From ff4c282a83788679bea884c723c21ea3592e821f Mon Sep 17 00:00:00 2001 From: John Turner Date: Tue, 29 Oct 2024 14:22:33 +0000 Subject: [PATCH 1/3] just a test for the linter --- CheckLinks.py | 88 ------------------------------------------ reusable-workflow-repo | 1 - test-lint.ipynb | 55 ++++++++++++++++++++++++++ 3 files changed, 55 insertions(+), 89 deletions(-) delete mode 100644 CheckLinks.py delete mode 160000 reusable-workflow-repo create mode 100644 test-lint.ipynb diff --git a/CheckLinks.py b/CheckLinks.py deleted file mode 100644 index f05717d..0000000 --- a/CheckLinks.py +++ /dev/null @@ -1,88 +0,0 @@ -import http.client -import urllib.request,urllib.error -import os -import sys -import re - -# Get the response code of the url to see if it exists -def getResponseCode(url): - content = None - try: - req = urllib.request.Request(url, headers={'User-Agent': 'Mozilla/5.0'}) - conn = urllib.request.urlopen(req) - # Only get HTML if we have a potential anchor link - if "#" in url and "pdf" not in url: - content = conn.read().decode("utf-8") - except urllib.error.HTTPError as e: - return [e.code,content] - except urllib.error.URLError as e: - return [404,content] - except http.client.InvalidURL: - return [200,content] - return [conn.getcode(),content] - - -path = os.path.dirname(os.path.realpath(__file__)) -remove_characters = ['**', '\\n'] -# text that tends to be at the end of the url that we need truncate everything past them -end_characters = [')',",","'",'`',"\"",'','',"\\",">"] -big_regex = re.compile('|'.join(map(re.escape, remove_characters))) -if len(sys.argv) >1 and os.path.exists(sys.argv[1]): - path = sys.argv[1] - -err = 0 -# Loop through all files in path -for root, dirs, files in os.walk(path): - for file in files: - # only read file that match template ( txt, md or python notebook) - if file.endswith(".md") or file.endswith(".txt") or file.endswith(".ipynb"): - - # get content and separate into lines and then separate by spaces - raw_content = open(os.path.join(root, file), "r").read() - content = raw_content.split("\n") - content = [x.split(" ") for x in content] - - # have an incrementer for line number later export - line_num=0 - for line in content: - char=0 - for item in line: - - if "https://" in item or "http://" in item: - - # this is a command being ran so difficult to validate in this script, skip it - if '$(uname' in item: - continue - - # get just from the http portion if there was more in from of the string we grabbed - item = item[item.find("http"):] - - # if there is a period at the end, truncate to that period. Other periods may be valid - if item.endswith("."): - item = item[:item.rfind(".")] - if item.endswith("'"): - item = item[:item.rfind("'")] - if item.endswith("\""): - item = item[:item.rfind("\"")] - # strip various characters that may be in the string - item_stripped = big_regex.sub("",item.strip()) - for end_c in end_characters: - end_index = item_stripped.find(end_c) - if end_index != -1: - item_stripped = item_stripped[:end_index] - - # try and get the url, if its 404 or 500 then its invalid, let us know and trigger the error flag - code = getResponseCode(item_stripped) - if code[0] in [404,403,500]: - err = 1 - print(file+" Code:"+str(code[0])+" Line "+str(line_num)+"("+str(char)+"):"+item_stripped) - - # check for missing anchors - elif "#" in item_stripped and \ - code[1] is not None \ - and 'href=\"'+item_stripped[item_stripped.find("#"):]+'\"' not in code[1]: - print(file + " Missing Anchor Line " + str(line_num) + "(" + str( - char) + "):" + item_stripped) - char+=len(item) - line_num+=1 -exit(err) \ No newline at end of file diff --git a/reusable-workflow-repo b/reusable-workflow-repo deleted file mode 160000 index 3237900..0000000 --- a/reusable-workflow-repo +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 3237900c16e854cf76b24e58b3543dbb63e1a2eb diff --git a/test-lint.ipynb b/test-lint.ipynb new file mode 100644 index 0000000..e4987fb --- /dev/null +++ b/test-lint.ipynb @@ -0,0 +1,55 @@ +{ + "cells": [ + { + "cell_type": "code", + "id": "initial_id", + "metadata": { + "collapsed": true, + "ExecuteTime": { + "end_time": "2024-10-29T14:21:59.998233Z", + "start_time": "2024-10-29T14:21:59.970969Z" + } + }, + "source": "print(\"test cell\")", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "test cell\n" + ] + } + ], + "execution_count": 1 + }, + { + "metadata": {}, + "cell_type": "code", + "outputs": [], + "execution_count": null, + "source": "", + "id": "18ababdccf0c49c6" + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From 9244fcdf975c55299f058a30706e475c611d8d4d Mon Sep 17 00:00:00 2001 From: github-action Date: Tue, 29 Oct 2024 14:23:46 +0000 Subject: [PATCH 2/3] Github Action: Lint Notebooks --- docs/HowToMountABucketWithGcsfuse.ipynb | 157 +- docs/HowToUseCondaEnvsAsKernels.ipynb | 963 +--- docs/HowToUseNextflowandGCPLifeSciences.ipynb | 4088 +---------------- test-lint.ipynb | 52 +- 4 files changed, 107 insertions(+), 5153 deletions(-) diff --git a/docs/HowToMountABucketWithGcsfuse.ipynb b/docs/HowToMountABucketWithGcsfuse.ipynb index 348b94a..7a85d04 100644 --- a/docs/HowToMountABucketWithGcsfuse.ipynb +++ b/docs/HowToMountABucketWithGcsfuse.ipynb @@ -10,28 +10,10 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "1eb9b734-f956-424d-9b7a-240f7075aa49", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[core]\n", - "account = 25874201052-compute@developer.gserviceaccount.com\n", - "disable_usage_reporting = True\n", - "project = keen-clarity-352623\n", - "\n", - "Your active configuration is: [default]\n", - "\n", - "\n", - "To take a quick anonymous survey, run:\n", - " $ gcloud survey\n", - "\n" - ] - } - ], + "outputs": [], "source": [ "# Pre-check steps: check account and project\n", "!gcloud config list\n", @@ -43,18 +25,10 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "5310328f-53ef-430c-92b3-86a7fec33149", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "gs://test_user_managed_gcsfuse/us-states.txt\n" - ] - } - ], + "outputs": [], "source": [ "#afterwards check permission with the following command(replace with your bucket name)\n", "#If you can't list the contents..add the compute engine service account to your bucket permissions..or whichever account listed in the above command\n", @@ -63,7 +37,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "id": "aa57c680-d4af-4688-8c1a-a6d613e7f8ce", "metadata": {}, "outputs": [], @@ -74,21 +48,10 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "id": "12b590c0-c77e-4c47-ba02-2ff912b91059", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "2022/08/15 17:34:22.729724 Start gcsfuse/0.41.4 (Go version go1.17.6) for app \"\" using mount point: /home/jupyter/gcs\n", - "2022/08/15 17:34:22.749754 Opening GCS connection...\n", - "2022/08/15 17:34:22.836734 Mounting file system \"test_user_managed_gcsfuse\"...\n", - "2022/08/15 17:34:22.959908 File system has been successfully mounted.\n" - ] - } - ], + "outputs": [], "source": [ "#mount the bucket contents to the folder above(replace with your bucket name)\n", "!gcsfuse test_user_managed_gcsfuse /home/jupyter/gcs" @@ -96,18 +59,10 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "id": "026f4f16-5cc8-4656-a637-523e83a80661", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "us-states.txt\n" - ] - } - ], + "outputs": [], "source": [ "#list files with terminal\n", "!ls /home/jupyter/gcs" @@ -115,27 +70,10 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "id": "90101b0e-08f6-4672-97fb-08d9d6eaf714", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "name,post_abbr\n", - "Alabama,AL\n", - "Alaska,AK\n", - "Arizona,AZ\n", - "Arkansas,AR\n", - "California,CA\n", - "Colorado,CO\n", - "Connecticut,CT\n", - "Delaware,DE\n", - "Florida,FL\n" - ] - } - ], + "outputs": [], "source": [ "#interact with file with terminal\n", "!head /home/jupyter/gcs/us-states.txt" @@ -143,21 +81,10 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "id": "5fbb978e-9ab7-4383-925c-182d23dceb2b", "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'/home/jupyter'" - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "#list and interact with bucket contents with python in python notebook\n", "import os\n", @@ -167,7 +94,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "id": "bd1c9077-c393-4338-ab62-190f74ac9d89", "metadata": {}, "outputs": [], @@ -177,72 +104,26 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "id": "874e7100-cc3f-42cd-8311-4f4ce89791cd", "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'/home/jupyter/gcs'" - ] - }, - "execution_count": 9, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "os.getcwd()" ] }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "id": "b0dc1d68-d2e5-4a39-859a-a1a470e627fc", "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['us-states.txt']" - ] - }, - "execution_count": 10, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "os.listdir()" ] } ], - "metadata": { - "environment": { - "kernel": "python3", - "name": "common-cpu.m94", - "type": "gcloud", - "uri": "gcr.io/deeplearning-platform-release/base-cpu:m94" - }, - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.7.12" - } - }, + "metadata": {}, "nbformat": 4, "nbformat_minor": 5 } diff --git a/docs/HowToUseCondaEnvsAsKernels.ipynb b/docs/HowToUseCondaEnvsAsKernels.ipynb index 09b3f07..4cdf43c 100644 --- a/docs/HowToUseCondaEnvsAsKernels.ipynb +++ b/docs/HowToUseCondaEnvsAsKernels.ipynb @@ -34,23 +34,10 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "58b3e45e-3710-46cf-89fd-a67f77578d46", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "# conda environments:\n", - "#\n", - "base * /opt/conda\n", - "\n", - "\n", - "Note: you may need to restart the kernel to use updated packages.\n" - ] - } - ], + "outputs": [], "source": [ "conda env list" ] @@ -65,19 +52,10 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "id": "8b664567-ca2c-4853-8cbc-6ad30cb88cdc", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Available kernels:\n", - " python3 /opt/conda/share/jupyter/kernels/python3\n" - ] - } - ], + "outputs": [], "source": [ "!jupyter kernelspec list" ] @@ -92,21 +70,10 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "id": "70937661-db33-4ac0-badb-4e51bcb31180", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[ListKernelSpecs] [nb_conda_kernels] enabled, 1 kernels found\n", - "Available kernels:\n", - " python3 /opt/conda/share/jupyter/kernels/python3\n", - " conda-root-py /opt/conda/share/jupyter/kernels/python3\n" - ] - } - ], + "outputs": [], "source": [ "!python -m nb_conda_kernels list" ] @@ -136,18 +103,10 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "id": "ea488951-77f5-4831-af5d-038bc8e74ab4", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "/home/jupyter/.jupyter\n" - ] - } - ], + "outputs": [], "source": [ "!jupyter --config-dir" ] @@ -200,41 +159,20 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "id": "e1ee6dd7-d44b-49c2-9621-682c22cfc35d", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[ListKernelSpecs] Installed kernelspec conda-root-py in /home/jupyter/.local/share/jupyter/kernels/conda-root-py\n", - "[ListKernelSpecs] [nb_conda_kernels] enabled, 1 kernels found\n", - "Available kernels:\n", - " conda-root-py /opt/conda/share/jupyter/kernels/python3\n" - ] - } - ], + "outputs": [], "source": [ "!python -m nb_conda_kernels list" ] }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "id": "071c0a7a-750e-4848-9cb6-31dfd513977a", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Available kernels:\n", - " conda-root-py /home/jupyter/.local/share/jupyter/kernels/conda-root-py\n", - " python3 /opt/conda/share/jupyter/kernels/python3\n" - ] - } - ], + "outputs": [], "source": [ "!jupyter kernelspec list" ] @@ -339,101 +277,10 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "id": "90aa282e-3eb8-41dc-a35b-6bafb3a924bb", - "metadata": { - "scrolled": true, - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Collecting package metadata (repodata.json): done\n", - "Solving environment: done\n", - "\n", - "Downloading and Extracting Packages\n", - "python_abi-3.9 | 4 KB | ##################################### | 100% \n", - "fonts-conda-ecosyste | 4 KB | ##################################### | 100% \n", - "harfbuzz-5.3.0 | 2.2 MB | ##################################### | 100% \n", - "xorg-libice-1.0.10 | 58 KB | ##################################### | 100% \n", - "xorg-libx11-1.7.2 | 941 KB | ##################################### | 100% \n", - "xorg-libxi-1.7.10 | 46 KB | ##################################### | 100% \n", - "pyzmq-24.0.1 | 483 KB | ##################################### | 100% \n", - "xorg-xproto-7.0.31 | 73 KB | ##################################### | 100% \n", - "ipykernel-6.16.1 | 100 KB | ##################################### | 100% \n", - "perl-5.32.1 | 14.4 MB | ##################################### | 100% \n", - "libstdcxx-ng-12.2.0 | 4.3 MB | ##################################### | 100% \n", - "xorg-kbproto-1.0.7 | 27 KB | ##################################### | 100% \n", - "giflib-5.2.1 | 77 KB | ##################################### | 100% \n", - "xorg-xextproto-7.3.0 | 28 KB | ##################################### | 100% \n", - "jupyter_client-7.4.3 | 91 KB | ##################################### | 100% \n", - "_openmp_mutex-4.5 | 23 KB | ##################################### | 100% \n", - "stack_data-0.5.1 | 24 KB | ##################################### | 100% \n", - "xorg-recordproto-1.1 | 8 KB | ##################################### | 100% \n", - "xorg-renderproto-0.1 | 9 KB | ##################################### | 100% \n", - "setuptools-65.5.0 | 768 KB | ##################################### | 100% \n", - "xorg-libxtst-1.2.3 | 31 KB | ##################################### | 100% \n", - "xorg-libxfixes-5.0.3 | 18 KB | ##################################### | 100% \n", - "cairo-1.16.0 | 1.5 MB | ##################################### | 100% \n", - "krb5-1.19.3 | 1.4 MB | ##################################### | 100% \n", - "sqlite-3.39.4 | 789 KB | ##################################### | 100% \n", - "six-1.16.0 | 14 KB | ##################################### | 100% \n", - "python-3.9.13 | 26.7 MB | ##################################### | 100% \n", - "readline-8.1.2 | 291 KB | ##################################### | 100% \n", - "xorg-inputproto-2.3. | 19 KB | ##################################### | 100% \n", - "libgomp-12.2.0 | 455 KB | ##################################### | 100% \n", - "openssl-3.0.5 | 2.8 MB | ##################################### | 100% \n", - "jupyter_core-4.11.1 | 81 KB | ##################################### | 100% \n", - "ncurses-6.3 | 1002 KB | ##################################### | 100% \n", - "_libgcc_mutex-0.1 | 3 KB | ##################################### | 100% \n", - "xorg-libxext-1.3.4 | 54 KB | ##################################### | 100% \n", - "asttokens-2.0.8 | 24 KB | ##################################### | 100% \n", - "debugpy-1.6.3 | 2.0 MB | ##################################### | 100% \n", - "fastqc-0.11.9 | 9.7 MB | ##################################### | 100% \n", - "xorg-fixesproto-5.0 | 9 KB | ##################################### | 100% \n", - "libzlib-1.2.13 | 64 KB | ##################################### | 100% \n", - "xorg-libxrender-0.9. | 32 KB | ##################################### | 100% \n", - "traitlets-5.5.0 | 85 KB | ##################################### | 100% \n", - "pixman-0.40.0 | 627 KB | ##################################### | 100% \n", - "openjdk-17.0.3 | 172.4 MB | ##################################### | 100% \n", - "pthread-stubs-0.4 | 5 KB | ##################################### | 100% \n", - "libgcc-ng-12.2.0 | 936 KB | ##################################### | 100% \n", - "fonts-conda-forge-1 | 4 KB | ##################################### | 100% \n", - "pip-22.3 | 1.5 MB | ##################################### | 100% \n", - "graphite2-1.3.13 | 102 KB | ##################################### | 100% \n", - "psutil-5.9.3 | 348 KB | ##################################### | 100% \n", - "libsqlite-3.39.4 | 803 KB | ##################################### | 100% \n", - "tzdata-2022e | 118 KB | ##################################### | 100% \n", - "gettext-0.21.1 | 4.1 MB | ##################################### | 100% \n", - "tornado-6.2 | 658 KB | ##################################### | 100% \n", - "pure_eval-0.2.2 | 14 KB | ##################################### | 100% \n", - "xorg-libsm-1.2.3 | 26 KB | ##################################### | 100% \n", - "zlib-1.2.13 | 92 KB | ##################################### | 100% \n", - "ld_impl_linux-64-2.3 | 759 KB | ##################################### | 100% \n", - "executing-1.1.1 | 23 KB | ##################################### | 100% \n", - "wheel-0.37.1 | 31 KB | ##################################### | 100% \n", - "ipython-8.5.0 | 552 KB | ##################################### | 100% \n", - "nest-asyncio-1.5.6 | 10 KB | ##################################### | 100% \n", - "Preparing transaction: done\n", - "Verifying transaction: done\n", - "Executing transaction: done\n", - "#\n", - "# To activate this environment, use\n", - "#\n", - "# $ conda activate sample4\n", - "#\n", - "# To deactivate an active environment, use\n", - "#\n", - "# $ conda deactivate\n", - "\n", - "Retrieving notices: ...working... done\n", - "\n", - "Note: you may need to restart the kernel to use updated packages.\n" - ] - } - ], + "metadata": {}, + "outputs": [], "source": [ "conda env create --file env.yml" ] @@ -448,24 +295,10 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "id": "0e6f58d4-3733-475c-8b51-4ca4251b60a3", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[ListKernelSpecs] Removing existing kernelspec in /home/jupyter/.local/share/jupyter/kernels/conda-root-py\n", - "[ListKernelSpecs] Installed kernelspec conda-root-py in /home/jupyter/.local/share/jupyter/kernels/conda-root-py\n", - "[ListKernelSpecs] Installed kernelspec conda-env-sample4-py in /home/jupyter/.local/share/jupyter/kernels/conda-env-sample4-py\n", - "[ListKernelSpecs] [nb_conda_kernels] enabled, 2 kernels found\n", - "Available kernels:\n", - " conda-env-sample4-py /opt/conda/envs/sample4/share/jupyter/kernels/python3\n", - " conda-root-py /opt/conda/share/jupyter/kernels/python3\n" - ] - } - ], + "outputs": [], "source": [ "!python -m nb_conda_kernels list" ] @@ -480,21 +313,10 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "id": "49db325a-3782-4219-8e26-e04c0f5cfdb7", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Available kernels:\n", - " conda-env-sample4-py /home/jupyter/.local/share/jupyter/kernels/conda-env-sample4-py\n", - " conda-root-py /home/jupyter/.local/share/jupyter/kernels/conda-root-py\n", - " python3 /opt/conda/share/jupyter/kernels/python3\n" - ] - } - ], + "outputs": [], "source": [ "!jupyter kernelspec list" ] @@ -544,755 +366,16 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "055fef60-b0dc-42c4-a210-afe81de98c7a", - "metadata": { - "scrolled": true, - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\u001b[?25l\u001b[2K\u001b[0G[+] 0.0s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 0.1s\n", - "conda-forge/linux-64 \u001b[90m━━━━━━━━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━\u001b[0m 0.0 B / ??.?MB @ ??.?MB/s 0.1s\n", - "conda-forge/noarch \u001b[90m━━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━\u001b[0m 0.0 B / ??.?MB @ ??.?MB/s 0.1s\n", - "bioconda/linux-64 \u001b[90m╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━\u001b[0m 0.0 B / ??.?MB @ ??.?MB/s 0.1s\n", - "bioconda/noarch \u001b[33m━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━━━\u001b[0m 0.0 B / ??.?MB @ ??.?MB/s 0.1s\n", - "pkgs/main/linux-64 \u001b[33m━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━\u001b[0m 0.0 B / ??.?MB @ ??.?MB/s 0.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gbioconda/linux-64 No change\n", - "bioconda/noarch No change\n", - "pkgs/main/linux-64 No change\n", - "pkgs/main/noarch No change\n", - "pkgs/r/noarch No change\n", - "pkgs/r/linux-64 No change\n", - "[+] 0.2s\n", - "conda-forge/linux-64 \u001b[90m━━━━━━━━━━━╸\u001b[0m\u001b[33m━━━━━━━━━━━\u001b[0m 104.1kB / ??.?MB @ 621.8kB/s 0.2s\n", - "conda-forge/noarch \u001b[90m━━━━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━\u001b[0m 158.7kB / ??.?MB @ 948.8kB/s 0.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 0.3s\n", - "conda-forge/linux-64 \u001b[90m━━━━━━━━━━━━━╸\u001b[0m\u001b[33m━━━━━━━━━\u001b[0m 534.8kB / ??.?MB @ 2.0MB/s 0.3s\n", - "conda-forge/noarch \u001b[90m━━━━━━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━━━\u001b[0m 530.2kB / ??.?MB @ 2.0MB/s 0.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 0.4s\n", - "conda-forge/linux-64 \u001b[33m━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━━━━\u001b[0m 843.0kB / ??.?MB @ 2.3MB/s 0.4s\n", - "conda-forge/noarch \u001b[90m━━━━━━━━━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━\u001b[0m 1.0MB / ??.?MB @ 2.7MB/s 0.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 0.5s\n", - "conda-forge/linux-64 \u001b[33m━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━━\u001b[0m 1.3MB / ??.?MB @ 2.8MB/s 0.5s\n", - 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"conda-forge/linux-64 \u001b[90m━━━━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━\u001b[0m 3.2MB / ??.?MB @ 3.6MB/s 0.9s\n", - "conda-forge/noarch \u001b[33m━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━\u001b[0m 3.4MB / ??.?MB @ 3.9MB/s 0.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 1.0s\n", - "conda-forge/linux-64 \u001b[90m━━━━━━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━━━\u001b[0m 3.6MB / ??.?MB @ 3.7MB/s 1.0s\n", - "conda-forge/noarch \u001b[90m╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━\u001b[0m 3.9MB / ??.?MB @ 4.0MB/s 1.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 1.1s\n", - "conda-forge/linux-64 \u001b[90m━━━━━━━━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━\u001b[0m 4.1MB / ??.?MB @ 3.8MB/s 1.1s\n", - "conda-forge/noarch \u001b[90m━━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━\u001b[0m 4.4MB / ??.?MB @ 4.1MB/s 1.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 1.2s\n", - "conda-forge/linux-64 \u001b[90m━━━━━━━━━━━╸\u001b[0m\u001b[33m━━━━━━━━━━━\u001b[0m 4.6MB / ??.?MB @ 3.9MB/s 1.2s\n", - 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"\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.0s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.1s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.2s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.3s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.4s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.5s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.6s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.7s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.8s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.9s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.0s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.1s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.2s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.3s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0Gconda-forge/linux-64 @ 4.0MB/s 7.9s\n", - "\u001b[?25h\n", - "\n", - "Looking for: ['snakemake', 'pip']\n", - "\n", - "\n", - "Transaction\n", - "\n", - " Prefix: /opt/conda/envs/snakemake\n", - "\n", - " Updating specs:\n", - "\n", - " - snakemake\n", - " - pip\n", - "\n", - "\n", - " Package Version Build Channel Size\n", - "─────────────────────────────────────────────────────────────────────────────────────────────────────\n", - " Install:\n", - "─────────────────────────────────────────────────────────────────────────────────────────────────────\n", - "\n", - "\u001b[32m + _libgcc_mutex \u001b[00m 0.1 conda_forge conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + _openmp_mutex \u001b[00m 4.5 2_gnu conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + abseil-cpp \u001b[00m 20211102.0 h27087fc_1 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + aioeasywebdav \u001b[00m 2.4.0 pyha770c72_0 conda-forge/noarch 13kB\n", - "\u001b[32m + aiohttp \u001b[00m 3.8.1 py310h5764c6d_1 conda-forge/linux-64 599kB\n", - "\u001b[32m + aiosignal \u001b[00m 1.2.0 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + amply \u001b[00m 0.1.5 pyhd8ed1ab_0 conda-forge/noarch 21kB\n", - "\u001b[32m + appdirs \u001b[00m 1.4.4 pyh9f0ad1d_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + async-timeout \u001b[00m 4.0.2 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + attmap \u001b[00m 0.13.2 pyhd8ed1ab_0 conda-forge/noarch 14kB\n", - "\u001b[32m + attrs \u001b[00m 22.1.0 pyh71513ae_1 conda-forge/noarch 49kB\n", - "\u001b[32m + backports \u001b[00m 1.0 py_2 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + backports.functools_lru_cache\u001b[00m 1.6.4 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + bcrypt \u001b[00m 3.2.2 py310h5764c6d_0 conda-forge/linux-64 45kB\n", - "\u001b[32m + boto3 \u001b[00m 1.24.44 pyhd8ed1ab_0 conda-forge/noarch 74kB\n", - "\u001b[32m + botocore \u001b[00m 1.27.44 pyhd8ed1ab_0 conda-forge/noarch 6MB\n", - "\u001b[32m + brotlipy \u001b[00m 0.7.0 py310h5764c6d_1004 conda-forge/linux-64 350kB\n", - "\u001b[32m + bzip2 \u001b[00m 1.0.8 h7f98852_4 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + c-ares \u001b[00m 1.18.1 h7f98852_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + ca-certificates \u001b[00m 2022.6.15 ha878542_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + cachetools \u001b[00m 5.0.0 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + certifi \u001b[00m 2022.6.15 py310hff52083_0 conda-forge/linux-64 159kB\n", - "\u001b[32m + cffi \u001b[00m 1.15.1 py310h255011f_0 conda-forge/linux-64 237kB\n", - "\u001b[32m + charset-normalizer \u001b[00m 2.1.0 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + coin-or-cbc \u001b[00m 2.10.8 h3786ebc_0 conda-forge/linux-64 1MB\n", - "\u001b[32m + coin-or-cgl \u001b[00m 0.60.6 h6f57e76_1 conda-forge/linux-64 603kB\n", - "\u001b[32m + coin-or-clp \u001b[00m 1.17.7 hc56784d_1 conda-forge/linux-64 1MB\n", - "\u001b[32m + coin-or-osi \u001b[00m 0.108.7 h2720bb7_1 conda-forge/linux-64 450kB\n", - "\u001b[32m + coin-or-utils \u001b[00m 2.11.6 h202d8b1_1 conda-forge/linux-64 758kB\n", - "\u001b[32m + coincbc \u001b[00m 2.10.8 0_metapackage conda-forge/noarch 10kB\n", - "\u001b[32m + commonmark \u001b[00m 0.9.1 py_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + configargparse \u001b[00m 1.5.3 pyhd8ed1ab_0 conda-forge/noarch 33kB\n", - "\u001b[32m + connection_pool \u001b[00m 0.0.3 pyhd3deb0d_0 conda-forge/noarch 8kB\n", - "\u001b[32m + cryptography \u001b[00m 37.0.1 py310h9ce1e76_0 pkgs/main/linux-64 2MB\n", - "\u001b[32m + dataclasses \u001b[00m 0.8 pyhc8e2a94_3 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + datrie \u001b[00m 0.8.2 py310h6acc77f_3 conda-forge/linux-64 772kB\n", - "\u001b[32m + decorator \u001b[00m 5.1.1 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + defusedxml \u001b[00m 0.7.1 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + docutils \u001b[00m 0.19 py310hff52083_0 conda-forge/linux-64 781kB\n", - "\u001b[32m + dpath \u001b[00m 2.0.6 py310hff52083_1 conda-forge/linux-64 24kB\n", - "\u001b[32m + dropbox \u001b[00m 11.33.0 pyhd8ed1ab_0 conda-forge/noarch 956kB\n", - "\u001b[32m + filechunkio \u001b[00m 1.8 py_2 conda-forge/noarch 5kB\n", - "\u001b[32m + filelock \u001b[00m 3.7.1 pyhd8ed1ab_0 conda-forge/noarch 12kB\n", - "\u001b[32m + frozenlist \u001b[00m 1.3.0 py310h5764c6d_1 conda-forge/linux-64 44kB\n", - "\u001b[32m + ftputil \u001b[00m 5.0.4 pyhd8ed1ab_0 conda-forge/noarch 43kB\n", - "\u001b[32m + future \u001b[00m 0.18.2 py310hff52083_5 conda-forge/linux-64 755kB\n", - "\u001b[32m + gitdb \u001b[00m 4.0.9 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + gitpython \u001b[00m 3.1.27 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + google-api-core \u001b[00m 2.8.2 pyhd8ed1ab_0 conda-forge/noarch 72kB\n", - "\u001b[32m + google-api-python-client \u001b[00m 2.55.0 pyhd8ed1ab_0 conda-forge/noarch 5MB\n", - "\u001b[32m + google-auth \u001b[00m 2.9.1 pyh6c4a22f_0 conda-forge/noarch 92kB\n", - "\u001b[32m + google-auth-httplib2 \u001b[00m 0.1.0 pyhd8ed1ab_1 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + google-cloud-core \u001b[00m 2.3.2 pyhd8ed1ab_0 conda-forge/noarch 28kB\n", - "\u001b[32m + google-cloud-storage \u001b[00m 2.4.0 pyh6c4a22f_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + google-crc32c \u001b[00m 1.1.2 py310he8fe98e_3 conda-forge/linux-64 24kB\n", - "\u001b[32m + google-resumable-media \u001b[00m 2.3.3 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + googleapis-common-protos \u001b[00m 1.56.4 py310hff52083_0 conda-forge/linux-64 126kB\n", - "\u001b[32m + grpc-cpp \u001b[00m 1.48.0 h00ec82a_0 conda-forge/linux-64 5MB\n", - "\u001b[32m + grpcio \u001b[00m 1.48.0 py310h70d52b7_0 conda-forge/linux-64 825kB\n", - "\u001b[32m + httplib2 \u001b[00m 0.20.4 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + idna \u001b[00m 3.3 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + importlib-metadata \u001b[00m 4.11.4 py310hff52083_0 conda-forge/linux-64 34kB\n", - "\u001b[32m + importlib_resources \u001b[00m 5.9.0 pyhd8ed1ab_0 conda-forge/noarch 28kB\n", - "\u001b[32m + iniconfig \u001b[00m 1.1.1 pyh9f0ad1d_0 conda-forge/noarch 8kB\n", - "\u001b[32m + jinja2 \u001b[00m 3.1.2 pyhd8ed1ab_1 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + jmespath \u001b[00m 1.0.1 pyhd8ed1ab_0 conda-forge/noarch 21kB\n", - "\u001b[32m + jsonschema \u001b[00m 4.9.1 pyhd8ed1ab_0 conda-forge/noarch 64kB\n", - "\u001b[32m + jupyter_core \u001b[00m 4.11.1 py310hff52083_0 conda-forge/linux-64 84kB\n", - "\u001b[32m + ld_impl_linux-64 \u001b[00m 2.36.1 hea4e1c9_2 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libblas \u001b[00m 3.9.0 15_linux64_openblas conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libcblas \u001b[00m 3.9.0 15_linux64_openblas conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libcrc32c \u001b[00m 1.1.2 h9c3ff4c_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libffi \u001b[00m 3.4.2 h7f98852_5 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libgcc-ng \u001b[00m 12.1.0 h8d9b700_16 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libgfortran-ng \u001b[00m 12.1.0 h69a702a_16 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libgfortran5 \u001b[00m 12.1.0 hdcd56e2_16 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libgomp \u001b[00m 12.1.0 h8d9b700_16 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + liblapack \u001b[00m 3.9.0 15_linux64_openblas conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + liblapacke \u001b[00m 3.9.0 15_linux64_openblas conda-forge/linux-64 13kB\n", - "\u001b[32m + libnsl \u001b[00m 2.0.0 h7f98852_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libopenblas \u001b[00m 0.3.20 pthreads_h78a6416_1 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libprotobuf \u001b[00m 3.20.1 h6239696_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libsodium \u001b[00m 1.0.18 h36c2ea0_1 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libstdcxx-ng \u001b[00m 12.1.0 ha89aaad_16 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libuuid \u001b[00m 2.32.1 h7f98852_1000 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libzlib \u001b[00m 1.2.12 h166bdaf_2 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + logmuse \u001b[00m 0.2.6 pyh8c360ce_0 conda-forge/noarch 11kB\n", - "\u001b[32m + markupsafe \u001b[00m 2.1.1 py310h5764c6d_1 conda-forge/linux-64 23kB\n", - "\u001b[32m + multidict \u001b[00m 6.0.2 py310h5764c6d_1 conda-forge/linux-64 53kB\n", - "\u001b[32m + nbformat \u001b[00m 5.4.0 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + ncurses \u001b[00m 6.3 h27087fc_1 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + numpy \u001b[00m 1.23.1 py310h53a5b5f_0 conda-forge/linux-64 7MB\n", - "\u001b[32m + oauth2client \u001b[00m 4.1.3 py_0 conda-forge/noarch 67kB\n", - "\u001b[32m + openssl \u001b[00m 3.0.5 h166bdaf_1 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + packaging \u001b[00m 21.3 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + pandas \u001b[00m 1.4.3 py310h769672d_0 conda-forge/linux-64 13MB\n", - "\u001b[32m + paramiko \u001b[00m 2.11.0 pyhd8ed1ab_0 conda-forge/noarch 143kB\n", - "\u001b[32m + peppy \u001b[00m 0.32.0 pyhd8ed1ab_1 conda-forge/noarch 26kB\n", - "\u001b[32m + pip \u001b[00m 22.2.1 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + pkgutil-resolve-name \u001b[00m 1.3.10 pyhd8ed1ab_0 conda-forge/noarch 9kB\n", - "\u001b[32m + plac \u001b[00m 1.3.5 pyhd8ed1ab_0 conda-forge/noarch 23kB\n", - "\u001b[32m + pluggy \u001b[00m 1.0.0 py310hff52083_3 conda-forge/linux-64 26kB\n", - "\u001b[32m + ply \u001b[00m 3.11 py_1 conda-forge/noarch 45kB\n", - "\u001b[32m + prettytable \u001b[00m 3.3.0 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + protobuf \u001b[00m 3.20.1 py310hd8f1fbe_0 conda-forge/linux-64 333kB\n", - "\u001b[32m + psutil \u001b[00m 5.9.1 py310h5764c6d_0 conda-forge/linux-64 359kB\n", - "\u001b[32m + pulp \u001b[00m 2.6.0 py310hff52083_1 conda-forge/linux-64 128kB\n", - "\u001b[32m + py \u001b[00m 1.11.0 pyh6c4a22f_0 conda-forge/noarch 76kB\n", - "\u001b[32m + pyasn1 \u001b[00m 0.4.8 py_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + pyasn1-modules \u001b[00m 0.2.7 py_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + pycparser \u001b[00m 2.21 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + pygments \u001b[00m 2.12.0 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + pynacl \u001b[00m 1.5.0 py310h5764c6d_1 conda-forge/linux-64 1MB\n", - "\u001b[32m + pyopenssl \u001b[00m 22.0.0 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + pyparsing \u001b[00m 3.0.9 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + pyrsistent \u001b[00m 0.18.1 py310h5764c6d_1 conda-forge/linux-64 95kB\n", - "\u001b[32m + pysftp \u001b[00m 0.2.9 py_1 conda-forge/noarch 16kB\n", - "\u001b[32m + pysocks \u001b[00m 1.7.1 py310hff52083_5 conda-forge/linux-64 29kB\n", - "\u001b[32m + pytest \u001b[00m 7.1.2 py310hff52083_0 conda-forge/linux-64 476kB\n", - "\u001b[32m + python \u001b[00m 3.10.5 ha86cf86_0_cpython conda-forge/linux-64 30MB\n", - "\u001b[32m + python-dateutil \u001b[00m 2.8.2 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + python-fastjsonschema \u001b[00m 2.16.1 pyhd8ed1ab_0 conda-forge/noarch 249kB\n", - "\u001b[32m + python-irodsclient \u001b[00m 1.1.4 pyhd8ed1ab_0 conda-forge/noarch 137kB\n", - "\u001b[32m + python_abi \u001b[00m 3.10 2_cp310 conda-forge/linux-64 4kB\n", - "\u001b[32m + pytz \u001b[00m 2022.1 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + pyu2f \u001b[00m 0.1.5 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + pyyaml \u001b[00m 6.0 py310h5764c6d_4 conda-forge/linux-64 183kB\n", - "\u001b[32m + ratelimiter \u001b[00m 1.2.0 py_1002 conda-forge/noarch 12kB\n", - "\u001b[32m + re2 \u001b[00m 2022.06.01 h27087fc_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + readline \u001b[00m 8.1.2 h0f457ee_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + requests \u001b[00m 2.28.1 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + retry \u001b[00m 0.9.2 py_0 conda-forge/noarch 9kB\n", - "\u001b[32m + rich \u001b[00m 12.5.1 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + rsa \u001b[00m 4.9 pyhd8ed1ab_0 conda-forge/noarch 30kB\n", - "\u001b[32m + s3transfer \u001b[00m 0.6.0 pyhd8ed1ab_0 conda-forge/noarch 57kB\n", - "\u001b[32m + setuptools \u001b[00m 63.3.0 py310hff52083_0 conda-forge/linux-64 1MB\n", - "\u001b[32m + setuptools-scm \u001b[00m 7.0.5 pyhd8ed1ab_0 conda-forge/noarch 36kB\n", - "\u001b[32m + six \u001b[00m 1.16.0 pyh6c4a22f_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + slacker \u001b[00m 0.14.0 py_0 conda-forge/noarch 16kB\n", - "\u001b[32m + smart_open \u001b[00m 6.0.0 pyhd8ed1ab_0 conda-forge/noarch 44kB\n", - "\u001b[32m + smmap \u001b[00m 3.0.5 pyh44b312d_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + snakemake \u001b[00m 7.12.0 hdfd78af_0 bioconda/noarch 8kB\n", - "\u001b[32m + snakemake-minimal \u001b[00m 7.12.0 pyhdfd78af_0 bioconda/noarch 249kB\n", - "\u001b[32m + sqlite \u001b[00m 3.39.2 h4ff8645_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + stone \u001b[00m 3.3.1 pyhd8ed1ab_0 conda-forge/noarch 149kB\n", - "\u001b[32m + stopit \u001b[00m 1.1.2 py_0 conda-forge/noarch 16kB\n", - "\u001b[32m + tabulate \u001b[00m 0.8.10 pyhd8ed1ab_0 conda-forge/noarch 30kB\n", - "\u001b[32m + tk \u001b[00m 8.6.12 h27826a3_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + tomli \u001b[00m 2.0.1 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + toposort \u001b[00m 1.7 pyhd8ed1ab_0 conda-forge/noarch 13kB\n", - "\u001b[32m + traitlets \u001b[00m 5.3.0 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + typing-extensions \u001b[00m 4.3.0 hd8ed1ab_0 conda-forge/noarch 8kB\n", - "\u001b[32m + typing_extensions \u001b[00m 4.3.0 pyha770c72_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + tzdata \u001b[00m 2022a h191b570_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + ubiquerg \u001b[00m 0.6.2 pyhd8ed1ab_0 conda-forge/noarch 16kB\n", - "\u001b[32m + uritemplate \u001b[00m 4.1.1 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + urllib3 \u001b[00m 1.26.11 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + veracitools \u001b[00m 0.1.3 py_0 conda-forge/noarch 6kB\n", - "\u001b[32m + wcwidth \u001b[00m 0.2.5 pyh9f0ad1d_2 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + wheel \u001b[00m 0.37.1 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + wrapt \u001b[00m 1.14.1 py310h5764c6d_0 conda-forge/linux-64 52kB\n", - "\u001b[32m + xz \u001b[00m 5.2.5 h516909a_1 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + yaml \u001b[00m 0.2.5 h7f98852_2 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + yarl \u001b[00m 1.7.2 py310h5764c6d_2 conda-forge/linux-64 136kB\n", - "\u001b[32m + yte \u001b[00m 1.5.1 py310hff52083_0 conda-forge/linux-64 17kB\n", - "\u001b[32m + zipp \u001b[00m 3.8.1 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + zlib \u001b[00m 1.2.12 h166bdaf_2 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\n", - " Summary:\n", - "\n", - " Install: 167 packages\n", - "\n", - " Total download: 85MB\n", - "\n", - "─────────────────────────────────────────────────────────────────────────────────────────────────────\n", - "\n", - "\u001b[?25l\u001b[2K\u001b[0G[+] 0.0s\n", - "Downloading \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m 0.0 B 0.0s\n", - "Extracting \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m 0 0.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 0.1s\n", - "Downloading (5) \u001b[33m━╸\u001b[0m\u001b[90m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 0.0 B coin-or-clp 0.0s\n", - "Extracting \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m 0 0.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gcoin-or-utils 757.5kB @ 5.9MB/s 0.1s\n", - "liblapacke 12.7kB @ 89.4kB/s 0.1s\n", - "coin-or-clp 1.3MB @ 8.3MB/s 0.2s\n", - "coin-or-osi 450.1kB @ 2.8MB/s 0.2s\n", - "ply 44.8kB @ 236.4kB/s 0.0s\n", - "ftputil 42.9kB @ 217.3kB/s 0.0s\n", - "[+] 0.2s\n", - "Downloading (5) \u001b[33m━━╸\u001b[0m\u001b[90m━━━━━━━━━━━━━━━━━━━━\u001b[0m 3.1MB grpc-cpp 0.1s\n", - "Extracting (3) \u001b[33m━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━━\u001b[0m 1 coin-or-clp 0.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gpython-fastjsonschema 248.8kB @ 1.2MB/s 0.0s\n", - "setuptools 1.4MB @ 6.9MB/s 0.1s\n", - "stopit 16.1kB @ 68.7kB/s 0.0s\n", - "ratelimiter 11.9kB @ 49.9kB/s 0.0s\n", - "configargparse 32.5kB @ 136.2kB/s 0.0s\n", - "importlib_resources 28.3kB @ 115.9kB/s 0.0s\n", - "markupsafe 22.7kB @ 83.9kB/s 0.0s\n", - "wrapt 52.0kB @ 191.5kB/s 0.0s\n", - "retry 8.8kB @ 32.3kB/s 0.0s\n", - "dpath 23.7kB @ 85.0kB/s 0.0s\n", - "grpc-cpp 5.4MB @ 19.2MB/s 0.3s\n", - "[+] 0.3s\n", - "Downloading (5) ━╸\u001b[33m━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━━━━━━\u001b[0m 9.9MB certifi 0.2s\n", - "Extracting (16) \u001b[33m━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━\u001b[0m 1 coin-or-clp 0.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gcertifi 158.9kB @ 532.3kB/s 0.0s\n", - "protobuf 333.2kB @ 1.0MB/s 0.1s\n", - "cffi 237.0kB @ 709.4kB/s 0.1s\n", - "google-crc32c 24.2kB @ 71.1kB/s 0.0s\n", - "docutils 781.1kB @ 2.3MB/s 0.1s\n", - "jsonschema 63.9kB @ 176.1kB/s 0.0s\n", - "googleapis-common-protos 125.7kB @ 345.5kB/s 0.0s\n", - "ubiquerg 16.0kB @ 41.1kB/s 0.1s\n", - "[+] 0.4s\n", - "Downloading (5) ━━╸\u001b[33m━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━━━\u001b[0m 13.2MB botocore 0.3s\n", - "Extracting (19) ╸\u001b[33m━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━━━━━━━\u001b[0m 7 coin-or-clp 0.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gparamiko 143.4kB @ 350.0kB/s 0.0s\n", - "slacker 15.6kB @ 34.6kB/s 0.1s\n", - "google-cloud-core 28.3kB @ 62.6kB/s 0.0s\n", - "[+] 0.5s\n", - "Downloading (5) ━━━╸\u001b[33m━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━\u001b[0m 17.9MB botocore 0.4s\n", - "Extracting (20) ━╸\u001b[33m━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━━━━━━\u001b[0m 8 coin-or-clp 0.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gcryptography 1.6MB @ 3.2MB/s 0.2s\n", - "snakemake 8.0kB @ 15.5kB/s 0.1s\n", - "coincbc 9.9kB @ 19.1kB/s 0.1s\n", - "logmuse 10.7kB @ 19.1kB/s 0.0s\n", - "attrs 49.5kB @ 86.6kB/s 0.0s\n", - "pkgutil-resolve-name 8.7kB @ 14.7kB/s 0.0s\n", - "iniconfig 8.3kB @ 13.9kB/s 0.1s\n", - "botocore 5.8MB @ 9.7MB/s 0.2s\n", - "[+] 0.6s\n", - "Downloading (4) ━━━━━╸\u001b[33m━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━\u001b[0m 26.0MB frozenlist 0.5s\n", - "Extracting (22) ━╸\u001b[33m━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━━━━━\u001b[0m 11 attrs 0.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gtyping-extensions 8.5kB @ 13.8kB/s 0.0s\n", - "oauth2client 67.5kB @ 107.7kB/s 0.0s\n", - "pyrsistent 94.5kB @ 149.9kB/s 0.0s\n", - "frozenlist 44.2kB @ 67.8kB/s 0.1s\n", - "psutil 358.7kB @ 545.3kB/s 0.0s\n", - "jupyter_core 83.7kB @ 126.8kB/s 0.0s\n", - "yarl 135.7kB @ 202.1kB/s 0.0s\n", - "attmap 13.6kB @ 19.8kB/s 0.0s\n", - "[+] 0.7s\n", - "Downloading (5) ━━━━━━╸\u001b[33m━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━\u001b[0m 29.6MB pandas 0.6s\n", - "Extracting (32) ━━╸\u001b[33m━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━━\u001b[0m 12 attrs 0.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gsetuptools-scm 35.8kB @ 51.2kB/s 0.0s\n", - "pulp 127.8kB @ 180.0kB/s 0.0s\n", - "s3transfer 56.7kB @ 79.2kB/s 0.0s\n", - "pandas 13.1MB @ 18.2MB/s 0.4s\n", - "boto3 73.7kB @ 99.8kB/s 0.0s\n", - "snakemake-minimal 249.0kB @ 335.3kB/s 0.0s\n", - "pynacl 1.4MB @ 1.9MB/s 0.1s\n", - "jmespath 21.0kB @ 27.5kB/s 0.0s\n", - "filelock 12.2kB @ 15.7kB/s 0.0s\n", - "[+] 0.8s\n", - "Downloading (6) ━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━\u001b[0m 36.2MB grpcio 0.7s\n", - "Extracting (37) ━━━╸\u001b[33m━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━\u001b[0m 16 attrs 0.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gtoposort 12.6kB @ 15.7kB/s 0.1s\n", - "pysocks 28.6kB @ 34.9kB/s 0.0s\n", - "stone 149.0kB @ 172.3kB/s 0.1s\n", - "brotlipy 350.1kB @ 393.6kB/s 0.1s\n", - "grpcio 825.2kB @ 921.9kB/s 0.1s\n", - "[+] 0.9s\n", - "Downloading (5) ━━━━━━━━━━╸\u001b[33m━━━━━━━━━━━━\u001b[0m 42.3MB aiohttp 0.8s\n", - "Extracting (36) ━━━━╸\u001b[33m━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━\u001b[0m 20 attrs 0.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gveracitools 6.1kB @ 6.7kB/s 0.0s\n", - "google-auth 92.1kB @ 98.6kB/s 0.0s\n", - "aiohttp 599.3kB @ 636.1kB/s 0.1s\n", - "python_abi 4.1kB @ 4.2kB/s 0.0s\n", - "filechunkio 5.1kB @ 5.2kB/s 0.0s\n", - "[+] 1.0s\n", - "Downloading (5) ━━━━━━━━━━━━╸\u001b[33m━━━━━━━━━━\u001b[0m 49.9MB connection_pool 0.9s\n", - "Extracting (37) ━━━━━╸\u001b[33m━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━\u001b[0m 26 aiohttp 0.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gconnection_pool 8.3kB @ 8.2kB/s 0.0s\n", - "rsa 29.9kB @ 29.4kB/s 0.0s\n", - "numpy 7.4MB @ 7.2MB/s 0.3s\n", - "pytest 475.9kB @ 451.9kB/s 0.0s\n", - "datrie 771.5kB @ 721.0kB/s 0.1s\n", - "pysftp 15.5kB @ 14.3kB/s 0.0s\n", - "google-api-python-client 5.2MB @ 4.7MB/s 0.2s\n", - "[+] 1.1s\n", - "Downloading (5) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 62.1MB coin-or-cgl 1.0s\n", - "Extracting (39) ━━━━━━╸\u001b[33m━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━\u001b[0m 30 aiohttp 0.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gpluggy 25.8kB @ 22.7kB/s 0.0s\n", - "coin-or-cgl 603.2kB @ 530.5kB/s 0.1s\n", - "py 76.0kB @ 66.9kB/s 0.0s\n", - "amply 20.9kB @ 17.9kB/s 0.0s\n", - "pyyaml 182.6kB @ 155.7kB/s 0.0s\n", - "bcrypt 45.4kB @ 38.7kB/s 0.0s\n", - "[+] 1.2s\n", - "Downloading (5) ━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━━\u001b[0m 68.3MB coin-or-cbc 1.1s\n", - "Extracting (43) ━━━━━━━╸\u001b[33m━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━\u001b[0m 33 aiohttp 1.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gpython-irodsclient 137.1kB @ 114.1kB/s 0.2s\n", - "coin-or-cbc 1.1MB @ 874.6kB/s 0.0s\n", - "tabulate 30.2kB @ 24.9kB/s 0.0s\n", - "importlib-metadata 34.2kB @ 28.1kB/s 0.0s\n", - "plac 23.4kB @ 18.9kB/s 0.0s\n", - "future 755.4kB @ 599.6kB/s 0.0s\n", - "multidict 52.7kB @ 41.0kB/s 0.0s\n", - "dropbox 956.0kB @ 743.9kB/s 0.1s\n", - "[+] 1.3s\n", - "Downloading (5) ━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━━\u001b[0m 79.3MB aioeasywebdav 1.2s\n", - "Extracting (50) ━━━━━━━╸\u001b[33m━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━\u001b[0m 34 aiohttp 1.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gaioeasywebdav 12.5kB @ 9.6kB/s 0.1s\n", - "google-api-core 71.9kB @ 54.8kB/s 0.1s\n", - "smart_open 44.2kB @ 33.5kB/s 0.0s\n", - "peppy 26.3kB @ 19.7kB/s 0.1s\n", - "yte 17.4kB @ 13.0kB/s 0.0s\n", - "python 30.0MB @ 22.3MB/s 0.6s\n", - "[+] 1.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (55) ━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━━\u001b[0m 35 amply 1.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 1.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (55) ━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━━\u001b[0m 35 amply 1.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 1.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (54) ━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━\u001b[0m 36 amply 1.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 1.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (53) ━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━\u001b[0m 37 aioeasywebdav 1.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 1.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (53) ━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━\u001b[0m 37 aioeasywebdav 1.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 1.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (52) ━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━\u001b[0m 38 aioeasywebdav 1.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (52) ━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━\u001b[0m 38 aioeasywebdav 1.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (52) ━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━\u001b[0m 38 aiohttp 1.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (51) ━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━\u001b[0m 39 aiohttp 2.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (49) ━━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━\u001b[0m 41 aiohttp 2.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (48) ━━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━\u001b[0m 42 aiohttp 2.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (48) ━━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━\u001b[0m 42 attmap 2.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (47) ━━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━\u001b[0m 43 attmap 2.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (47) ━━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━\u001b[0m 43 attmap 2.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (44) ━━━━━━━━━━╸\u001b[33m━━━━━━━━━━━━\u001b[0m 46 attmap 2.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (42) ━━━━━━━━━━━╸\u001b[33m━━━━━━━━━━━\u001b[0m 48 bcrypt 2.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (40) ━━━━━━━━━━━╸\u001b[33m━━━━━━━━━━━\u001b[0m 50 bcrypt 2.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (38) ━━━━━━━━━━━━╸\u001b[33m━━━━━━━━━━\u001b[0m 52 bcrypt 2.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (35) ━━━━━━━━━━━━━╸\u001b[33m━━━━━━━━━\u001b[0m 55 bcrypt 3.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (34) ━━━━━━━━━━━━━╸\u001b[33m━━━━━━━━━\u001b[0m 56 botocore 3.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (30) ━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━━\u001b[0m 60 botocore 3.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (28) ━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━━\u001b[0m 62 botocore 3.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (25) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 65 botocore 3.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (24) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 66 coin-or-cbc 3.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (23) ━━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━\u001b[0m 67 coin-or-cbc 3.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (20) ━━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━\u001b[0m 70 coin-or-cbc 3.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (18) ━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━━\u001b[0m 72 coin-or-cbc 3.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (15) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 75 connection_pool 3.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (13) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 77 connection_pool 4.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (9) ━━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━\u001b[0m 81 botocore 4.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (6) ━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━━\u001b[0m 84 botocore 4.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (5) ━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━━\u001b[0m 85 botocore 4.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (5) ━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━━\u001b[0m 85 botocore 4.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (3) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 87 google-api-python-client 4.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (3) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 87 google-api-python-client 4.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (3) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 87 google-api-python-client 4.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (3) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 87 google-api-python-client 4.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (3) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 87 python 4.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (3) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 87 python 5.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (3) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 87 python 5.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (3) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 87 python 5.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (3) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 87 botocore 5.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (3) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 87 botocore 5.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (3) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 87 botocore 5.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (3) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 87 botocore 5.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (3) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 87 google-api-python-client 5.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (3) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 87 google-api-python-client 5.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (3) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 87 google-api-python-client 5.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 88 botocore 6.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 88 botocore 6.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 88 botocore 6.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 88 botocore 6.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 88 python 6.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 88 python 6.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (1) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 89 python 6.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (1) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 89 python 6.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (1) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 89 python 6.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (1) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 89 python 6.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting (1) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 89 python 7.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 85.4MB 1.3s\n", - "Extracting ━━━━━━━━━━━━━━━━━━━━━━━ 90 7.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G\u001b[?25hPreparing transaction: done\n", - "Verifying transaction: done\n", - "Executing transaction: done\n", - "Installing pip dependencies: \\ Ran pip subprocess with arguments:\n", - "['/opt/conda/envs/snakemake/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/jupyter/condaenv.f9a1h2xy.requirements.txt']\n", - "Pip subprocess output:\n", - "Collecting jupyterlab\n", - " Using cached jupyterlab-3.4.4-py3-none-any.whl (8.8 MB)\n", - "Collecting jupyterlab-server~=2.10\n", - " Using cached jupyterlab_server-2.15.0-py3-none-any.whl (54 kB)\n", - "Collecting ipython\n", - " Using cached ipython-8.4.0-py3-none-any.whl (750 kB)\n", - "Collecting notebook<7\n", - " Using cached notebook-6.4.12-py3-none-any.whl (9.9 MB)\n", - "Requirement already satisfied: jupyter-core in /opt/conda/envs/snakemake/lib/python3.10/site-packages (from jupyterlab->-r /home/jupyter/condaenv.f9a1h2xy.requirements.txt (line 1)) (4.11.1)\n", - "Requirement already satisfied: packaging in /opt/conda/envs/snakemake/lib/python3.10/site-packages (from jupyterlab->-r /home/jupyter/condaenv.f9a1h2xy.requirements.txt (line 1)) (21.3)\n", - "Collecting tornado>=6.1.0\n", - " Using cached tornado-6.2-cp37-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (423 kB)\n", - "Collecting jupyter-server~=1.16\n", - " Using cached jupyter_server-1.18.1-py3-none-any.whl (344 kB)\n", - "Requirement already satisfied: jinja2>=2.1 in /opt/conda/envs/snakemake/lib/python3.10/site-packages (from jupyterlab->-r /home/jupyter/condaenv.f9a1h2xy.requirements.txt (line 1)) (3.1.2)\n", - "Collecting nbclassic\n", - " Using cached nbclassic-0.4.3-py3-none-any.whl (9.7 MB)\n", - "Requirement already satisfied: MarkupSafe>=2.0 in /opt/conda/envs/snakemake/lib/python3.10/site-packages (from jinja2>=2.1->jupyterlab->-r /home/jupyter/condaenv.f9a1h2xy.requirements.txt (line 1)) (2.1.1)\n", - "Collecting anyio<4,>=3.1.0\n", - " Using cached anyio-3.6.1-py3-none-any.whl (80 kB)\n", - "Collecting websocket-client\n", - " Using cached websocket_client-1.3.3-py3-none-any.whl (54 kB)\n", - "Collecting Send2Trash\n", - " Using cached Send2Trash-1.8.0-py3-none-any.whl (18 kB)\n", - "Requirement already satisfied: nbformat>=5.2.0 in /opt/conda/envs/snakemake/lib/python3.10/site-packages (from jupyter-server~=1.16->jupyterlab->-r /home/jupyter/condaenv.f9a1h2xy.requirements.txt (line 1)) (5.4.0)\n", - "Collecting jupyter-client>=6.1.12\n", - " Using cached jupyter_client-7.3.4-py3-none-any.whl (132 kB)\n", - "Collecting prometheus-client\n", - " Using cached prometheus_client-0.14.1-py3-none-any.whl (59 kB)\n", - "Collecting nbconvert>=6.4.4\n", - " Using cached nbconvert-6.5.0-py3-none-any.whl (561 kB)\n", - "Requirement already satisfied: traitlets>=5.1 in /opt/conda/envs/snakemake/lib/python3.10/site-packages (from jupyter-server~=1.16->jupyterlab->-r /home/jupyter/condaenv.f9a1h2xy.requirements.txt (line 1)) (5.3.0)\n", - "Collecting argon2-cffi\n", - " Using cached argon2_cffi-21.3.0-py3-none-any.whl (14 kB)\n", - "Collecting pyzmq>=17\n", - " Downloading pyzmq-23.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)\n", - " ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 9.9 MB/s eta 0:00:00\n", - "Collecting terminado>=0.8.3\n", - " Using cached terminado-0.15.0-py3-none-any.whl (16 kB)\n", - "Collecting babel\n", - " Using cached Babel-2.10.3-py3-none-any.whl (9.5 MB)\n", - "Requirement already satisfied: requests in /opt/conda/envs/snakemake/lib/python3.10/site-packages (from jupyterlab-server~=2.10->jupyterlab->-r /home/jupyter/condaenv.f9a1h2xy.requirements.txt (line 1)) (2.28.1)\n", - "Requirement already satisfied: jsonschema>=3.0.1 in /opt/conda/envs/snakemake/lib/python3.10/site-packages (from jupyterlab-server~=2.10->jupyterlab->-r /home/jupyter/condaenv.f9a1h2xy.requirements.txt (line 1)) (4.9.1)\n", - "Collecting json5\n", - " Using cached json5-0.9.9-py2.py3-none-any.whl (18 kB)\n", - 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"Installing collected packages: webencodings, Send2Trash, pure-eval, ptyprocess, pickleshare, mistune, json5, ipython-genutils, executing, backcall, websocket-client, tornado, tinycss2, soupsieve, sniffio, pyzmq, prompt-toolkit, prometheus-client, pexpect, parso, pandocfilters, nest-asyncio, matplotlib-inline, jupyterlab-pygments, entrypoints, debugpy, bleach, babel, asttokens, terminado, stack-data, jupyter-client, jedi, beautifulsoup4, argon2-cffi-bindings, anyio, nbclient, ipython, argon2-cffi, nbconvert, ipykernel, notebook, jupyter-server, notebook-shim, jupyterlab-server, nbclassic, jupyterlab\n", - "Successfully installed Send2Trash-1.8.0 anyio-3.6.1 argon2-cffi-21.3.0 argon2-cffi-bindings-21.2.0 asttokens-2.0.5 babel-2.10.3 backcall-0.2.0 beautifulsoup4-4.11.1 bleach-5.0.1 debugpy-1.6.2 entrypoints-0.4 executing-0.9.1 ipykernel-6.15.1 ipython-8.4.0 ipython-genutils-0.2.0 jedi-0.18.1 json5-0.9.9 jupyter-client-7.3.4 jupyter-server-1.18.1 jupyterlab-3.4.4 jupyterlab-pygments-0.2.2 jupyterlab-server-2.15.0 matplotlib-inline-0.1.3 mistune-0.8.4 nbclassic-0.4.3 nbclient-0.6.6 nbconvert-6.5.0 nest-asyncio-1.5.5 notebook-6.4.12 notebook-shim-0.1.0 pandocfilters-1.5.0 parso-0.8.3 pexpect-4.8.0 pickleshare-0.7.5 prometheus-client-0.14.1 prompt-toolkit-3.0.30 ptyprocess-0.7.0 pure-eval-0.2.2 pyzmq-23.2.0 sniffio-1.2.0 soupsieve-2.3.2.post1 stack-data-0.3.0 terminado-0.15.0 tinycss2-1.1.1 tornado-6.2 webencodings-0.5.1 websocket-client-1.3.3\n", - "\n", - "done\n", - "#\n", - "# To activate this environment, use\n", - "#\n", - "# $ conda activate snakemake\n", - "#\n", - "# To deactivate an active environment, use\n", - "#\n", - "# $ conda deactivate\n", - "\n" - ] - } - ], + "metadata": {}, + "outputs": [], "source": [ "!mamba env create -f env.yml" ] } ], - "metadata": { - "environment": { - "kernel": "python3", - "name": "common-cpu.m94", - "type": "gcloud", - "uri": "gcr.io/deeplearning-platform-release/base-cpu:m94" - }, - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.7.12" - } - }, + "metadata": {}, "nbformat": 4, "nbformat_minor": 5 } diff --git a/docs/HowToUseNextflowandGCPLifeSciences.ipynb b/docs/HowToUseNextflowandGCPLifeSciences.ipynb index 21a0197..2d29038 100644 --- a/docs/HowToUseNextflowandGCPLifeSciences.ipynb +++ b/docs/HowToUseNextflowandGCPLifeSciences.ipynb @@ -3,9 +3,7 @@ { "cell_type": "markdown", "id": "0f8f4b85-9459-497d-97ec-5909e8aeacae", - "metadata": { - "tags": [] - }, + "metadata": {}, "source": [ "# 1. Submit a Job directly to Life Science API" ] @@ -22,18 +20,10 @@ }, { "cell_type": "code", - "execution_count": 57, + "execution_count": null, "id": "3cb5bd4b-032a-47f0-bee4-299a547c3b48", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Running [projects/25874201052/locations/us-central1/operations/17977600789736315778].\n" - ] - } - ], + "outputs": [], "source": [ "!gcloud beta lifesciences pipelines run \\\n", " --location us-central1 \\\n", @@ -45,70 +35,17 @@ { "cell_type": "markdown", "id": "f4892a16-f4d9-4db9-a171-6e9245df2a72", - "metadata": { - "tags": [] - }, + "metadata": {}, "source": [ "### 1.2 Check job status" ] }, { "cell_type": "code", - "execution_count": 58, + "execution_count": null, "id": "9cba7c4e-4b8c-4e4c-80e4-8de1f11b5790", - "metadata": { - "scrolled": true, - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "metadata:\n", - " '@type': type.googleapis.com/google.cloud.lifesciences.v2beta.Metadata\n", - " createTime: '2022-07-27T18:22:48.187635Z'\n", - " events:\n", - " - description: Worker \"google-pipelines-worker-a90f18302bb692140844568b5f65ee4c\"\n", - " assigned in \"us-east1-b\" on a \"n1-standard-1\" machine\n", - " timestamp: '2022-07-27T18:22:57.589812819Z'\n", - " workerAssigned:\n", - " instance: google-pipelines-worker-a90f18302bb692140844568b5f65ee4c\n", - " machineType: n1-standard-1\n", - " zone: us-east1-b\n", - " pipeline:\n", - " actions:\n", - " - commands:\n", - " - -c\n", - " - echo \"hello world!\"\n", - " entrypoint: bash\n", - " imageUri: google/cloud-sdk:slim\n", - " - alwaysRun: true\n", - " commands:\n", - " - /bin/sh\n", - " - -c\n", - " - gsutil -m -q cp /google/logs/output gs://nextflowdemobucket/zy-test/example.log\n", - " imageUri: google/cloud-sdk:slim\n", - " resources:\n", - " regions:\n", - " - us-east1\n", - " virtualMachine:\n", - " bootDiskSizeGb: 10\n", - " bootImage: projects/cos-cloud/global/images/family/cos-stable\n", - " labels:\n", - " goog-pipelines-worker: 'true'\n", - " machineType: n1-standard-1\n", - " nvidiaDriverVersion: 450.51.06\n", - " serviceAccount:\n", - " email: default\n", - " scopes:\n", - " - https://www.googleapis.com/auth/cloud-platform\n", - " timeout: 604800s\n", - " startTime: '2022-07-27T18:22:57.589812819Z'\n", - "name: projects/25874201052/locations/us-central1/operations/17977600789736315778\n" - ] - } - ], + "metadata": {}, + "outputs": [], "source": [ "#To check the job status enter operation ID from the gcloud output in command below : \n", "#Running [projects/PROJECT_ID/locations/LOCATION/operations/OPERATION_ID]\n", @@ -125,21 +62,10 @@ }, { "cell_type": "code", - "execution_count": 59, + "execution_count": null, "id": "02faf944-0143-49c7-bf4c-6b8e377fcd81", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Copying gs://nextflowdemobucket/zy-test/example.log...\n", - "/ [1 files][ 13.0 B/ 13.0 B] \n", - "Operation completed over 1 objects/13.0 B. \n", - "hello world!\n" - ] - } - ], + "outputs": [], "source": [ "!gsutil cp gs://nextflowdemobucket/zy-test/example.log .\n", "!cat example.log" @@ -156,9 +82,7 @@ { "cell_type": "markdown", "id": "783043ae-1598-4157-a3a9-58064197665d", - "metadata": { - "tags": [] - }, + "metadata": {}, "source": [ "### 2.1 Create a Nexflow Service Account" ] @@ -243,53 +167,17 @@ { "cell_type": "markdown", "id": "292bbf27-57db-4503-8a5f-acf540fedb4f", - "metadata": { - "tags": [] - }, + "metadata": {}, "source": [ "### 2.4 Install Nextflow" ] }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "id": "06043e64-ba89-43f0-8397-7f2fa0cd6789", - "metadata": { - "scrolled": true, - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Hit:2 http://packages.cloud.google.com/apt cloud-sdk-buster InRelease \u001b[0m\n", - "Hit:3 http://packages.cloud.google.com/apt google-cloud-packages-archive-keyring-buster InRelease\n", - "Hit:4 http://packages.cloud.google.com/apt gcsfuse-buster InRelease \u001b[0m\n", - "Hit:1 https://packages.cloud.google.com/apt kubernetes-xenial InRelease \u001b[0m\n", - "Get:5 http://packages.cloud.google.com/apt google-compute-engine-buster-stable InRelease [5526 B]\n", - "Hit:6 http://deb.debian.org/debian buster InRelease \u001b[0m\u001b[33m\n", - "Hit:7 http://security.debian.org/debian-security buster/updates InRelease \u001b[0m\n", - "Hit:8 https://cloud.r-project.org/bin/linux/debian buster-cran40/ InRelease \u001b[0m\n", - "Hit:9 http://deb.debian.org/debian buster-updates InRelease \u001b[0m \n", - "Hit:10 http://deb.debian.org/debian buster-backports InRelease\n", - "Get:11 https://download.docker.com/linux/debian buster InRelease [54.0 kB]\n", - "Fetched 59.5 kB in 1s (66.3 kB/s) \u001b[0m\u001b[33m\u001b[33m\u001b[33m\u001b[33m\u001b[33m\u001b[33m\u001b[33m\u001b[33m\u001b[33m\u001b[33m\n", - "Reading package lists... Done\n", - "Building dependency tree \n", - "Reading state information... Done\n", - "1 package can be upgraded. Run 'apt list --upgradable' to see it.\n", - "Reading package lists... Done\n", - "Building dependency tree \n", - "Reading state information... Done\n", - "default-jdk is already the newest version (2:1.11-71).\n", - "0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.\n", - "openjdk version \"11.0.16\" 2022-07-19\n", - "OpenJDK Runtime Environment (build 11.0.16+8-post-Debian-1deb10u1)\n", - "OpenJDK 64-Bit Server VM (build 11.0.16+8-post-Debian-1deb10u1, mixed mode, sharing)\n" - ] - } - ], + "metadata": {}, + "outputs": [], "source": [ "#First install java\n", "!sudo apt update\n", @@ -299,47 +187,10 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "12458efd-38d1-4710-a4be-11d266b6a1d2", - "metadata": { - "scrolled": true, - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - " % Total % Received % Xferd Average Speed Time Time Time Current\n", - " Dload Upload Total Spent Left Speed\n", - "100 14624 100 14624 0 0 88726 0 --:--:-- --:--:-- --:--:-- 89170\n", - "\u001b[Knloading nextflow dependencies. It may require a few seconds, please wait .. Downloading nextflow dependencies. It may require a few seconds, please wait .. \n", - " N E X T F L O W\n", - " version 22.04.5 build 5708\n", - " created 15-07-2022 16:09 UTC \n", - " cite doi:10.1038/nbt.3820\n", - " http://nextflow.io\n", - "\n", - "\n", - "Nextflow installation completed. Please note:\n", - "- the executable file `nextflow` has been created in the folder: /home/jupyter\n", - "- you may complete the installation by moving it to a directory in your $PATH\n", - "\n", - "\u001b[Knloading nextflow dependencies. It may require a few seconds, please wait .. Downloading nextflow dependencies. It may require a few seconds, please wait .. \n", - " N E X T F L O W\n", - " version 22.04.5 build 5708\n", - " created 15-07-2022 16:09 UTC \n", - " cite doi:10.1038/nbt.3820\n", - " http://nextflow.io\n", - "\n", - "\n", - "Nextflow installation completed. Please note:\n", - "- the executable file `nextflow` has been created in the folder: .\n", - "- you may complete the installation by moving it to a directory in your $PATH\n", - "\n" - ] - } - ], + "metadata": {}, + "outputs": [], "source": [ "#Specify platfrom\n", "!export NXF_MODE=google\n", @@ -398,44 +249,20 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "6efad386-185b-4faf-be39-6c5a3f84ffe4", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "N E X T F L O W ~ version 22.04.5\n", - "Launching `hello.nf` [soggy_cuvier] DSL2 - revision: f5c6efda4a\n", - "[- ] process > sayHello [ 0%] 0 of 1\u001b[K\n", - "\u001b[2A\n", - "executor > local (1)\u001b[K\n", - "[cf/4cfacf] process > sayHello [100%] 1 of 1 ✔\u001b[K\n", - "Hello!\u001b[K\n", - "\u001b[K\n", - "\n" - ] - } - ], + "outputs": [], "source": [ "!./nextflow run hello.nf --str 'Hello!'" ] }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "89a13f0c-4b12-4dd3-92ad-795d301f9805", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "hello\n" - ] - } - ], + "outputs": [], "source": [ "!cat /home/jupyter/work/34/35a36d596ad458c0d2dc2e2a8193f9/hello.txt" ] @@ -443,9 +270,7 @@ { "cell_type": "markdown", "id": "7619875d-7f10-4699-b4d2-120d5d7d4cd7", - "metadata": { - "tags": [] - }, + "metadata": {}, "source": [ "### 2.6 Create and modify your own config file to include a 'gls' profile block" ] @@ -495,9 +320,7 @@ { "cell_type": "markdown", "id": "340f7300-449a-4a12-bbc5-073547d58cac", - "metadata": { - "tags": [] - }, + "metadata": {}, "source": [ "### Optional: Listing nf-core tools with docker and viewing their commands\n", "Using the command below you can see all the tools that nfcore holds and their versions/lastes releases" @@ -505,115 +328,10 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "ca1ff164-cee2-446e-ab2e-a3ed984e0dc0", - "metadata": { - "scrolled": true, - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n", - " ,--./,-.\n", - " ___ __ __ __ ___ /,-._.--~\\\n", - " |\\ | |__ __ / ` / \\ |__) |__ } {\n", - " | \\| | \\__, \\__/ | \\ |___ \\`-._,-`-,\n", - " `._,._,'\n", - "\n", - " nf-core/tools version 2.4.1 - https://nf-co.re\n", - "\n", - "\n", - "┏━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓\n", - "┃ Pipeline ┃ ┃ Latest ┃ ┃ ┃ Have latest ┃\n", - "┃ Name ┃ Stars ┃ Release ┃ Released ┃ Last Pulled ┃ release? ┃\n", - "┡━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━┩\n", - "│ sarek │ 180 │ 3.0 │ 1 week ago │ - │ - │\n", - "│ viralrecon │ 73 │ 2.5 │ 2 weeks ago │ - │ - │\n", - "│ rnafusion │ 76 │ 2.1.0 │ 2 weeks ago │ - │ - │\n", - "│ isoseq │ 4 │ 1.1.0 │ 2 weeks ago │ - │ - │\n", - "│ fetchngs │ 58 │ 1.7 │ 4 weeks ago │ - │ - │\n", - "│ circdna │ 8 │ 1.0.1 │ 1 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ nanoseq │ 79 │ 3.0.0 │ 1 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ rnavar │ 8 │ 1.0.0 │ 1 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ scrnaseq │ 59 │ 2.0.0 │ 1 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ mag │ 94 │ 2.2.0 │ 1 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ cutandrun │ 29 │ 2.0 │ 2 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ airrflow │ 19 │ 2.2.0 │ 2 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ smrnaseq │ 41 │ 2.0.0 │ 2 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ rnaseq │ 489 │ 3.8.1 │ 2 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ ampliseq │ 91 │ 2.3.2 │ 2 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ mnaseseq │ 7 │ 1.0.0 │ 2 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ atacseq │ 110 │ 1.2.2 │ 3 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ mhcquant │ 19 │ 2.3.1 │ 3 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ hicar │ 2 │ 1.0.0 │ 3 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ quantms │ 3 │ 1.0 │ 3 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ eager │ 70 │ 2.4.4 │ 4 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ epitopepre… │ 19 │ 2.0.0 │ 7 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ bacass │ 36 │ 2.0.0 │ 11 months │ - │ - │\n", - "│ │ │ │ ago │ │ │\n", - "│ bactmap │ 30 │ 1.0.0 │ 1 years ago │ - │ - │\n", - "│ hic │ 37 │ 1.3.0 │ 1 years ago │ - │ - │\n", - "│ metaboigni… │ 8 │ 1.0.1 │ 1 years ago │ - │ - │\n", - "│ methylseq │ 88 │ 1.6.1 │ 1 years ago │ - │ - │\n", - "│ diaproteom… │ 10 │ 1.2.4 │ 1 years ago │ - │ - │\n", - "│ clipseq │ 11 │ 1.0.0 │ 1 years ago │ - │ - │\n", - "│ pgdb │ 3 │ 1.0.0 │ 1 years ago │ - │ - │\n", - "│ chipseq │ 114 │ 1.2.2 │ 1 years ago │ - │ - │\n", - "│ dualrnaseq │ 7 │ 1.0.0 │ 1 years ago │ - │ - │\n", - "│ cageseq │ 8 │ 1.0.2 │ 2 years ago │ - │ - │\n", - "│ proteomics… │ 23 │ 1.0.0 │ 2 years ago │ - │ - │\n", - "│ hlatyping │ 29 │ 1.2.0 │ 2 years ago │ - │ - │\n", - "│ imcyto │ 16 │ 1.0.0 │ 2 years ago │ - │ - │\n", - "│ slamseq │ 4 │ 1.0.0 │ 2 years ago │ - │ - │\n", - "│ coproid │ 5 │ 1.1 │ 2 years ago │ - │ - │\n", - "│ nascent │ 3 │ 1.0 │ 3 years ago │ - │ - │\n", - "│ circrna │ 18 │ dev │ - │ - │ - │\n", - "│ crisprseq │ 1 │ dev │ - │ - │ - │\n", - "│ crisprvar │ 4 │ dev │ - │ - │ - │\n", - "│ demultiplex │ 11 │ dev │ - │ - │ - │\n", - "│ denovohybr… │ 3 │ dev │ - │ - │ - │\n", - "│ funcscan │ 2 │ dev │ - │ - │ - │\n", - "│ genomeanno… │ 2 │ dev │ - │ - │ - │\n", - "│ genomeasse… │ 7 │ dev │ - │ - │ - │\n", - "│ gwas │ 9 │ dev │ - │ - │ - │\n", - "│ hgtseq │ 4 │ dev │ - │ - │ - │\n", - "│ kmermaid │ 15 │ dev │ - │ - │ - │\n", - "│ liverctana… │ 0 │ dev │ - │ - │ - │\n", - "│ lncpipe │ 23 │ dev │ - │ - │ - │\n", - "│ metapep │ 0 │ dev │ - │ - │ - │\n", - "│ nanostring │ 1 │ dev │ - │ - │ - │\n", - "│ pangenome │ 16 │ dev │ - │ - │ - │\n", - "│ proteinfold │ 1 │ dev │ - │ - │ - │\n", - "│ raredisease │ 19 │ dev │ - │ - │ - │\n", - "│ rnadnavar │ 0 │ dev │ - │ - │ - │\n", - "│ scflow │ 12 │ dev │ - │ - │ - │\n", - "│ spatialtra… │ 10 │ dev │ - │ - │ - │\n", - "│ ssds │ 0 │ dev │ - │ - │ - │\n", - "│ taxprofiler │ 17 │ dev │ - │ - │ - │\n", - "└─────────────┴───────┴─────────────┴─────────────┴─────────────┴──────────────┘\n" - ] - } - ], + "metadata": {}, + "outputs": [], "source": [ "!docker run nfcore/tools list" ] @@ -628,96 +346,10 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "id": "05ea2893-60b3-4934-ae86-b07d4bc59728", - "metadata": { - "scrolled": true, - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "N E X T F L O W ~ version 22.04.5\n", - "Launching `https://github.com/nf-core/methylseq` [tiny_sanger] DSL1 - revision: 03972a686b [1.6.1]\n", - "\n", - "\n", - "-\u001b[2m----------------------------------------------------\u001b[0m-\n", - " \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n", - "\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n", - "\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n", - "\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n", - " \u001b[0;32m`._,._,'\u001b[0m\n", - "\u001b[0;35m nf-core/methylseq v1.6.1\u001b[0m\n", - "-\u001b[2m----------------------------------------------------\u001b[0m-\n", - "\n", - "Typical pipeline command:\n", - "\n", - " \u001b[0;36mnextflow run nf-core/methylseq --input '*_R{1,2}.fastq.gz' -profile docker\u001b[0m\n", - "\n", - "\u001b[4m\u001b[1mInput/output options\u001b[0m\n", - " --input \u001b[2m[string] \u001b[0mInput FastQ files.\u001b[2m\u001b[0m\n", - " --single_end \u001b[2m[boolean] \u001b[0mSpecifies that the input is single-end reads.\u001b[2m\u001b[0m\n", - " --outdir \u001b[2m[string] \u001b[0mThe output directory where the results will be saved.\u001b[2m [default: ./results]\u001b[0m\n", - " --email \u001b[2m[string] \u001b[0mEmail address for completion summary.\u001b[2m\u001b[0m\n", - "\n", - "\u001b[4m\u001b[1mAlignment options\u001b[0m\n", - " --aligner \u001b[2m[string] \u001b[0mAlignment tool to use.\u001b[2m [default: bismark]\u001b[0m\n", - " --comprehensive \u001b[2m[boolean] \u001b[0mOutput information for all cytosine contexts.\u001b[2m\u001b[0m\n", - "\n", - "\u001b[4m\u001b[1mSpecial library types\u001b[0m\n", - " --pbat \u001b[2m[boolean] \u001b[0mPreset for working with PBAT libraries.\u001b[2m\u001b[0m\n", - " --rrbs \u001b[2m[boolean] \u001b[0mTurn on if dealing with MspI digested material.\u001b[2m\u001b[0m\n", - " --slamseq \u001b[2m[boolean] \u001b[0mRun bismark in SLAM-seq mode.\u001b[2m\u001b[0m\n", - " --em_seq \u001b[2m[boolean] \u001b[0mPreset for EM-seq libraries.\u001b[2m\u001b[0m\n", - " --single_cell \u001b[2m[boolean] \u001b[0mTrimming preset for single-cell bisulfite libraries.\u001b[2m\u001b[0m\n", - " --accel \u001b[2m[boolean] \u001b[0mTrimming preset for the Accel kit.\u001b[2m\u001b[0m\n", - " --cegx \u001b[2m[boolean] \u001b[0mTrimming preset for the CEGX bisulfite kit.\u001b[2m\u001b[0m\n", - " --epignome \u001b[2m[boolean] \u001b[0mTrimming preset for the Epignome kit.\u001b[2m\u001b[0m\n", - " --zymo \u001b[2m[boolean] \u001b[0mTrimming preset for the Zymo kit.\u001b[2m\u001b[0m\n", - "\n", - "\u001b[4m\u001b[1mReference genome options\u001b[0m\n", - " --genome \u001b[2m[string] \u001b[0mName of iGenomes reference.\u001b[2m\u001b[0m\n", - " --fasta \u001b[2m[string] \u001b[0mPath to FASTA genome file.\u001b[2m\u001b[0m\n", - " --fasta_index \u001b[2m[string] \u001b[0mPath to Fasta index file.\u001b[2m\u001b[0m\n", - " --bismark_index \u001b[2m[string] \u001b[0mPath to a directory containing a Bismark reference index.\u001b[2m\u001b[0m\n", - " --bwa_meth_index \u001b[2m[string] \u001b[0mbwameth index filename base\u001b[2m\u001b[0m\n", - " --save_reference \u001b[2m[boolean] \u001b[0mSave reference(s) to results directory\u001b[2m\u001b[0m\n", - "\n", - "\u001b[4m\u001b[1mAdapter Trimming\u001b[0m\n", - " --clip_r1 \u001b[2m[integer] \u001b[0mTrim bases from the 5' end of read 1 (or single-end reads).\u001b[2m\u001b[0m\n", - " --clip_r2 \u001b[2m[integer] \u001b[0mTrim bases from the 5' end of read 2 (paired-end only).\u001b[2m\u001b[0m\n", - " --three_prime_clip_r1 \u001b[2m[integer] \u001b[0mTrim bases from the 3' end of read 1 AFTER adapter/quality trimming.\u001b[2m\u001b[0m\n", - " --three_prime_clip_r2 \u001b[2m[integer] \u001b[0mTrim bases from the 3' end of read 2 AFTER adapter/quality trimming\u001b[2m\u001b[0m\n", - "\n", - "\u001b[4m\u001b[1mBismark options\u001b[0m\n", - " --non_directional \u001b[2m[boolean] \u001b[0mRun alignment against all four possible strands.\u001b[2m\u001b[0m\n", - " --cytosine_report \u001b[2m[boolean] \u001b[0mOutput stranded cytosine report during Bismark's bismark_methylation_extractor step.\u001b[2m\u001b[0m\n", - " --relax_mismatches \u001b[2m[boolean] \u001b[0mTurn on to relax stringency for alignment (set allowed penalty with --num_mismatches).\u001b[2m\u001b[0m\n", - " --num_mismatches \u001b[2m[number] \u001b[0m0.6 will allow a penalty of bp * -0.6 - for 100bp reads (bismark default is 0.2)\u001b[2m [default: 0.6]\u001b[0m\n", - " --unmapped \u001b[2m[boolean] \u001b[0mSave unmapped reads to FastQ files\u001b[2m\u001b[0m\n", - " --meth_cutoff \u001b[2m[integer] \u001b[0mSpecify a minimum read coverage to report a methylation call\u001b[2m\u001b[0m\n", - " --known_splices \u001b[2m[string] \u001b[0mSupply a .gtf file containing known splice sites (bismark_hisat only).\u001b[2m\u001b[0m\n", - " --local_alignment \u001b[2m[boolean] \u001b[0mAllow soft-clipping of reads (potentially useful for single-cell experiments).\u001b[2m\u001b[0m\n", - " --minins \u001b[2m[integer] \u001b[0mThe minimum insert size for valid paired-end alignments.\u001b[2m\u001b[0m\n", - " --maxins \u001b[2m[integer] \u001b[0mThe maximum insert size for valid paired-end alignments.\u001b[2m\u001b[0m\n", - "\n", - "\u001b[4m\u001b[1mbwa-meth options\u001b[0m\n", - " --min_depth \u001b[2m[integer] \u001b[0mSpecify a minimum read coverage for MethylDackel to report a methylation call.\u001b[2m\u001b[0m\n", - " --ignore_flags \u001b[2m[boolean] \u001b[0mMethylDackel - ignore SAM flags\u001b[2m\u001b[0m\n", - " --methyl_kit \u001b[2m[boolean] \u001b[0mSave files for use with methylKit\u001b[2m\u001b[0m\n", - "\n", - "\u001b[4m\u001b[1mSkip pipeline steps\u001b[0m\n", - " --skip_trimming \u001b[2m[boolean] \u001b[0mSkip read trimming.\u001b[2m\u001b[0m\n", - " --skip_deduplication \u001b[2m[boolean] \u001b[0mSkip deduplication step after alignment.\u001b[2m\u001b[0m\n", - "\n", - "-\u001b[2m----------------------------------------------------\u001b[0m-\u001b[2m\n", - " Hiding 26 params, use --show_hidden_params to show.\n", - "\u001b[0m-\u001b[2m----------------------------------------------------\u001b[0m-\n" - ] - } - ], + "metadata": {}, + "outputs": [], "source": [ "!./nextflow run nf-core/methylseq -r 1.6.1 --help" ] @@ -725,9 +357,7 @@ { "cell_type": "markdown", "id": "b4dbef59-d619-4444-8870-18c1f0ba3b5c", - "metadata": { - "tags": [] - }, + "metadata": {}, "source": [ "### 2.7 Test Methylseq" ] @@ -744,1485 +374,10 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "id": "4b21f170-37fa-4fbc-ab83-3f6b4d386ef9", - "metadata": { - "scrolled": true, - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "N E X T F L O W ~ version 22.04.5\n", - "Launching `https://github.com/nf-core/methylseq` [grave_noether] DSL1 - revision: 03972a686b [1.6.1]\n", - "\n", - "\n", - "-\u001b[2m----------------------------------------------------\u001b[0m-\n", - " \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n", - "\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n", - "\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n", - "\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n", - " \u001b[0;32m`._,._,'\u001b[0m\n", - "\u001b[0;35m nf-core/methylseq v1.6.1\u001b[0m\n", - "-\u001b[2m----------------------------------------------------\u001b[0m-\n", - "\n", - "\u001b[1mCore Nextflow options\u001b[0m\n", - " \u001b[0;34mrevision : \u001b[0;32m1.6.1\u001b[0m\n", - " \u001b[0;34mrunName : \u001b[0;32mgrave_noether\u001b[0m\n", - " \u001b[0;34mcontainer : \u001b[0;32mnfcore/methylseq:1.6.1\u001b[0m\n", - " \u001b[0;34mlaunchDir : \u001b[0;32m/home/jupyter\u001b[0m\n", - " \u001b[0;34mworkDir : \u001b[0;32m/zy-test\u001b[0m\n", - " \u001b[0;34mprojectDir : \u001b[0;32m/home/jupyter/.nextflow/assets/nf-core/methylseq\u001b[0m\n", - " \u001b[0;34muserName : \u001b[0;32mjupyter\u001b[0m\n", - " \u001b[0;34mprofile : \u001b[0;32mtest,gls\u001b[0m\n", - " \u001b[0;34mconfigFiles : \u001b[0;32m/home/jupyter/.nextflow/assets/nf-core/methylseq/nextflow.config, /home/jupyter/nextflow.config, /home/jupyter/nextflow.config\u001b[0m\n", - "\n", - "\u001b[1mInput/output options\u001b[0m\n", - " \u001b[0;34msingle_end : \u001b[0;32mtrue\u001b[0m\n", - " \u001b[0;34moutdir : \u001b[0;32mgs://nextflowdemobucket/zy-test/test\u001b[0m\n", - "\n", - "\u001b[1mReference genome options\u001b[0m\n", - " \u001b[0;34mfasta : \u001b[0;32mhttps://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa\u001b[0m\n", - " \u001b[0;34mfasta_index : \u001b[0;32mhttps://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai\u001b[0m\n", - "\n", - "\u001b[1mGeneric options\u001b[0m\n", - " \u001b[0;34mmax_multiqc_email_size : \u001b[0;32m25 MB\u001b[0m\n", - " \u001b[0;34mtracedir : \u001b[0;32m./results/pipeline_info\u001b[0m\n", - "\n", - "\u001b[1mMax job request options\u001b[0m\n", - " \u001b[0;34mmax_cpus : \u001b[0;32m2\u001b[0m\n", - " \u001b[0;34mmax_memory : \u001b[0;32m6 GB\u001b[0m\n", - " \u001b[0;34mmax_time : \u001b[0;32m2d\u001b[0m\n", - "\n", - "\u001b[1mInstitutional config options\u001b[0m\n", - " \u001b[0;34mconfig_profile_name : \u001b[0;32mTest profile\u001b[0m\n", - " \u001b[0;34mconfig_profile_description: \u001b[0;32mMinimal test dataset to check pipeline function\u001b[0m\n", - "\n", - "-\u001b[2m----------------------------------------------------\u001b[0m-\u001b[2m\n", - " Only displaying parameters that differ from defaults.\n", - "\u001b[0m-\u001b[2m----------------------------------------------------\u001b[0m-\n", - "\u001b[33mWARN: Access to undefined parameter `bwa_meth_index` -- Initialise it to a default value eg. `params.bwa_meth_index = some_value`\u001b[39m\u001b[K\n", - "Uploading local `bin` scripts folder to gs://nextflowdemobucket/zy-test/tmp/41/689050d47ad996a3bfbef278f62276/bin\n", - "[- ] process > get_software_versions -\u001b[K\n", - "[- ] process > makeBismarkIndex -\u001b[K\n", - "\u001b[3A\n", - "[- ] process > get_software_versions -\u001b[K\n", - "[- ] process > makeBismarkIndex -\u001b[K\n", - "[- ] process > fastqc -\u001b[K\n", - "[- ] process > trim_galore -\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "\u001b[12A\n", - "[- ] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[- ] process > makeBismarkIndex -\u001b[K\n", - "[- ] process > fastqc -\u001b[K\n", - "[- ] process > trim_galore -\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[- ] process > output_documentation -\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (1)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[- ] process > makeBismarkIndex -\u001b[K\n", - "[- ] process > fastqc [ 0%] 0 of 2\u001b[K\n", - "[- ] process > trim_galore [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[- ] process > output_documentation -\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (1)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[- ] process > makeBismarkIndex [ 0%] 0 of 1\u001b[K\n", - "[- ] process > fastqc [ 0%] 0 of 2\u001b[K\n", - "[- ] process > trim_galore [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[- ] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (2)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[- ] process > makeBismarkIndex [ 0%] 0 of 1\u001b[K\n", - "[- ] process > fastqc [ 0%] 0 of 2\u001b[K\n", - "[ec/2900a5] process > trim_galore (SRR389222_sub1) [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[- ] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (3)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[- ] process > makeBismarkIndex [ 0%] 0 of 1\u001b[K\n", - "[a2/658755] process > fastqc (SRR389222_sub1) [ 0%] 0 of 2\u001b[K\n", - "[ec/2900a5] process > trim_galore (SRR389222_sub1) [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - 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"[40/f0dddd] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [ 0%] 0 of 1\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[e7/ba86f5] process > trim_galore (SRR389222_sub2) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [ 0%] 0 of 1\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [ 0%] 0 of 1\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [ 0%] 0 of 1\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [ 0%] 0 of 1\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [ 0%] 0 of 1\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [ 0%] 0 of 1\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [ 0%] 0 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [ 0%] 0 of 1\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [ 0%] 0 of 1\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [ 0%] 0 of 1\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[ec/2900a5] process > trim_galore (SRR389222_sub1) [ 33%] 1 of 3\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [ 0%] 0 of 1\u001b[K\n", - "[a2/658755] process > fastqc (SRR389222_sub1) [ 33%] 1 of 3\u001b[K\n", - "[ec/2900a5] process > trim_galore (SRR389222_sub1) [ 33%] 1 of 3\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [ 0%] 0 of 1\u001b[K\n", - "[63/bfd055] process > fastqc (SRR389222_sub2) [ 66%] 2 of 3\u001b[K\n", - "[ec/2900a5] process > trim_galore (SRR389222_sub1) [ 33%] 1 of 3\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [ 0%] 0 of 1\u001b[K\n", - "[63/bfd055] process > fastqc (SRR389222_sub2) [ 66%] 2 of 3\u001b[K\n", - "[e7/ba86f5] process > trim_galore (SRR389222_sub2) [ 66%] 2 of 3\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[63/bfd055] process > fastqc (SRR389222_sub2) [ 66%] 2 of 3\u001b[K\n", - "[e7/ba86f5] process > trim_galore (SRR389222_sub2) [ 66%] 2 of 3\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[63/bfd055] process > fastqc (SRR389222_sub2) [ 66%] 2 of 3\u001b[K\n", - "[e7/ba86f5] process > trim_galore (SRR389222_sub2) [ 66%] 2 of 3\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[63/bfd055] process > fastqc (SRR389222_sub2) [ 66%] 2 of 3 ✔\u001b[K\n", - "[e7/ba86f5] process > trim_galore (SRR389222_sub2) [ 66%] 2 of 3\u001b[K\n", - "[- ] process > bismark_align [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (10)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[e7/ba86f5] process > trim_galore (SRR389222_sub2) [ 66%] 2 of 3\u001b[K\n", - "[4f/08dcd8] process > bismark_align (SRR389222_sub1) [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (11)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[e7/ba86f5] process > trim_galore (SRR389222_sub2) [ 66%] 2 of 3\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (11)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[e7/ba86f5] process > trim_galore (SRR389222_sub2) [ 66%] 2 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (11)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (11)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (12)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[9d/be6b46] process > bismark_align (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (12)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[9d/be6b46] process > bismark_align (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (12)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[9d/be6b46] process > bismark_align (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (12)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[4f/08dcd8] process > bismark_align (SRR389222_sub1) [ 33%] 1 of 3\u001b[K\n", - "[- ] process > bismark_deduplicate [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq [ 0%] 0 of 1\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (13)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[4f/08dcd8] process > bismark_align (SRR389222_sub1) [ 33%] 1 of 3\u001b[K\n", - "[- ] process > bismark_deduplicate [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[78/f1c9c3] process > preseq (SRR389222_sub1) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (14)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[4f/08dcd8] process > bismark_align (SRR389222_sub1) [ 33%] 1 of 3\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[78/f1c9c3] process > preseq (SRR389222_sub1) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (14)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[9d/be6b46] process > bismark_align (SRR389222_sub3) [ 66%] 2 of 3\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[78/f1c9c3] process > preseq (SRR389222_sub1) [ 0%] 0 of 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (15)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[9d/be6b46] process > bismark_align (SRR389222_sub3) [ 66%] 2 of 3\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[78/f1c9c3] process > preseq (SRR389222_sub1) [ 0%] 0 of 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (16)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[9d/be6b46] process > bismark_align (SRR389222_sub3) [ 66%] 2 of 3\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 0%] 0 of 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (16)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (16)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (17)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[92/10a8f6] process > bismark_deduplicate (SRR389... [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (18)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[92/10a8f6] process > bismark_deduplicate (SRR389... [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[c0/7c754d] process > preseq (SRR389222_sub2) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (18)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[92/10a8f6] process > bismark_deduplicate (SRR389... [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[c0/7c754d] process > preseq (SRR389222_sub2) [ 0%] 0 of 3\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33mWARN: Google Pipelines > A resource limit has delayed the operation: generic::resource_exhausted: allocating: selecting resources: selecting region and zone: no available zones: us-central1: 30 C2_CPUS (20/500 available) usage too high\u001b[39m\u001b[K\n", - "\u001b[16A\n", - "executor > google-lifesciences (18)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[92/10a8f6] process > bismark_deduplicate (SRR389... [ 0%] 0 of 3\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33m[78/f1c9c3] NOTE: Process `preseq (SRR389222_sub1)` terminated with an error exit status (139) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[33m[f0/fb5ad1] NOTE: Process `preseq (SRR389222_sub3)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[K\n", - "\u001b[18A\n", - "executor > google-lifesciences (18)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[92/10a8f6] process > bismark_deduplicate (SRR389... [ 33%] 1 of 3\u001b[K\n", - "[- ] process > bismark_methXtract [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap [ 0%] 0 of 1\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33m[78/f1c9c3] NOTE: Process `preseq (SRR389222_sub1)` terminated with an error exit status (139) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[33m[f0/fb5ad1] NOTE: Process `preseq (SRR389222_sub3)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[K\n", - "\u001b[18A\n", - "executor > google-lifesciences (19)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[92/10a8f6] process > bismark_deduplicate (SRR389... [ 33%] 1 of 3\u001b[K\n", - "[- ] process > bismark_methXtract [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[67/b4fb43] process > qualimap (SRR389222_sub2) [ 0%] 0 of 1\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33m[78/f1c9c3] NOTE: Process `preseq (SRR389222_sub1)` terminated with an error exit status (139) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[33m[f0/fb5ad1] NOTE: Process `preseq (SRR389222_sub3)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[17A\n", - "executor > google-lifesciences (20)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[92/10a8f6] process > bismark_deduplicate (SRR389... [ 33%] 1 of 3\u001b[K\n", - "[82/5ff01a] process > bismark_methXtract (SRR3892... [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[67/b4fb43] process > qualimap (SRR389222_sub2) [ 0%] 0 of 1\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33m[78/f1c9c3] NOTE: Process `preseq (SRR389222_sub1)` terminated with an error exit status (139) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[33m[f0/fb5ad1] NOTE: Process `preseq (SRR389222_sub3)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[17A\n", - "executor > google-lifesciences (20)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[92/10a8f6] process > bismark_deduplicate (SRR389... [ 33%] 1 of 3\u001b[K\n", - "[82/5ff01a] process > bismark_methXtract (SRR3892... [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[67/b4fb43] process > qualimap (SRR389222_sub2) [ 0%] 0 of 1\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33m[78/f1c9c3] NOTE: Process `preseq (SRR389222_sub1)` terminated with an error exit status (139) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[33m[f0/fb5ad1] NOTE: Process `preseq (SRR389222_sub3)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[17A\n", - "executor > google-lifesciences (20)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[92/10a8f6] process > bismark_deduplicate (SRR389... [ 33%] 1 of 3\u001b[K\n", - "[82/5ff01a] process > bismark_methXtract (SRR3892... [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[67/b4fb43] process > qualimap (SRR389222_sub2) [ 0%] 0 of 1\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33m[78/f1c9c3] NOTE: Process `preseq (SRR389222_sub1)` terminated with an error exit status (139) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[33m[f0/fb5ad1] NOTE: Process `preseq (SRR389222_sub3)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[17A\n", - "executor > google-lifesciences (20)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[82/5ff01a] process > bismark_methXtract (SRR3892... [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[67/b4fb43] process > qualimap (SRR389222_sub2) [ 0%] 0 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33m[78/f1c9c3] NOTE: Process `preseq (SRR389222_sub1)` terminated with an error exit status (139) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[33m[f0/fb5ad1] NOTE: Process `preseq (SRR389222_sub3)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[17A\n", - "executor > google-lifesciences (21)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[82/5ff01a] process > bismark_methXtract (SRR3892... [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[a6/058bd2] process > qualimap (SRR389222_sub1) [ 0%] 0 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33m[78/f1c9c3] NOTE: Process `preseq (SRR389222_sub1)` terminated with an error exit status (139) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[33m[f0/fb5ad1] NOTE: Process `preseq (SRR389222_sub3)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[17A\n", - "executor > google-lifesciences (22)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[4a/560a3c] process > bismark_methXtract (SRR3892... [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[a6/058bd2] process > qualimap (SRR389222_sub1) [ 0%] 0 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33m[78/f1c9c3] NOTE: Process `preseq (SRR389222_sub1)` terminated with an error exit status (139) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[33m[f0/fb5ad1] NOTE: Process `preseq (SRR389222_sub3)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[17A\n", - "executor > google-lifesciences (22)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[4a/560a3c] process > bismark_methXtract (SRR3892... [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[a6/058bd2] process > qualimap (SRR389222_sub1) [ 0%] 0 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33m[78/f1c9c3] NOTE: Process `preseq (SRR389222_sub1)` terminated with an error exit status (139) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[33m[f0/fb5ad1] NOTE: Process `preseq (SRR389222_sub3)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[17A\n", - "executor > google-lifesciences (22)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[4a/560a3c] process > bismark_methXtract (SRR3892... [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[a6/058bd2] process > qualimap (SRR389222_sub1) [ 0%] 0 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33m[78/f1c9c3] NOTE: Process `preseq (SRR389222_sub1)` terminated with an error exit status (139) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[33m[f0/fb5ad1] NOTE: Process `preseq (SRR389222_sub3)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[17A\n", - "executor > google-lifesciences (22)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[4a/560a3c] process > bismark_methXtract (SRR3892... [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[67/b4fb43] process > qualimap (SRR389222_sub2) [ 50%] 1 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[K\n", - "\u001b[K\n", - "\u001b[17A\n", - "executor > google-lifesciences (22)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[4a/560a3c] process > bismark_methXtract (SRR3892... [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[67/b4fb43] process > qualimap (SRR389222_sub2) [ 50%] 1 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33mWARN: Failed to publish file: gs://nextflowdemobucket/zy-test/67/b4fb434d3c0259f99d06defc243652/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_qualimap; to: gs://nextflowdemobucket/zy-test/test/qualimap/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_qualimap [copy] -- See log file for details\u001b[39m\u001b[K\n", - "\u001b[K\n", - "\u001b[17A\n", - "executor > google-lifesciences (22)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[82/5ff01a] process > bismark_methXtract (SRR3892... [ 50%] 1 of 2\u001b[K\n", - "[- ] process > bismark_report [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[67/b4fb43] process > qualimap (SRR389222_sub2) [ 50%] 1 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33mWARN: Failed to publish file: gs://nextflowdemobucket/zy-test/67/b4fb434d3c0259f99d06defc243652/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_qualimap; to: gs://nextflowdemobucket/zy-test/test/qualimap/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_qualimap [copy] -- See log file for details\u001b[39m\u001b[K\n", - "\u001b[16A\n", - "executor > google-lifesciences (23)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[82/5ff01a] process > bismark_methXtract (SRR3892... [ 50%] 1 of 2\u001b[K\n", - "[7b/16d27f] process > bismark_report (SRR389222_s... [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[a6/058bd2] process > qualimap (SRR389222_sub1) [100%] 2 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33mWARN: Failed to publish file: gs://nextflowdemobucket/zy-test/67/b4fb434d3c0259f99d06defc243652/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_qualimap; to: gs://nextflowdemobucket/zy-test/test/qualimap/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_qualimap [copy] -- See log file for details\u001b[39m\u001b[K\n", - "\u001b[16A\n", - "executor > google-lifesciences (23)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[82/5ff01a] process > bismark_methXtract (SRR3892... [ 50%] 1 of 2\u001b[K\n", - "[7b/16d27f] process > bismark_report (SRR389222_s... [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[a6/058bd2] process > qualimap (SRR389222_sub1) [100%] 2 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33mWARN: Failed to publish file: gs://nextflowdemobucket/zy-test/67/b4fb434d3c0259f99d06defc243652/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_qualimap; to: gs://nextflowdemobucket/zy-test/test/qualimap/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_qualimap [copy] -- See log file for details\u001b[39m\u001b[K\n", - "\u001b[33mWARN: Failed to publish file: gs://nextflowdemobucket/zy-test/a6/058bd257af28d1454fedb253667590/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_qualimap; to: gs://nextflowdemobucket/zy-test/test/qualimap/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_qualimap [copy] -- See log file for details\u001b[39m\u001b[K\n", - "\u001b[17A\n", - "executor > google-lifesciences (23)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[82/5ff01a] process > bismark_methXtract (SRR3892... [ 50%] 1 of 2\u001b[K\n", - "[7b/16d27f] process > bismark_report (SRR389222_s... [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[a6/058bd2] process > qualimap (SRR389222_sub1) [100%] 2 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33mWARN: Failed to publish file: gs://nextflowdemobucket/zy-test/67/b4fb434d3c0259f99d06defc243652/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_qualimap; to: gs://nextflowdemobucket/zy-test/test/qualimap/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_qualimap [copy] -- See log file for details\u001b[39m\u001b[K\n", - "\u001b[33mWARN: Failed to publish file: gs://nextflowdemobucket/zy-test/a6/058bd257af28d1454fedb253667590/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_qualimap; to: gs://nextflowdemobucket/zy-test/test/qualimap/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_qualimap [copy] -- See log file for details\u001b[39m\u001b[K\n", - "\u001b[17A\n", - "executor > google-lifesciences (23)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[4a/560a3c] process > bismark_methXtract (SRR3892... [100%] 2 of 2\u001b[K\n", - "[7b/16d27f] process > bismark_report (SRR389222_s... [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[a6/058bd2] process > qualimap (SRR389222_sub1) [100%] 2 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33mWARN: Failed to publish file: gs://nextflowdemobucket/zy-test/a6/058bd257af28d1454fedb253667590/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_qualimap; to: gs://nextflowdemobucket/zy-test/test/qualimap/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_qualimap [copy] -- See log file for details\u001b[39m\u001b[K\n", - "\u001b[K\n", - "\u001b[17A\n", - "executor > google-lifesciences (24)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[4a/560a3c] process > bismark_methXtract (SRR3892... [100%] 2 of 2\u001b[K\n", - "[cf/10ce4b] process > bismark_report (SRR389222_s... [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[a6/058bd2] process > qualimap (SRR389222_sub1) [100%] 2 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33mWARN: Failed to publish file: gs://nextflowdemobucket/zy-test/a6/058bd257af28d1454fedb253667590/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_qualimap; to: gs://nextflowdemobucket/zy-test/test/qualimap/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_qualimap [copy] -- See log file for details\u001b[39m\u001b[K\n", - "\u001b[K\n", - "\u001b[17A\n", - "executor > google-lifesciences (24)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[4a/560a3c] process > bismark_methXtract (SRR3892... [100%] 2 of 2\u001b[K\n", - "[cf/10ce4b] process > bismark_report (SRR389222_s... [ 0%] 0 of 2\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[a6/058bd2] process > qualimap (SRR389222_sub1) [100%] 2 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33mWARN: Failed to publish file: gs://nextflowdemobucket/zy-test/a6/058bd257af28d1454fedb253667590/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_qualimap; to: gs://nextflowdemobucket/zy-test/test/qualimap/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_qualimap [copy] -- See log file for details\u001b[39m\u001b[K\n", - "\u001b[16A\n", - "executor > google-lifesciences (24)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[4a/560a3c] process > bismark_methXtract (SRR3892... [100%] 2 of 2\u001b[K\n", - "[7b/16d27f] process > bismark_report (SRR389222_s... [ 50%] 1 of 2\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[a6/058bd2] process > qualimap (SRR389222_sub1) [100%] 2 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[K\n", - "\u001b[16A\n", - "executor > google-lifesciences (24)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3\u001b[K\n", - "[4a/560a3c] process > bismark_methXtract (SRR3892... [100%] 2 of 2\u001b[K\n", - "[cf/10ce4b] process > bismark_report (SRR389222_s... [100%] 2 of 2\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[a6/058bd2] process > qualimap (SRR389222_sub1) [100%] 2 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[K\n", - "\u001b[16A\n", - "executor > google-lifesciences (24)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[86/02f12c] process > bismark_deduplicate (SRR389... [ 66%] 2 of 3 ✔\u001b[K\n", - "[4a/560a3c] process > bismark_methXtract (SRR3892... [100%] 2 of 2\u001b[K\n", - "[cf/10ce4b] process > bismark_report (SRR389222_s... [100%] 2 of 2\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[a6/058bd2] process > qualimap (SRR389222_sub1) [100%] 2 of 2\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (24)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[4a/560a3c] process > bismark_methXtract (SRR3892... [ 66%] 2 of 3\u001b[K\n", - "[cf/10ce4b] process > bismark_report (SRR389222_s... [100%] 2 of 2\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[a6/058bd2] process > qualimap (SRR389222_sub1) [ 66%] 2 of 3\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (25)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[4a/560a3c] process > bismark_methXtract (SRR3892... [ 66%] 2 of 3\u001b[K\n", - "[cf/10ce4b] process > bismark_report (SRR389222_s... [100%] 2 of 2\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [ 66%] 2 of 3\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (26)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [ 66%] 2 of 3\u001b[K\n", - "[cf/10ce4b] process > bismark_report (SRR389222_s... [100%] 2 of 2\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [ 66%] 2 of 3\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (26)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [ 66%] 2 of 3\u001b[K\n", - "[cf/10ce4b] process > bismark_report (SRR389222_s... [100%] 2 of 2\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [ 66%] 2 of 3\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (26)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [ 66%] 2 of 3\u001b[K\n", - "[cf/10ce4b] process > bismark_report (SRR389222_s... [100%] 2 of 2\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [ 66%] 2 of 3 ✔\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (26)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [ 66%] 2 of 3\u001b[K\n", - "[cf/10ce4b] process > bismark_report (SRR389222_s... [100%] 2 of 2\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (26)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [100%] 3 of 3 ✔\u001b[K\n", - "[cf/10ce4b] process > bismark_report (SRR389222_s... [ 66%] 2 of 3\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (27)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [100%] 3 of 3 ✔\u001b[K\n", - "[d5/714f3d] process > bismark_report (SRR389222_s... [ 66%] 2 of 3\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (27)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [100%] 3 of 3 ✔\u001b[K\n", - "[d5/714f3d] process > bismark_report (SRR389222_s... [ 66%] 2 of 3\u001b[K\n", - "[- ] process > bismark_summary [ 0%] 0 of 1\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (28)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [100%] 3 of 3 ✔\u001b[K\n", - "[d5/714f3d] process > bismark_report (SRR389222_s... [ 66%] 2 of 3\u001b[K\n", - "[7e/52c38f] process > bismark_summary [ 0%] 0 of 1\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (28)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [100%] 3 of 3 ✔\u001b[K\n", - "[d5/714f3d] process > bismark_report (SRR389222_s... [ 66%] 2 of 3\u001b[K\n", - "[7e/52c38f] process > bismark_summary [ 0%] 0 of 1\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[f0/fb5ad1] process > preseq (SRR389222_sub3) [ 66%] 2 of 3, failed: 2\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (28)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [100%] 3 of 3 ✔\u001b[K\n", - "[d5/714f3d] process > bismark_report (SRR389222_s... [ 66%] 2 of 3\u001b[K\n", - "[7e/52c38f] process > bismark_summary [ 0%] 0 of 1\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[c0/7c754d] process > preseq (SRR389222_sub2) [100%] 3 of 3, failed: 3 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[33m[c0/7c754d] NOTE: Process `preseq (SRR389222_sub2)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", - "\u001b[16A\n", - "executor > google-lifesciences (28)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [100%] 3 of 3 ✔\u001b[K\n", - "[d5/714f3d] process > bismark_report (SRR389222_s... [100%] 3 of 3 ✔\u001b[K\n", - "[7e/52c38f] process > bismark_summary [ 0%] 0 of 1\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[c0/7c754d] process > preseq (SRR389222_sub2) [100%] 3 of 3, failed: 3 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[K\n", - "\u001b[16A\n", - "executor > google-lifesciences (28)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [100%] 3 of 3 ✔\u001b[K\n", - "[d5/714f3d] process > bismark_report (SRR389222_s... [100%] 3 of 3 ✔\u001b[K\n", - "[7e/52c38f] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[c0/7c754d] process > preseq (SRR389222_sub2) [100%] 3 of 3, failed: 3 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[K\n", - "\u001b[16A\n", - "executor > google-lifesciences (28)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [100%] 3 of 3 ✔\u001b[K\n", - "[d5/714f3d] process > bismark_report (SRR389222_s... [100%] 3 of 3 ✔\u001b[K\n", - "[7e/52c38f] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[c0/7c754d] process > preseq (SRR389222_sub2) [100%] 3 of 3, failed: 3 ✔\u001b[K\n", - "[- ] process > multiqc [ 0%] 0 of 1\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (29)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [100%] 3 of 3 ✔\u001b[K\n", - "[d5/714f3d] process > bismark_report (SRR389222_s... [100%] 3 of 3 ✔\u001b[K\n", - "[7e/52c38f] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[c0/7c754d] process > preseq (SRR389222_sub2) [100%] 3 of 3, failed: 3 ✔\u001b[K\n", - "[ab/f27db5] process > multiqc (1) [ 0%] 0 of 1\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (29)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [100%] 3 of 3 ✔\u001b[K\n", - "[d5/714f3d] process > bismark_report (SRR389222_s... [100%] 3 of 3 ✔\u001b[K\n", - "[7e/52c38f] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[c0/7c754d] process > preseq (SRR389222_sub2) [100%] 3 of 3, failed: 3 ✔\u001b[K\n", - "[ab/f27db5] process > multiqc (1) [ 0%] 0 of 1\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (29)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [100%] 3 of 3 ✔\u001b[K\n", - "[d5/714f3d] process > bismark_report (SRR389222_s... [100%] 3 of 3 ✔\u001b[K\n", - "[7e/52c38f] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[c0/7c754d] process > preseq (SRR389222_sub2) [100%] 3 of 3, failed: 3 ✔\u001b[K\n", - "[ab/f27db5] process > multiqc (1) [ 0%] 0 of 1 ✔\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (29)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [100%] 3 of 3 ✔\u001b[K\n", - "[d5/714f3d] process > bismark_report (SRR389222_s... [100%] 3 of 3 ✔\u001b[K\n", - "[7e/52c38f] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[c0/7c754d] process > preseq (SRR389222_sub2) [100%] 3 of 3, failed: 3 ✔\u001b[K\n", - "[ab/f27db5] process > multiqc (1) [100%] 1 of 1 ✔\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "-\u001b[0;35mWarning, pipeline completed, but with errored process(es) \u001b[0m-\u001b[K\n", - "-\u001b[0;31mNumber of ignored errored process(es) : 3 \u001b[0m-\u001b[K\n", - "-\u001b[0;32mNumber of successfully ran process(es) : 26 \u001b[0m-\u001b[K\n", - "-\u001b[0;35m[nf-core/methylseq]\u001b[0;32m Pipeline completed successfully\u001b[0m-\u001b[K\n", - "\u001b[19A\n", - "executor > google-lifesciences (29)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [100%] 3 of 3 ✔\u001b[K\n", - "[d5/714f3d] process > bismark_report (SRR389222_s... [100%] 3 of 3 ✔\u001b[K\n", - "[7e/52c38f] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[c0/7c754d] process > preseq (SRR389222_sub2) [100%] 3 of 3, failed: 3 ✔\u001b[K\n", - "[ab/f27db5] process > multiqc (1) [100%] 1 of 1 ✔\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "-\u001b[0;35mWarning, pipeline completed, but with errored process(es) \u001b[0m-\u001b[K\n", - "-\u001b[0;31mNumber of ignored errored process(es) : 3 \u001b[0m-\u001b[K\n", - "-\u001b[0;32mNumber of successfully ran process(es) : 26 \u001b[0m-\u001b[K\n", - "-\u001b[0;35m[nf-core/methylseq]\u001b[0;32m Pipeline completed successfully\u001b[0m-\u001b[K\n", - "Waiting files transfer to complete (2 files)\u001b[K\n", - "\u001b[20A\n", - "executor > google-lifesciences (29)\u001b[K\n", - "[40/f0dddd] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[0f/afed09] process > makeBismarkIndex (1) [100%] 1 of 1 ✔\u001b[K\n", - "[e8/9b38e1] process > fastqc (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[71/cc59ed] process > trim_galore (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[15/e29fff] process > bismark_align (SRR389222_sub2) [100%] 3 of 3 ✔\u001b[K\n", - "[90/1a2136] process > bismark_deduplicate (SRR389... [100%] 3 of 3 ✔\u001b[K\n", - "[ac/d70665] process > bismark_methXtract (SRR3892... [100%] 3 of 3 ✔\u001b[K\n", - "[d5/714f3d] process > bismark_report (SRR389222_s... [100%] 3 of 3 ✔\u001b[K\n", - "[7e/52c38f] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[0f/6fc3c8] process > qualimap (SRR389222_sub3) [100%] 3 of 3 ✔\u001b[K\n", - "[c0/7c754d] process > preseq (SRR389222_sub2) [100%] 3 of 3, failed: 3 ✔\u001b[K\n", - "[ab/f27db5] process > multiqc (1) [100%] 1 of 1 ✔\u001b[K\n", - "[80/279ac6] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "-\u001b[0;35mWarning, pipeline completed, but with errored process(es) \u001b[0m-\u001b[K\n", - "-\u001b[0;31mNumber of ignored errored process(es) : 3 \u001b[0m-\u001b[K\n", - "-\u001b[0;32mNumber of successfully ran process(es) : 26 \u001b[0m-\u001b[K\n", - "-\u001b[0;35m[nf-core/methylseq]\u001b[0;32m Pipeline completed successfully\u001b[0m-\u001b[K\n", - "Waiting files transfer to complete (2 files)\u001b[K\n", - "\u001b[32;1mCompleted at: 28-Jul-2022 18:35:56\n", - "Duration : 29m 48s\n", - "CPU hours : 0.5 (87.7% failed)\n", - "Succeeded : 26\n", - "Ignored : 3\n", - "Failed : 3\n", - "\u001b[22;39m\u001b[K\n", - "\n" - ] - } - ], + "metadata": {}, + "outputs": [], "source": [ "!./nextflow run nf-core/methylseq -r 1.6.1 -profile test,gls -c nextflow.config" ] @@ -2261,332 +416,10 @@ }, { "cell_type": "code", - "execution_count": 35, + "execution_count": null, "id": "0ba49168-f63c-4ca4-8882-f043302d40a4", - "metadata": { - "scrolled": true, - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - " % Total % Received % Xferd Average Speed Time Time Time Current\n", - " Dload Upload Total Spent Left Speed\n", - " 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0\n", - " 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0\n", - "100 88.1M 100 88.1M 0 0 47.6M 0 0:00:01 0:00:01 --:--:-- 66.4M\n", - "PREFIX=/home/jupyter/mambaforge\n", - "Unpacking payload ...\n", - "Extracting \"pybind11-abi-4-hd8ed1ab_3.tar.bz2\"\n", - "Extracting \"pysocks-1.7.1-py39hf3d152e_5.tar.bz2\"\n", - "Extracting \"_openmp_mutex-4.5-2_gnu.tar.bz2\"\n", - "Extracting \"icu-70.1-h27087fc_0.tar.bz2\"\n", - "Extracting \"_libgcc_mutex-0.1-conda_forge.tar.bz2\"\n", - "Extracting \"cryptography-37.0.2-py39hd97740a_0.tar.bz2\"\n", - "Extracting \"libffi-3.4.2-h7f98852_5.tar.bz2\"\n", - "Extracting \"mamba-0.22.1-py39hfa8f2c8_1.tar.bz2\"\n", - "Extracting \"conda-package-handling-1.8.1-py39hb9d737c_1.tar.bz2\"\n", - "Extracting \"reproc-14.2.3-h7f98852_0.tar.bz2\"\n", - "Extracting \"pycosat-0.6.3-py39hb9d737c_1010.tar.bz2\"\n", - "Extracting \"charset-normalizer-2.0.12-pyhd8ed1ab_0.tar.bz2\"\n", - "Extracting \"colorama-0.4.4-pyh9f0ad1d_0.tar.bz2\"\n", - "Extracting \"libnsl-2.0.0-h7f98852_0.tar.bz2\"\n", - "Extracting \"certifi-2022.5.18.1-py39hf3d152e_0.tar.bz2\"\n", - "Extracting \"ca-certificates-2022.5.18.1-ha878542_0.tar.bz2\"\n", - "Extracting \"ncurses-6.3-h27087fc_1.tar.bz2\"\n", - "Extracting \"libgcc-ng-12.1.0-h8d9b700_16.tar.bz2\"\n", - "Extracting \"yaml-0.2.5-h7f98852_2.tar.bz2\"\n", - "Extracting \"libstdcxx-ng-12.1.0-ha89aaad_16.tar.bz2\"\n", - "Extracting \"tzdata-2022a-h191b570_0.tar.bz2\"\n", - "Extracting \"zlib-1.2.12-h166bdaf_0.tar.bz2\"\n", - "Extracting \"requests-2.27.1-pyhd8ed1ab_0.tar.bz2\"\n", - "Extracting \"yaml-cpp-0.6.3-he1b5a44_4.tar.bz2\"\n", - "Extracting \"libxml2-2.9.14-h22db469_0.tar.bz2\"\n", - "Extracting \"c-ares-1.18.1-h7f98852_0.tar.bz2\"\n", - "Extracting \"ruamel_yaml-0.15.80-py39hb9d737c_1007.tar.bz2\"\n", - "Extracting \"sqlite-3.38.5-h4ff8645_0.tar.bz2\"\n", - "Extracting \"libsolv-0.7.22-h6239696_0.tar.bz2\"\n", - "Extracting \"xz-5.2.5-h516909a_1.tar.bz2\"\n", - "Extracting \"six-1.16.0-pyh6c4a22f_0.tar.bz2\"\n", - "Extracting \"lz4-c-1.9.3-h9c3ff4c_1.tar.bz2\"\n", - "Extracting \"libev-4.33-h516909a_1.tar.bz2\"\n", - "Extracting \"libmambapy-0.22.1-py39hd55135b_1.tar.bz2\"\n", - "Extracting \"libzlib-1.2.12-h166bdaf_0.tar.bz2\"\n", - "Extracting \"brotlipy-0.7.0-py39hb9d737c_1004.tar.bz2\"\n", - "Extracting \"urllib3-1.26.9-pyhd8ed1ab_0.tar.bz2\"\n", - "Extracting \"reproc-cpp-14.2.3-h9c3ff4c_0.tar.bz2\"\n", - "Extracting \"pycparser-2.21-pyhd8ed1ab_0.tar.bz2\"\n", - "Extracting \"tqdm-4.64.0-pyhd8ed1ab_0.tar.bz2\"\n", - "Extracting \"python-3.9.13-h9a8a25e_0_cpython.tar.bz2\"\n", - "Extracting \"krb5-1.19.3-h3790be6_0.tar.bz2\"\n", - "Extracting \"pip-22.1.2-pyhd8ed1ab_0.tar.bz2\"\n", - "Extracting \"conda-4.12.0-py39hf3d152e_0.tar.bz2\"\n", - "Extracting \"wheel-0.37.1-pyhd8ed1ab_0.tar.bz2\"\n", - "Extracting \"pyopenssl-22.0.0-pyhd8ed1ab_0.tar.bz2\"\n", - "Extracting \"zstd-1.5.2-h8a70e8d_1.tar.bz2\"\n", - "Extracting \"libedit-3.1.20191231-he28a2e2_2.tar.bz2\"\n", - "Extracting \"libiconv-1.16-h516909a_0.tar.bz2\"\n", - "Extracting \"libcurl-7.83.1-h7bff187_0.tar.bz2\"\n", - "Extracting \"libnghttp2-1.47.0-h727a467_0.tar.bz2\"\n", - "Extracting \"libarchive-3.5.2-hb890918_2.tar.bz2\"\n", - "Extracting \"setuptools-62.3.2-py39hf3d152e_0.tar.bz2\"\n", - "Extracting \"ld_impl_linux-64-2.36.1-hea4e1c9_2.tar.bz2\"\n", - "Extracting \"idna-3.3-pyhd8ed1ab_0.tar.bz2\"\n", - "Extracting \"cffi-1.15.0-py39h4bc2ebd_0.tar.bz2\"\n", - "Extracting \"libssh2-1.10.0-ha56f1ee_2.tar.bz2\"\n", - "Extracting \"readline-8.1-h46c0cb4_0.tar.bz2\"\n", - "Extracting \"tk-8.6.12-h27826a3_0.tar.bz2\"\n", - "Extracting \"openssl-1.1.1o-h166bdaf_0.tar.bz2\"\n", - "Extracting \"python_abi-3.9-2_cp39.tar.bz2\"\n", - "Extracting \"libuuid-2.32.1-h7f98852_1000.tar.bz2\"\n", - "Extracting \"bzip2-1.0.8-h7f98852_4.tar.bz2\"\n", - "Extracting \"keyutils-1.6.1-h166bdaf_0.tar.bz2\"\n", - "Extracting \"libgomp-12.1.0-h8d9b700_16.tar.bz2\"\n", - "Extracting \"lzo-2.10-h516909a_1000.tar.bz2\"\n", - "Extracting \"libmamba-0.22.1-hd8a31e3_1.tar.bz2\"\n", - "\n", - " __\n", - " __ ______ ___ ____ _____ ___ / /_ ____ _\n", - " / / / / __ `__ \\/ __ `/ __ `__ \\/ __ \\/ __ `/\n", - " / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /\n", - " / .___/_/ /_/ /_/\\__,_/_/ /_/ /_/_.___/\\__,_/\n", - " /_/\n", - "\n", - "conda-forge/linux-64 Using cache\n", - "conda-forge/noarch Using cache\n", - "\n", - "Transaction\n", - "\n", - " Prefix: /home/jupyter/mambaforge\n", - "\n", - " Updating specs:\n", - "\n", - " - python==3.9.13=h9a8a25e_0_cpython\n", - " - _libgcc_mutex==0.1=conda_forge\n", - " - ca-certificates==2022.5.18.1=ha878542_0\n", - " - ld_impl_linux-64==2.36.1=hea4e1c9_2\n", - " - libstdcxx-ng==12.1.0=ha89aaad_16\n", - " - pybind11-abi==4=hd8ed1ab_3\n", - " - tzdata==2022a=h191b570_0\n", - " - libgomp==12.1.0=h8d9b700_16\n", - " - _openmp_mutex==4.5=2_gnu\n", - " - libgcc-ng==12.1.0=h8d9b700_16\n", - " - bzip2==1.0.8=h7f98852_4\n", - " - c-ares==1.18.1=h7f98852_0\n", - " - icu==70.1=h27087fc_0\n", - " - keyutils==1.6.1=h166bdaf_0\n", - " - libev==4.33=h516909a_1\n", - " - libffi==3.4.2=h7f98852_5\n", - " - libiconv==1.16=h516909a_0\n", - " - libnsl==2.0.0=h7f98852_0\n", - " - libuuid==2.32.1=h7f98852_1000\n", - " - libzlib==1.2.12=h166bdaf_0\n", - " - lz4-c==1.9.3=h9c3ff4c_1\n", - " - lzo==2.10=h516909a_1000\n", - " - ncurses==6.3=h27087fc_1\n", - " - openssl==1.1.1o=h166bdaf_0\n", - " - reproc==14.2.3=h7f98852_0\n", - " - xz==5.2.5=h516909a_1\n", - " - yaml==0.2.5=h7f98852_2\n", - " - yaml-cpp==0.6.3=he1b5a44_4\n", - " - libedit==3.1.20191231=he28a2e2_2\n", - " - libsolv==0.7.22=h6239696_0\n", - " - readline==8.1=h46c0cb4_0\n", - " - reproc-cpp==14.2.3=h9c3ff4c_0\n", - " - tk==8.6.12=h27826a3_0\n", - " - zlib==1.2.12=h166bdaf_0\n", - " - zstd==1.5.2=h8a70e8d_1\n", - " - krb5==1.19.3=h3790be6_0\n", - " - libnghttp2==1.47.0=h727a467_0\n", - " - libssh2==1.10.0=ha56f1ee_2\n", - " - libxml2==2.9.14=h22db469_0\n", - " - sqlite==3.38.5=h4ff8645_0\n", - " - libarchive==3.5.2=hb890918_2\n", - " - libcurl==7.83.1=h7bff187_0\n", - " - charset-normalizer==2.0.12=pyhd8ed1ab_0\n", - " - colorama==0.4.4=pyh9f0ad1d_0\n", - " - idna==3.3=pyhd8ed1ab_0\n", - " - libmamba==0.22.1=hd8a31e3_1\n", - " - pycparser==2.21=pyhd8ed1ab_0\n", - " - python_abi==3.9=2_cp39\n", - " - six==1.16.0=pyh6c4a22f_0\n", - " - wheel==0.37.1=pyhd8ed1ab_0\n", - " - certifi==2022.5.18.1=py39hf3d152e_0\n", - " - cffi==1.15.0=py39h4bc2ebd_0\n", - " - libmambapy==0.22.1=py39hd55135b_1\n", - " - pycosat==0.6.3=py39hb9d737c_1010\n", - " - pysocks==1.7.1=py39hf3d152e_5\n", - " - ruamel_yaml==0.15.80=py39hb9d737c_1007\n", - " - setuptools==62.3.2=py39hf3d152e_0\n", - " - tqdm==4.64.0=pyhd8ed1ab_0\n", - " - brotlipy==0.7.0=py39hb9d737c_1004\n", - " - conda-package-handling==1.8.1=py39hb9d737c_1\n", - " - cryptography==37.0.2=py39hd97740a_0\n", - " - pip==22.1.2=pyhd8ed1ab_0\n", - " - pyopenssl==22.0.0=pyhd8ed1ab_0\n", - " - urllib3==1.26.9=pyhd8ed1ab_0\n", - " - requests==2.27.1=pyhd8ed1ab_0\n", - " - conda==4.12.0=py39hf3d152e_0\n", - " - mamba==0.22.1=py39hfa8f2c8_1\n", - "\n", - "\n", - " Package Version Build Channel Size\n", - "───────────────────────────────────────────────────────────────────────────────────────────────\n", - " Install:\n", - "───────────────────────────────────────────────────────────────────────────────────────────────\n", - "\n", - "\u001b[32m + _libgcc_mutex \u001b[00m 0.1 conda_forge conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + _openmp_mutex \u001b[00m 4.5 2_gnu conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + brotlipy \u001b[00m 0.7.0 py39hb9d737c_1004 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + bzip2 \u001b[00m 1.0.8 h7f98852_4 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + c-ares \u001b[00m 1.18.1 h7f98852_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + ca-certificates \u001b[00m 2022.5.18.1 ha878542_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + certifi \u001b[00m 2022.5.18.1 py39hf3d152e_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + cffi \u001b[00m 1.15.0 py39h4bc2ebd_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + charset-normalizer \u001b[00m 2.0.12 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + colorama \u001b[00m 0.4.4 pyh9f0ad1d_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + conda \u001b[00m 4.12.0 py39hf3d152e_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + conda-package-handling\u001b[00m 1.8.1 py39hb9d737c_1 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + cryptography \u001b[00m 37.0.2 py39hd97740a_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + icu \u001b[00m 70.1 h27087fc_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + idna \u001b[00m 3.3 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + keyutils \u001b[00m 1.6.1 h166bdaf_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + krb5 \u001b[00m 1.19.3 h3790be6_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + ld_impl_linux-64 \u001b[00m 2.36.1 hea4e1c9_2 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libarchive \u001b[00m 3.5.2 hb890918_2 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libcurl \u001b[00m 7.83.1 h7bff187_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libedit \u001b[00m 3.1.20191231 he28a2e2_2 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libev \u001b[00m 4.33 h516909a_1 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libffi \u001b[00m 3.4.2 h7f98852_5 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libgcc-ng \u001b[00m 12.1.0 h8d9b700_16 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libgomp \u001b[00m 12.1.0 h8d9b700_16 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libiconv \u001b[00m 1.16 h516909a_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libmamba \u001b[00m 0.22.1 hd8a31e3_1 conda-forge/linux-64\u001b[32m 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lz4-c \u001b[00m 1.9.3 h9c3ff4c_1 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + lzo \u001b[00m 2.10 h516909a_1000 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + mamba \u001b[00m 0.22.1 py39hfa8f2c8_1 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + ncurses \u001b[00m 6.3 h27087fc_1 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + openssl \u001b[00m 1.1.1o h166bdaf_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + pip \u001b[00m 22.1.2 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + pybind11-abi \u001b[00m 4 hd8ed1ab_3 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + pycosat \u001b[00m 0.6.3 py39hb9d737c_1010 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + pycparser \u001b[00m 2.21 pyhd8ed1ab_0 conda-forge/noarch \u001b[32m Cached\u001b[00m\n", - "\u001b[32m + pyopenssl \u001b[00m 22.0.0 pyhd8ed1ab_0 conda-forge/noarch 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conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + zlib \u001b[00m 1.2.12 h166bdaf_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + zstd \u001b[00m 1.5.2 h8a70e8d_1 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\n", - " Summary:\n", - "\n", - " Install: 67 packages\n", - "\n", - " Total download: 0 B\n", - "\n", - "───────────────────────────────────────────────────────────────────────────────────────────────\n", - "\n", - "\n", - "Transaction starting\n", - "\u001b[?25l\u001b[2K\u001b[0G\u001b[?25hLinking _libgcc_mutex-0.1-conda_forge\n", - "Linking ca-certificates-2022.5.18.1-ha878542_0\n", - "Linking ld_impl_linux-64-2.36.1-hea4e1c9_2\n", - "Linking libstdcxx-ng-12.1.0-ha89aaad_16\n", - "Linking libgomp-12.1.0-h8d9b700_16\n", - "Linking _openmp_mutex-4.5-2_gnu\n", - "Linking libgcc-ng-12.1.0-h8d9b700_16\n", - "Linking yaml-cpp-0.6.3-he1b5a44_4\n", - "Linking yaml-0.2.5-h7f98852_2\n", - "Linking xz-5.2.5-h516909a_1\n", - "Linking 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libssh2-1.10.0-ha56f1ee_2\n", - "Linking libnghttp2-1.47.0-h727a467_0\n", - "Linking libarchive-3.5.2-hb890918_2\n", - "Linking libcurl-7.83.1-h7bff187_0\n", - "Linking libmamba-0.22.1-hd8a31e3_1\n", - "Linking pybind11-abi-4-hd8ed1ab_3\n", - "Linking tzdata-2022a-h191b570_0\n", - "Linking python-3.9.13-h9a8a25e_0_cpython\n", - "Linking python_abi-3.9-2_cp39\n", - "Linking setuptools-62.3.2-py39hf3d152e_0\n", - "Linking wheel-0.37.1-pyhd8ed1ab_0\n", - "Linking pip-22.1.2-pyhd8ed1ab_0\n", - "Linking six-1.16.0-pyh6c4a22f_0\n", - "Linking pycparser-2.21-pyhd8ed1ab_0\n", - "Linking idna-3.3-pyhd8ed1ab_0\n", - "Linking colorama-0.4.4-pyh9f0ad1d_0\n", - "Linking charset-normalizer-2.0.12-pyhd8ed1ab_0\n", - "Linking tqdm-4.64.0-pyhd8ed1ab_0\n", - "Linking ruamel_yaml-0.15.80-py39hb9d737c_1007\n", - "Linking pysocks-1.7.1-py39hf3d152e_5\n", - "Linking pycosat-0.6.3-py39hb9d737c_1010\n", - "Linking libmambapy-0.22.1-py39hd55135b_1\n", - "Linking certifi-2022.5.18.1-py39hf3d152e_0\n", - "Linking cffi-1.15.0-py39h4bc2ebd_0\n", - "Linking conda-package-handling-1.8.1-py39hb9d737c_1\n", - "Linking cryptography-37.0.2-py39hd97740a_0\n", - "Linking brotlipy-0.7.0-py39hb9d737c_1004\n", - "Linking pyopenssl-22.0.0-pyhd8ed1ab_0\n", - "Linking urllib3-1.26.9-pyhd8ed1ab_0\n", - "Linking requests-2.27.1-pyhd8ed1ab_0\n", - "Linking conda-4.12.0-py39hf3d152e_0\n", - "Linking mamba-0.22.1-py39hfa8f2c8_1\n", - "Transaction finished\n", - "installation finished.\n" - ] - } - ], + "metadata": {}, + "outputs": [], "source": [ "!curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh\n", "!bash Mambaforge-$(uname)-$(uname -m).sh -b -p $HOME/mambaforge" @@ -2602,849 +435,10 @@ }, { "cell_type": "code", - "execution_count": 36, + "execution_count": null, "id": "7c4527e0-7c43-4b80-a9d0-3d9cecd35b03", - "metadata": { - "scrolled": true, - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n", - " __ __ __ __\n", - " / \\ / \\ / \\ / \\\n", - " / \\/ \\/ \\/ \\\n", - "███████████████/ /██/ /██/ /██/ /████████████████████████\n", - " / / \\ / \\ / \\ / \\ \\____\n", - " / / \\_/ \\_/ \\_/ \\ o \\__,\n", - " / _/ \\_____/ `\n", - " |/\n", - " ███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗\n", - " ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗\n", - " ██╔████╔██║███████║██╔████╔██║██████╔╝███████║\n", - " ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║\n", - " ██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║\n", - " ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝\n", - "\n", - " mamba (0.22.1) supported by @QuantStack\n", - "\n", - " GitHub: https://github.com/mamba-org/mamba\n", - " Twitter: https://twitter.com/QuantStack\n", - "\n", - "█████████████████████████████████████████████████████████████\n", - "\n", - "\n", - "Looking for: ['sra-tools']\n", - "\n", - "\u001b[?25l\u001b[2K\u001b[0G[+] 0.0s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 0.1s\n", - "bioconda/linux-64 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"pkgs/r/noarch \u001b[90m╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━\u001b[0m 520.2kB / ??.?MB @ 311.1kB/s 0.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.2s\n", - "bioconda/noarch \u001b[90m━━━━━━━━━━━╸\u001b[0m\u001b[33m━━━━━━━━━━━\u001b[0m 3.2MB / ??.?MB @ 1.5MB/s 2.2s\n", - "conda-forge/linux-64 \u001b[33m━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━\u001b[0m 2.8MB / ??.?MB @ 1.3MB/s 2.2s\n", - "conda-forge/noarch \u001b[90m━━━━━━━━━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━\u001b[0m 1.5MB / ??.?MB @ 709.4kB/s 2.2s\n", - "pkgs/main/noarch \u001b[90m━━━━━━━━━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━\u001b[0m 0.0 B / ??.?MB @ ??.?MB/s 0.5s\n", - "pkgs/r/linux-64 \u001b[90m━━━━━━━━━━━━━╸\u001b[0m\u001b[33m━━━━━━━━━\u001b[0m 0.0 B / ??.?MB @ ??.?MB/s 0.1s\n", - "pkgs/r/noarch \u001b[90m━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━\u001b[0m 770.1kB / ??.?MB @ 366.7kB/s 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━━━━━━━━━━━━━━━━━━━━━━ 24.4MB @ 2.9MB/s Finalizing 9.9s\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.0s\n", - "conda-forge/linux-64 ━━━━━━━━━━━━━━━━━━━━━━ 24.4MB @ 2.9MB/s Finalizing 10.0s\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.1s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.2s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.3s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.4s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.5s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.6s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.7s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.8s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.9s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.0s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.1s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.2s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.3s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.4s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.5s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.6s\n", - "\u001b[2K\u001b[1A\u001b[2K\u001b[0Gconda-forge/linux-64 @ 2.9MB/s 10.1s\n", - "\u001b[?25h\n", - "Pinned packages:\n", - " - python 3.7.*\n", - "\n", - "\n", - "Transaction\n", - "\n", - " Prefix: /opt/conda\n", - "\n", - " Updating specs:\n", - "\n", - " - sra-tools\n", - " - ca-certificates\n", - " - certifi\n", - " - openssl\n", - "\n", - "\n", - " Package Version Build Channel Size\n", - "────────────────────────────────────────────────────────────────────────────────────────────────────\n", - " Install:\n", - "────────────────────────────────────────────────────────────────────────────────────────────────────\n", - "\n", - "\u001b[32m + curl \u001b[00m 7.83.1 h2283fc2_0 conda-forge/linux-64 91kB\n", - "\u001b[32m + hdf5 \u001b[00m 1.10.6 h3ffc7dd_1 pkgs/main/linux-64 4MB\n", - "\u001b[32m + keyutils \u001b[00m 1.6.1 h166bdaf_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + krb5 \u001b[00m 1.19.3 h08a2579_0 conda-forge/linux-64 2MB\n", - "\u001b[32m + libcurl \u001b[00m 7.83.1 h2283fc2_0 conda-forge/linux-64 352kB\n", - "\u001b[32m + libedit \u001b[00m 3.1.20191231 he28a2e2_2 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libev \u001b[00m 4.33 h516909a_1 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libiconv \u001b[00m 1.16 h516909a_0 conda-forge/linux-64\u001b[32m Cached\u001b[00m\n", - "\u001b[32m + libnghttp2 \u001b[00m 1.47.0 he49606f_0 conda-forge/linux-64 844kB\n", - "\u001b[32m + libssh2 \u001b[00m 1.10.0 ha35d2d1_2 conda-forge/linux-64 238kB\n", - "\u001b[32m + libxml2 \u001b[00m 2.9.14 h22db469_3 conda-forge/linux-64 800kB\n", - "\u001b[32m + ncbi-ngs-sdk \u001b[00m 2.11.2 pl5321h629fbf0_1 bioconda/linux-64 172kB\n", - "\u001b[32m + ossuuid \u001b[00m 1.6.2 hf484d3e_1000 conda-forge/linux-64 57kB\n", - "\u001b[32m + perl \u001b[00m 5.32.1 2_h7f98852_perl5 conda-forge/linux-64 15MB\n", - "\u001b[32m + perl-alien-build \u001b[00m 2.48 pl5321hec16e2b_0 bioconda/linux-64 176kB\n", - "\u001b[32m + perl-alien-libxml2 \u001b[00m 0.17 pl5321hec16e2b_0 bioconda/linux-64 13kB\n", - "\u001b[32m + perl-business-isbn \u001b[00m 3.007 pl5321hdfd78af_0 bioconda/noarch 18kB\n", - "\u001b[32m + perl-business-isbn-data \u001b[00m 20210112.006 pl5321hdfd78af_0 bioconda/noarch 21kB\n", - "\u001b[32m + perl-capture-tiny \u001b[00m 0.48 pl5321hdfd78af_2 bioconda/noarch 19kB\n", - "\u001b[32m + perl-carp \u001b[00m 1.38 pl5321hdfd78af_4 bioconda/noarch 17kB\n", - "\u001b[32m + perl-constant \u001b[00m 1.33 pl5321hdfd78af_2 bioconda/noarch 12kB\n", - "\u001b[32m + perl-data-dumper \u001b[00m 2.183 pl5321hec16e2b_1 bioconda/linux-64 38kB\n", - "\u001b[32m + perl-encode \u001b[00m 3.18 pl5321hec16e2b_0 bioconda/linux-64 2MB\n", - "\u001b[32m + perl-exporter \u001b[00m 5.72 pl5321hdfd78af_2 bioconda/noarch 16kB\n", - "\u001b[32m + perl-extutils-makemaker \u001b[00m 6.66 0 bioconda/linux-64 2kB\n", - "\u001b[32m + perl-ffi-checklib \u001b[00m 0.28 pl5321hdfd78af_0 bioconda/noarch 16kB\n", - "\u001b[32m + perl-file-chdir \u001b[00m 0.1010 pl5321hdfd78af_3 bioconda/noarch 13kB\n", - "\u001b[32m + perl-file-path \u001b[00m 2.09 0 bioconda/linux-64 2kB\n", - "\u001b[32m + perl-file-temp \u001b[00m 0.2304 pl5321hd8ed1ab_0 conda-forge/noarch 32kB\n", - "\u001b[32m + perl-file-which \u001b[00m 1.20 0 bioconda/linux-64 5kB\n", - "\u001b[32m + perl-importer \u001b[00m 0.026 pl5321hdfd78af_0 bioconda/noarch 24kB\n", - "\u001b[32m + perl-mime-base64 \u001b[00m 3.16 pl5321hec16e2b_2 bioconda/linux-64 18kB\n", - "\u001b[32m + perl-parent \u001b[00m 0.236 pl5321hdfd78af_2 bioconda/noarch 8kB\n", - "\u001b[32m + perl-path-tiny \u001b[00m 0.122 pl5321hdfd78af_0 bioconda/noarch 41kB\n", - "\u001b[32m + perl-pathtools \u001b[00m 3.75 pl5321hec16e2b_3 bioconda/linux-64 43kB\n", - "\u001b[32m + perl-scope-guard \u001b[00m 0.21 pl5321hdfd78af_3 bioconda/noarch 10kB\n", - "\u001b[32m + perl-sub-info \u001b[00m 0.002 pl5321hdfd78af_1 bioconda/noarch 10kB\n", - "\u001b[32m + perl-term-table \u001b[00m 0.016 pl5321hdfd78af_0 bioconda/noarch 24kB\n", - "\u001b[32m + perl-test2-suite \u001b[00m 0.000145 pl5321hdfd78af_0 bioconda/noarch 200kB\n", - "\u001b[32m + perl-threaded \u001b[00m 5.32.1 hdfd78af_1 bioconda/noarch 6kB\n", - "\u001b[32m + perl-uri \u001b[00m 5.12 pl5321hdfd78af_0 bioconda/noarch 61kB\n", - "\u001b[32m + perl-xml-libxml \u001b[00m 2.0207 pl5321h661654b_0 bioconda/linux-64 259kB\n", - "\u001b[32m + perl-xml-namespacesupport\u001b[00m 1.12 pl5321hdfd78af_1 bioconda/noarch 14kB\n", - "\u001b[32m + perl-xml-sax \u001b[00m 1.02 pl5321hdfd78af_1 bioconda/noarch 38kB\n", - "\u001b[32m + perl-xml-sax-base \u001b[00m 1.09 pl5321hdfd78af_1 bioconda/noarch 22kB\n", - "\u001b[32m + sra-tools \u001b[00m 2.11.0 pl5321ha49a11a_3 bioconda/linux-64 67MB\n", - "\n", - " Change:\n", - "────────────────────────────────────────────────────────────────────────────────────────────────────\n", - "\n", - "\u001b[31m - nodejs \u001b[00m 17.9.0 h96d913c_0 installed \n", - "\u001b[32m + nodejs \u001b[00m 17.9.0 h8839609_0 conda-forge/linux-64 16MB\n", - "\u001b[31m - python \u001b[00m 3.7.12 hb7a2778_100_cpython installed \n", - "\u001b[32m + python \u001b[00m 3.7.12 hf930737_100_cpython conda-forge/linux-64 60MB\n", - "\n", - " Upgrade:\n", - "────────────────────────────────────────────────────────────────────────────────────────────────────\n", - "\n", - "\u001b[31m - grpc-cpp \u001b[00m 1.47.0 hbd84cd8_1 installed \n", - "\u001b[32m + grpc-cpp \u001b[00m 1.48.0 h00ec82a_0 conda-forge/linux-64 5MB\n", - "\u001b[31m - grpcio \u001b[00m 1.47.0 py37h64c7598_1 installed \n", - "\u001b[32m + grpcio \u001b[00m 1.48.0 py37hb40ad2a_0 conda-forge/linux-64 835kB\n", - "\u001b[31m - openssl \u001b[00m 1.1.1p h166bdaf_0 installed \n", - "\u001b[32m + openssl \u001b[00m 3.0.5 h166bdaf_0 conda-forge/linux-64 3MB\n", - "\n", - " Downgrade:\n", - "────────────────────────────────────────────────────────────────────────────────────────────────────\n", - "\n", - "\u001b[31m - cryptography \u001b[00m 37.0.2 py37h38fbfac_0 installed \n", - "\u001b[32m + cryptography \u001b[00m 37.0.1 py37h9ce1e76_0 pkgs/main/linux-64 1MB\n", - "\n", - " Summary:\n", - "\n", - " Install: 46 packages\n", - " Change: 2 packages\n", - " Upgrade: 3 packages\n", - " Downgrade: 1 packages\n", - "\n", - " Total download: 180MB\n", - "\n", - "────────────────────────────────────────────────────────────────────────────────────────────────────\n", - "\n", - "\u001b[?25l\u001b[2K\u001b[0G[+] 0.0s\n", - "Downloading \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m 0.0 B 0.0s\n", - "Extracting \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m 0 0.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 0.1s\n", - "Downloading (5) \u001b[33m━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━━━━━\u001b[0m 0.0 B libssh2 0.0s\n", - "Extracting \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m 0 0.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gossuuid 56.9kB @ 366.8kB/s 0.2s\n", - "[+] 0.2s\n", - "Downloading (5) \u001b[33m━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━━━━\u001b[0m 2.1MB libssh2 0.1s\n", - "Extracting \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m 1 0.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Ggrpcio 835.1kB @ 3.2MB/s 0.1s\n", - "openssl 3.0MB @ 10.3MB/s 0.3s\n", - "[+] 0.3s\n", - "Downloading (5) ━╸\u001b[33m━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━━\u001b[0m 17.3MB libssh2 0.2s\n", - "Extracting (2) \u001b[90m╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━\u001b[0m 1 grpcio 0.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gperl-scope-guard 10.1kB @ 26.8kB/s 0.1s\n", - "[+] 0.4s\n", - "Downloading (5) ━━╸\u001b[33m━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━\u001b[0m 32.1MB libssh2 0.3s\n", - "Extracting (2) \u001b[90m━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━\u001b[0m 2 openssl 0.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Ghdf5 3.8MB @ 8.9MB/s 0.2s\n", - "perl 15.1MB @ 33.5MB/s 0.5s\n", - "perl-exporter 15.9kB @ 35.4kB/s 0.1s\n", - "[+] 0.5s\n", - "Downloading (5) ━━━━╸\u001b[33m━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━\u001b[0m 45.3MB perl-capture-tiny 0.4s\n", - "Extracting (5) \u001b[90m━━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━\u001b[0m 2 openssl 0.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gperl-data-dumper 38.5kB @ 75.0kB/s 0.1s\n", - "perl-mime-base64 17.5kB @ 32.1kB/s 0.1s\n", - "libssh2 238.3kB @ 432.3kB/s 0.6s\n", - "perl-capture-tiny 19.3kB @ 32.7kB/s 0.2s\n", - "[+] 0.6s\n", - "Downloading (5) ━━━━━╸\u001b[33m━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━\u001b[0m 53.4MB perl-carp 0.5s\n", - "Extracting (9) \u001b[90m━━━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━\u001b[0m 2 openssl 0.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gperl-carp 17.1kB @ 28.0kB/s 0.1s\n", - "perl-sub-info 10.2kB @ 16.4kB/s 0.1s\n", - "perl-uri 60.8kB @ 93.6kB/s 0.1s\n", - "perl-alien-libxml2 13.0kB @ 19.5kB/s 0.1s\n", - "perl-file-chdir 13.4kB @ 19.8kB/s 0.1s\n", - "[+] 0.7s\n", - "Downloading (5) ━━━━━━╸\u001b[33m━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━\u001b[0m 60.3MB curl 0.6s\n", - "Extracting (14) \u001b[90m━━━━╸\u001b[0m\u001b[33m━━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━\u001b[0m 2 openssl 0.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gcurl 91.3kB @ 123.4kB/s 0.1s\n", - "libnghttp2 843.6kB @ 1.1MB/s 0.1s\n", - "perl-importer 23.6kB @ 31.1kB/s 0.1s\n", - "[+] 0.8s\n", - "Downloading (5) ━━━━━━━╸\u001b[33m━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━\u001b[0m 69.7MB grpc-cpp 0.7s\n", - "Extracting (15) ╸\u001b[33m━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━━━━\u001b[0m 4 curl 0.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gperl-constant 12.5kB @ 15.3kB/s 0.1s\n", - "grpc-cpp 5.4MB @ 6.5MB/s 0.2s\n", - "perl-file-path 1.7kB @ 2.0kB/s 0.1s\n", - "perl-term-table 23.6kB @ 26.7kB/s 0.1s\n", - "perl-test2-suite 199.7kB @ 224.8kB/s 0.1s\n", - "[+] 0.9s\n", - "Downloading (5) ━━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━\u001b[0m 83.3MB krb5 0.8s\n", - "Extracting (18) ━╸\u001b[33m━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━━\u001b[0m 6 curl 0.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gperl-xml-sax 38.4kB @ 41.4kB/s 0.1s\n", - "perl-threaded 5.5kB @ 5.6kB/s 0.1s\n", - "[+] 1.0s\n", - "Downloading (5) ━━━━━━━━━━╸\u001b[33m━━━━━━━━━━━━\u001b[0m 91.4MB krb5 0.9s\n", - "Extracting (20) ━╸\u001b[33m━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━━\u001b[0m 6 curl 0.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gkrb5 1.5MB @ 1.5MB/s 0.1s\n", - "perl-extutils-makemaker 1.6kB @ 1.5kB/s 0.0s\n", - "perl-path-tiny 40.6kB @ 37.4kB/s 0.1s\n", - "[+] 1.1s\n", - "Downloading (5) ━━━━━━━━━━━╸\u001b[33m━━━━━━━━━━━\u001b[0m 101.1MB perl-business-isbn-data 1.0s\n", - "Extracting (23) ━╸\u001b[33m━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━━━\u001b[0m 6 curl 0.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gperl-business-isbn-data 21.3kB @ 19.0kB/s 0.1s\n", - "python 60.1MB @ 53.0MB/s 1.1s\n", - "perl-file-temp 31.5kB @ 27.6kB/s 0.1s\n", - "[+] 1.2s\n", - "Downloading (5) ━━━━━━━━━━━━╸\u001b[33m━━━━━━━━━━\u001b[0m 108.0MB cryptography 1.1s\n", - "Extracting (26) ━╸\u001b[33m━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━━\u001b[0m 6 grpc-cpp 0.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gperl-xml-namespacesupport 14.3kB @ 11.8kB/s 0.5s\n", - "perl-ffi-checklib 16.1kB @ 12.8kB/s 0.1s\n", - "cryptography 1.3MB @ 1.1MB/s 0.1s\n", - "[+] 1.3s\n", - "Downloading (5) ━━━━━━━━━━━━━╸\u001b[33m━━━━━━━━━\u001b[0m 113.1MB nodejs 1.2s\n", - "Extracting (29) ━╸\u001b[33m━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━━\u001b[0m 6 grpc-cpp 1.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gperl-business-isbn 18.1kB @ 13.6kB/s 0.1s\n", - "perl-xml-libxml 258.5kB @ 193.1kB/s 0.1s\n", - "[+] 1.4s\n", - "Downloading (5) ━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━━\u001b[0m 123.5MB nodejs 1.3s\n", - "Extracting (31) ━╸\u001b[33m━━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━━━\u001b[0m 6 grpc-cpp 1.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Glibxml2 800.1kB @ 571.3kB/s 0.1s\n", - "perl-file-which 5.5kB @ 3.9kB/s 0.1s\n", - "perl-xml-sax-base 21.8kB @ 15.3kB/s 0.2s\n", - "ncbi-ngs-sdk 172.4kB @ 118.4kB/s 0.1s\n", - "[+] 1.5s\n", - "Downloading (5) ━━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━\u001b[0m 134.4MB nodejs 1.4s\n", - "Extracting (35) ━╸\u001b[33m━━━━━━━━━━━━━━━━━╸\u001b[0m\u001b[90m━━━\u001b[0m 6 grpc-cpp 1.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gperl-alien-build 175.7kB @ 116.1kB/s 0.1s\n", - "perl-encode 2.3MB @ 1.5MB/s 0.1s\n", - "nodejs 15.9MB @ 10.4MB/s 0.4s\n", - "libcurl 352.4kB @ 228.2kB/s 0.1s\n", - "perl-parent 7.9kB @ 5.1kB/s 0.1s\n", - "perl-pathtools 43.1kB @ 27.5kB/s 0.0s\n", - "[+] 1.6s\n", - "Downloading (1) ━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━━\u001b[0m 143.5MB sra-tools 1.5s\n", - "Extracting (41) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 krb5 1.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 1.7s\n", - "Downloading (1) ━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━━\u001b[0m 147.6MB sra-tools 1.6s\n", - "Extracting (41) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 krb5 1.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 1.8s\n", - "Downloading (1) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 153.4MB sra-tools 1.7s\n", - "Extracting (41) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 krb5 1.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 1.9s\n", - "Downloading (1) ━━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━\u001b[0m 159.1MB sra-tools 1.8s\n", - "Extracting (41) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 krb5 1.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.0s\n", - "Downloading (1) ━━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━\u001b[0m 163.8MB sra-tools 1.9s\n", - "Extracting (41) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 libcurl 1.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.1s\n", - "Downloading (1) ━━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━\u001b[0m 165.2MB sra-tools 2.0s\n", - "Extracting (41) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 libcurl 1.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.2s\n", - "Downloading (1) ━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━━\u001b[0m 168.1MB sra-tools 2.1s\n", - "Extracting (41) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 libcurl 1.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.3s\n", - "Downloading (1) ━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━━\u001b[0m 168.9MB sra-tools 2.2s\n", - "Extracting (41) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 libcurl 2.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.4s\n", - "Downloading (1) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 174.6MB sra-tools 2.3s\n", - "Extracting (41) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 libnghttp2 2.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gsra-tools 67.0MB @ 27.1MB/s 1.6s\n", - "[+] 2.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (42) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 libnghttp2 2.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (42) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 libnghttp2 2.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (42) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 libnghttp2 2.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (42) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 libssh2 2.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (42) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 libssh2 2.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (42) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 libssh2 2.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (42) ━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━━\u001b[0m 6 libssh2 2.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (41) ━━╸\u001b[33m━━━━━━━━━━━━━━━━━━━━\u001b[0m 7 libxml2 2.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (33) ━━━━━━╸\u001b[33m━━━━━━━━━━━━━━━━\u001b[0m 15 libxml2 3.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (31) ━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━━\u001b[0m 17 libxml2 3.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (28) ━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━\u001b[0m 20 libxml2 3.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (28) ━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━\u001b[0m 20 ncbi-ngs-sdk 3.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (28) ━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━\u001b[0m 20 ncbi-ngs-sdk 3.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (28) ━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━\u001b[0m 20 ncbi-ngs-sdk 3.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (28) ━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━\u001b[0m 20 ncbi-ngs-sdk 3.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (28) ━━━━━━━━╸\u001b[33m━━━━━━━━━━━━━━\u001b[0m 20 nodejs 3.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (25) ━━━━━━━━━━╸\u001b[33m━━━━━━━━━━━━\u001b[0m 23 nodejs 3.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (22) ━━━━━━━━━━━╸\u001b[33m━━━━━━━━━━━\u001b[0m 26 nodejs 3.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (22) ━━━━━━━━━━━╸\u001b[33m━━━━━━━━━━━\u001b[0m 26 nodejs 4.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (15) ━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━━\u001b[0m 33 perl-alien-build 4.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-alien-build 4.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-alien-build 4.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-alien-build 4.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-business-isbn 4.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-business-isbn 4.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-business-isbn 4.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-business-isbn 4.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-encode 4.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-encode 5.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-encode 5.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-encode 5.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-file-which 5.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-file-which 5.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-file-which 5.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-file-which 5.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-parent 5.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-parent 5.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-parent 5.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-parent 6.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-pathtools 6.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-pathtools 6.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-pathtools 6.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-pathtools 6.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-xml-libxml 6.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-xml-libxml 6.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-xml-libxml 6.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-xml-libxml 6.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-xml-sax-base 6.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-xml-sax-base 7.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-xml-sax-base 7.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 perl-xml-sax-base 7.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 python 7.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 python 7.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 python 7.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 python 7.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 sra-tools 7.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 sra-tools 7.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 sra-tools 7.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 sra-tools 8.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 libcurl 8.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 libcurl 8.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 libcurl 8.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 libcurl 8.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 libxml2 8.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 libxml2 8.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 libxml2 8.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 libxml2 8.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 ncbi-ngs-sdk 8.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 ncbi-ngs-sdk 9.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 ncbi-ngs-sdk 9.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 ncbi-ngs-sdk 9.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 nodejs 9.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (14) ━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━━\u001b[0m 34 nodejs 9.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (12) ━━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━\u001b[0m 36 nodejs 9.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (11) ━━━━━━━━━━━━━━━━╸\u001b[33m━━━━━━\u001b[0m 37 nodejs 9.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (8) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 40 perl-encode 9.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (8) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 40 perl-encode 9.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (8) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 40 perl-encode 9.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 libcurl 10.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 libcurl 10.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 libcurl 10.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 libcurl 10.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 ncbi-ngs-sdk 10.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 ncbi-ngs-sdk 10.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 ncbi-ngs-sdk 10.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 ncbi-ngs-sdk 10.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 nodejs 10.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 nodejs 10.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 nodejs 11.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 nodejs 11.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 perl-file-which 11.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 perl-file-which 11.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 perl-file-which 11.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 perl-file-which 11.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 perl-parent 11.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 perl-parent 11.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 perl-parent 11.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 perl-parent 11.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 perl-pathtools 12.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (7) ━━━━━━━━━━━━━━━━━━╸\u001b[33m━━━━\u001b[0m 41 perl-pathtools 12.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (4) ━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━━\u001b[0m 44 libcurl 12.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 12.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 12.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 12.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 12.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 12.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 12.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 12.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 13.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 13.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 13.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 13.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 13.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 13.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 13.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 14.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 13.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 14.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 13.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 14.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 13.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 14.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 14.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 14.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 14.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 14.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 14.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 14.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 14.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 14.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 14.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 14.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 14.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 14.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 14.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 15.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 14.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 15.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 14.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 15.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 14.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 15.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 15.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 15.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 15.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 15.5s\n", - "Downloading 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16.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 15.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 16.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 15.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 16.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 15.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 16.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 16.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 16.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 16.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 16.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 16.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 16.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 16.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 16.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 16.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 16.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 16.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 16.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) 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- "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 17.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 17.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 17.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 17.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 17.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 17.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 17.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 17.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 17.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 17.9s\n", - "Downloading 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18.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 18.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 18.5s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 18.2s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 18.6s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 18.3s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 18.7s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 18.4s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 18.8s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 18.5s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 18.9s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 18.6s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 19.0s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 18.7s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 19.1s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 18.8s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 19.2s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 18.9s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 19.3s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 ncbi-ngs-sdk 19.0s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 19.4s\n", - "Downloading ━━━━━━━━━━━━━━━━━━━━━━━ 180.0MB 2.4s\n", - "Extracting (2) ━━━━━━━━━━━━━━━━━━━━━╸\u001b[33m━\u001b[0m 46 sra-tools 19.1s\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G\u001b[?25hPreparing transaction: done\n", - "Verifying transaction: done\n", - "Executing transaction: done\n" - ] - } - ], + "metadata": {}, + "outputs": [], "source": [ "!mambaforge/bin/mamba install -c bioconda sra-tools -y" ] @@ -3459,25 +453,10 @@ }, { "cell_type": "code", - "execution_count": 37, + "execution_count": null, "id": "13d67c37-9426-45b9-9818-faaba4226bde", - "metadata": { - "scrolled": true, - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "join :| 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 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93.093.093.093.093.093.093.093.093.093.093.193.193.193.193.193.193.193.193.193.193.293.293.293.293.293.293.293.293.293.293.393.393.393.393.393.393.393.393.393.393.493.493.493.493.493.493.493.493.493.493.593.593.593.593.593.593.593.593.593.593.693.693.693.693.693.693.693.693.693.693.793.793.793.793.793.793.793.793.793.793.893.893.893.893.893.893.893.893.893.893.993.993.993.993.993.993.993.993.993.994.094.094.094.094.094.094.094.094.094.094.194.194.194.194.194.194.194.194.194.194.294.294.294.294.294.294.294.294.294.294.394.394.394.394.394.394.394.394.394.394.494.494.494.494.494.494.494.494.494.494.594.594.594.594.594.594.594.594.594.594.694.694.694.694.694.694.694.694.694.694.794.794.794.794.794.794.794.794.794.794.894.894.894.894.894.894.894.894.894.894.994.994.994.994.994.994.994.994.994.99- 95.095.095.095.095.095.095.095.095.095.095.195.195.195.195.195.195.195.195.195.195.295.295.295.295.295.295.295.295.295.295.395.395.395.395.395.395.395.395.395.395.495.495.495.495.495.495.495.495.495.495.595.595.595.595.595.595.595.595.595.595.695.695.695.695.695.695.695.695.695.695.795.795.795.795.795.795.795.795.795.795.895.895.895.895.895.895.895.895.895.895.995.995.995.995.995.995.995.995.995.996.096.096.096.096.096.096.096.096.096.096.196.196.196.196.196.196.196.196.196.196.296.296.296.296.296.296.296.296.296.296.396.396.396.396.396.396.396.396.396.396.496.496.496.496.496.496.496.496.496.496.596.596.596.596.596.596.596.596.596.596.696.696.696.696.696.696.696.696.696.696.796.796.796.796.796.796.796.796.796.796.896.896.896.896.896.896.896.896.896.896.996.996.996.996.996.996.996.996.996.99- 97.097.097.097.097.097.097.097.097.097.097.197.197.197.197.197.197.197.197.197.197.297.297.297.297.297.297.297.297.297.297.397.397.397.397.397.397.397.397.397.397.497.497.497.497.497.497.497.497.497.497.597.597.597.597.597.597.597.597.597.597.697.697.697.697.697.697.697.697.697.697.797.797.797.797.797.797.797.797.797.797.897.897.897.897.897.897.897.897.897.897.997.997.997.997.997.997.997.997.997.998.098.098.098.098.098.098.098.098.098.098.198.198.198.198.198.198.198.198.198.198.298.298.298.298.298.298.298.298.298.298.398.398.398.398.398.398.398.398.398.398.498.498.498.498.498.498.498.498.498.498.598.598.598.598.598.598.598.598.598.598.698.698.698.698.698.698.698.698.698.698.798.798.798.798.798.798.798.798.798.798.898.898.898.898.898.898.898.898.898.898.998.998.998.998.998.998.998.998.998.99- 99.099.099.099.099.099.099.099.099.099.099.199.199.199.199.199.199.199.199.199.199.299.299.299.299.299.299.299.299.299.299.399.399.399.399.399.399.399.399.399.399.499.499.499.499.499.499.499.499.499.499.599.599.599.599.599.599.599.599.599.599.699.699.699.699.699.699.699.699.699.699.799.799.799.799.799.799.799.799.799.799.899.899.899.899.899.899.899.899.899.899.999.999.999.999.999.999.999.999.999.9100% \n", - "spots read : 29,521,950\n", - "reads read : 29,521,950\n", - "reads written : 29,521,950\n" - ] - } - ], + "metadata": {}, + "outputs": [], "source": [ "!fasterq-dump --threads 4 --progress SRR067701" ] @@ -3485,9 +464,7 @@ { "cell_type": "markdown", "id": "561abd2a-f88e-4265-a275-bf0604b4cb47", - "metadata": { - "tags": [] - }, + "metadata": {}, "source": [ "#### b. Run Methylseq with your own profile and data. Ensure you include:\n", "- nf-core tool version [-r]\n", @@ -3502,889 +479,10 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "id": "85da7655-f2f6-42c1-b189-7941afbecf23", - "metadata": { - "scrolled": true, - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "N E X T F L O W ~ version 22.04.3\n", - "Launching `https://github.com/nf-core/methylseq` [stoic_booth] DSL1 - revision: 03972a686b [1.6.1]\n", - "\n", - "\n", - "-\u001b[2m----------------------------------------------------\u001b[0m-\n", - " \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n", - "\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n", - "\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n", - "\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n", - " \u001b[0;32m`._,._,'\u001b[0m\n", - "\u001b[0;35m nf-core/methylseq v1.6.1\u001b[0m\n", - "-\u001b[2m----------------------------------------------------\u001b[0m-\n", - "\n", - "\u001b[1mCore Nextflow options\u001b[0m\n", - " \u001b[0;34mrevision : \u001b[0;32m1.6.1\u001b[0m\n", - " \u001b[0;34mrunName : \u001b[0;32mstoic_booth\u001b[0m\n", - " \u001b[0;34mcontainer : \u001b[0;32mnfcore/methylseq:1.6.1\u001b[0m\n", - " \u001b[0;34mlaunchDir : \u001b[0;32m/home/jupyter\u001b[0m\n", - " \u001b[0;34mworkDir : \u001b[0;32m/zy-test/methyl-seq\u001b[0m\n", - " \u001b[0;34mprojectDir : \u001b[0;32m/home/jupyter/.nextflow/assets/nf-core/methylseq\u001b[0m\n", - " \u001b[0;34muserName : \u001b[0;32mjupyter\u001b[0m\n", - " \u001b[0;34mprofile : \u001b[0;32mgls\u001b[0m\n", - " \u001b[0;34mconfigFiles : \u001b[0;32m/home/jupyter/.nextflow/assets/nf-core/methylseq/nextflow.config, /home/jupyter/test_hw2.config\u001b[0m\n", - "\n", - "\u001b[1mInput/output options\u001b[0m\n", - " \u001b[0;34minput : \u001b[0;32mSRR067701.fastq.gz\u001b[0m\n", - " \u001b[0;34msingle_end : \u001b[0;32mtrue\u001b[0m\n", - " \u001b[0;34moutdir : \u001b[0;32mgs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1\u001b[0m\n", - "\n", - "\u001b[1mReference genome options\u001b[0m\n", - " \u001b[0;34mgenome : \u001b[0;32mGRCh37\u001b[0m\n", - " \u001b[0;34mfasta : \u001b[0;32ms3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa\u001b[0m\n", - " \u001b[0;34mbismark_index : \u001b[0;32ms3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/\u001b[0m\n", - "\n", - "\u001b[1mGeneric options\u001b[0m\n", - " \u001b[0;34mmax_multiqc_email_size: \u001b[0;32m25 MB\u001b[0m\n", - " \u001b[0;34mtracedir : \u001b[0;32m./results/pipeline_info\u001b[0m\n", - "\n", - "\u001b[1mMax job request options\u001b[0m\n", - " \u001b[0;34mmax_cpus : \u001b[0;32m32\u001b[0m\n", - " \u001b[0;34mmax_memory : \u001b[0;32m110.GB\u001b[0m\n", - " \u001b[0;34mmax_time : \u001b[0;32m10d\u001b[0m\n", - "\n", - "-\u001b[2m----------------------------------------------------\u001b[0m-\u001b[2m\n", - " Only displaying parameters that differ from defaults.\n", - "\u001b[0m-\u001b[2m----------------------------------------------------\u001b[0m-\n", - "\u001b[33mWARN: Access to undefined parameter `bwa_meth_index` -- Initialise it to a default value eg. `params.bwa_meth_index = some_value`\u001b[39m\u001b[K\n", - "\u001b[33mWARN: Access to undefined parameter `fasta_index` -- Initialise it to a default value eg. `params.fasta_index = some_value`\u001b[39m\u001b[K\n", - "Uploading local `bin` scripts folder to gs://nextflowdemobucket/zy-test/methyl-seq/tmp/f1/9b276f393a4271c2f3f0cfc1db3018/bin\n", - "[- ] process > get_software_versions -\u001b[K\n", - "[- ] process > fastqc -\u001b[K\n", - "[- ] process > trim_galore -\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "\u001b[9A\n", - "[- ] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[- ] process > fastqc -\u001b[K\n", - "[- ] process > trim_galore -\u001b[K\n", - 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"\u001b[13A\n", - "[- ] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[- ] process > fastqc [ 0%] 0 of 1\u001b[K\n", - "[- ] process > trim_galore [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[- ] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[13A\n", - "executor > google-lifesciences (1)\u001b[K\n", - "[bb/29da00] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[- ] process > fastqc [ 0%] 0 of 1\u001b[K\n", - "[- ] process > trim_galore [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[- ] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (2)\u001b[K\n", - "[bb/29da00] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > trim_galore [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[- ] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (3)\u001b[K\n", - "[bb/29da00] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[- ] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (4)\u001b[K\n", - "[bb/29da00] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - 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"[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (4)\u001b[K\n", - "[bb/29da00] process > get_software_versions [ 0%] 0 of 1\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (4)\u001b[K\n", - "[bb/29da00] process > get_software_versions [ 0%] 0 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (4)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [ 0%] 0 of 1\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (4)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [ 0%] 0 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (4)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (4)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [ 0%] 0 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (4)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (4)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [ 0%] 0 of 1 ✔\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (4)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (4)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > bismark_align -\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "Staging foreign file: s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (4)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > bismark_align [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "Staging foreign file: s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (5)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "Staging foreign file: s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (5)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "Staging foreign file: s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (5)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [ 0%] 0 of 1 ✔\u001b[K\n", - "[- ] process > bismark_deduplicate -\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq -\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (5)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > bismark_deduplicate [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[- ] process > preseq [ 0%] 0 of 1\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (6)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > bismark_deduplicate [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (7)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (7)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (7)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (7)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [ 0%] 0 of 1 ✔\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap -\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (7)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[- ] process > qualimap [ 0%] 0 of 1\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (8)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > bismark_methXtract -\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (8)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > bismark_methXtract [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [ 0%] 0 of 1 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [ 0%] 0 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > bismark_report -\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (9)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > bismark_report [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (10)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[35/476b0d] process > bismark_report (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_summary -\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (10)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[35/476b0d] process > bismark_report (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[- ] process > bismark_summary [ 0%] 0 of 1\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (11)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[35/476b0d] process > bismark_report (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[1b/a2f528] process > bismark_summary [ 0%] 0 of 1\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (11)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[35/476b0d] process > bismark_report (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[1b/a2f528] process > bismark_summary [ 0%] 0 of 1\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (11)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[35/476b0d] process > bismark_report (SRR067701) [ 0%] 0 of 1\u001b[K\n", - "[1b/a2f528] process > bismark_summary [ 0%] 0 of 1\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (11)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[35/476b0d] process > bismark_report (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[1b/a2f528] process > bismark_summary [ 0%] 0 of 1\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (11)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[35/476b0d] process > bismark_report (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[1b/a2f528] process > bismark_summary [ 0%] 0 of 1 ✔\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (11)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[35/476b0d] process > bismark_report (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[1b/a2f528] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > multiqc -\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (11)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[35/476b0d] process > bismark_report (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[1b/a2f528] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[- ] process > multiqc [ 0%] 0 of 1\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (12)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[35/476b0d] process > bismark_report (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[1b/a2f528] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[10/70b01d] process > multiqc (1) [ 0%] 0 of 1\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (12)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[35/476b0d] process > bismark_report (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[1b/a2f528] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[10/70b01d] process > multiqc (1) [ 0%] 0 of 1\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (12)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[35/476b0d] process > bismark_report (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[1b/a2f528] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[10/70b01d] process > multiqc (1) [ 0%] 0 of 1 ✔\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[14A\n", - "executor > google-lifesciences (12)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[35/476b0d] process > bismark_report (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[1b/a2f528] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[10/70b01d] process > multiqc (1) [100%] 1 of 1 ✔\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "-\u001b[0;35m[nf-core/methylseq]\u001b[0;32m Pipeline completed successfully\u001b[0m-\u001b[K\n", - "\u001b[15A\n", - "executor > google-lifesciences (12)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[35/476b0d] process > bismark_report (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[1b/a2f528] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[10/70b01d] process > multiqc (1) [100%] 1 of 1 ✔\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "-\u001b[0;35m[nf-core/methylseq]\u001b[0;32m Pipeline completed successfully\u001b[0m-\u001b[K\n", - "Waiting files transfer to complete (2 files)\u001b[K\n", - "\u001b[16A\n", - "executor > google-lifesciences (12)\u001b[K\n", - "[bb/29da00] process > get_software_versions [100%] 1 of 1 ✔\u001b[K\n", - "[73/d29c66] process > fastqc (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[69/ba20f1] process > trim_galore (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[23/bcdb7b] process > bismark_align (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[b2/b37048] process > bismark_deduplicate (SRR067... [100%] 1 of 1 ✔\u001b[K\n", - "[15/2b913d] process > bismark_methXtract (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[35/476b0d] process > bismark_report (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[1b/a2f528] process > bismark_summary [100%] 1 of 1 ✔\u001b[K\n", - "[1b/006fce] process > qualimap (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[25/1f6785] process > preseq (SRR067701) [100%] 1 of 1 ✔\u001b[K\n", - "[10/70b01d] process > multiqc (1) [100%] 1 of 1 ✔\u001b[K\n", - "[46/1e1ee8] process > output_documentation [100%] 1 of 1 ✔\u001b[K\n", - "\u001b[K\n", - "\u001b[K\n", - "\u001b[32;1mCompleted at: 17-Jun-2022 05:49:04\n", - "Duration : 1h 5m 19s\n", - "CPU hours : 10.3\n", - "Succeeded : 12\n", - "\u001b[22;39m\u001b[K\n", - "\n" - ] - } - ], + "metadata": {}, + "outputs": [], "source": [ "!./nextflow run nf-core/methylseq -r 1.6.1 \\\n", " --input 'SRR067701.fastq.gz' \\ \n", @@ -4399,38 +497,17 @@ { "cell_type": "markdown", "id": "a8fbe5a4-8ab0-4766-a954-f8b4dcc0f6b6", - "metadata": { - "tags": [] - }, + "metadata": {}, "source": [ "#### c. Check to see if files are in your output directory bucket" ] }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "id": "4a12997e-a890-464d-9145-412154bda4a7", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "gs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1/\n", - "gs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1/MultiQC/\n", - "gs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1/bismark_alignments/\n", - "gs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1/bismark_deduplicated/\n", - "gs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1/bismark_methylation_calls/\n", - "gs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1/bismark_reports/\n", - "gs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1/bismark_summary/\n", - "gs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1/fastqc/\n", - "gs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1/pipeline_info/\n", - "gs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1/preseq/\n", - "gs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1/qualimap/\n", - "gs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1/trim_galore/\n" - ] - } - ], + "outputs": [], "source": [ "!gsutil ls gs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1" ] @@ -4445,53 +522,20 @@ }, { "cell_type": "code", - "execution_count": 39, + "execution_count": null, "id": "9ba6f2bb-a4a4-4cd2-8c30-1912851ebd5c", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Copying gs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1/MultiQC/multiqc_report.html...\n", - "/ [1 files][ 1.2 MiB/ 1.2 MiB] \n", - "Operation completed over 1 objects/1.2 MiB. \n" - ] - } - ], + "outputs": [], "source": [ "!gsutil cp -r gs://nextflowdemobucket/zy-test/methyl-seq/methylseq-1/MultiQC/multiqc_report.html ." ] }, { "cell_type": "code", - "execution_count": 46, + "execution_count": null, "id": "dccc7b1f-a5ac-4cec-a2c3-f7fe42fe8f73", "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - " \n", - " " - ], - "text/plain": [ - "" - ] - }, - "execution_count": 46, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "from IPython.display import IFrame\n", "\n", @@ -4537,31 +581,7 @@ ] } ], - "metadata": { - "environment": { - "kernel": "python3", - "name": "r-cpu.4-2.m103", - "type": "gcloud", - "uri": "gcr.io/deeplearning-platform-release/r-cpu.4-2:m103" - }, - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.7.12" - } - }, + "metadata": {}, "nbformat": 4, "nbformat_minor": 5 } diff --git a/test-lint.ipynb b/test-lint.ipynb index e4987fb..75b0d9c 100644 --- a/test-lint.ipynb +++ b/test-lint.ipynb @@ -2,54 +2,24 @@ "cells": [ { "cell_type": "code", + "execution_count": null, "id": "initial_id", - "metadata": { - "collapsed": true, - "ExecuteTime": { - "end_time": "2024-10-29T14:21:59.998233Z", - "start_time": "2024-10-29T14:21:59.970969Z" - } - }, - "source": "print(\"test cell\")", - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "test cell\n" - ] - } - ], - "execution_count": 1 + "metadata": {}, + "outputs": [], + "source": [ + "print(\"test cell\")" + ] }, { - "metadata": {}, "cell_type": "code", - "outputs": [], "execution_count": null, - "source": "", - "id": "18ababdccf0c49c6" + "id": "18ababdccf0c49c6", + "metadata": {}, + "outputs": [], + "source": [] } ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 2 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.6" - } - }, + "metadata": {}, "nbformat": 4, "nbformat_minor": 5 } From 35357e11acac2192c7a1c63cbb836e324cf61ae8 Mon Sep 17 00:00:00 2001 From: John Turner Date: Tue, 29 Oct 2024 14:30:08 +0000 Subject: [PATCH 3/3] removing test file --- test-lint.ipynb | 25 ------------------------- 1 file changed, 25 deletions(-) delete mode 100644 test-lint.ipynb diff --git a/test-lint.ipynb b/test-lint.ipynb deleted file mode 100644 index 75b0d9c..0000000 --- a/test-lint.ipynb +++ /dev/null @@ -1,25 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "id": "initial_id", - "metadata": {}, - "outputs": [], - "source": [ - "print(\"test cell\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "18ababdccf0c49c6", - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": {}, - "nbformat": 4, - "nbformat_minor": 5 -}