Cartoflow is not working on my input chemical file on palmetto #3
Comments
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Hi! It seems that a recent update with cartogene & genebridge may have led to a few errors in installing the packages it needs from a requirement list, which is leading to them not being installed and thus the program being unable to run. A patch is being implemented soon! |
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Hello! An update was just applied that should fix it so even if something like Palmetto doesn't have access to the specific version that is requested in 'requirements.txt', it will attempt to get the closest version too that one. That should fix it for supercomputers that only have access to specific package versions for safety reasons! Hope this helps @madmont02 ! Tell me if it works and I will close this issue. |
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I am still receiving the same error. |
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Hey @madmont02 . Sorry for the delay, but I think this last update should have fixed all these issues! Please reinstall the newest version of CartoFlow and tell me if it works or not. If it doesn't work, please post the new errors here! |
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I tried reinstalling the newest version and this was the error I received: If git wasn't 'found', then you may have to run this: Cartogene Phase... loading network from edgelist...Traceback (most recent call last): |
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My chemical list was the same as before: |
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Hey @madmont02 , are you sure your chemical file is only listed as 'beets_chemicals'? |
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yes i had it saved as that, i tried making another file and making it a .txt and tried that way but received the same error: If git wasn't 'found', then you may have to run this: Cartogene Phase... loading network from edgelist...Traceback (most recent call last): Traceback (most recent call last): |
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@madmont02 So, that actually not the same error! The last error was resolved it seems and could find beets_chem.txt . Installing collected packages: certifi, charset-normalizer, numpy, pytz, pandas, str2bool, tzdata, wheel The error message you provided indicates that the issue is occurring during the installation of Python packages using pip. The PermissionError: [Errno 13] Permission denied: '/usr/local/lib/python3.6' is indicates that the process does not have the necessary permissions to write to the /usr/local/lib/python3.6 directory. This error typically happens when trying to install packages globally without sufficient privileges. You could try running these commands while you are in the cartogene AND genebridge directory: If neither of these work, try to ask someone you know of who can give you rewrite access on the machine or, if you still do not have permission to download the packages required like pandas to for the program to run, then you would have to run it on a machine you DO have those permissions on. This could include a laptop, pc, or a virtual machine that you have access to. |
Here is my chemical list:
Gamma-aminobutyric acid Betaxanthin
Betaine
Betanin
Indicaxanthin
Isobetanin
Isoleucine Betaxanthin
leucine Betaxanthin
Miraxanthin V
Muscaaurin VII
Phenylalanine Betaxanthin
Serine Betaxanthin
Tryptophan Betaxanthin
Valine Betaxanthin
Vulgaxanthin I
Vulgaxanthin IV
Here are the errors I'm getting:
[maddenm@login002 cartoflow]$ bash cartoflow.sh -i golden_beets
fatal: destination path 'cartogene' already exists and is not an empty directory.
fatal: destination path 'linkcomm' already exists and is not an empty directory.
fatal: destination path 'genebridge' already exists and is not an empty directory.
If git wasn't 'found', then you may have to run this:
sudo apt install git
Cartogene Phase...
Collecting certifi==2023.11.17 (from -r requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/64/62/428ef076be88fa93716b576e4a01f919d25968913e817077a386fcbe4f42/certifi-202
3.11.17-py3-none-any.whl
Collecting charset-normalizer==3.3.2 (from -r requirements.txt (line 2))
Could not find a version that satisfies the requirement charset-normalizer==3.3.2 (from -r requirements.txt (line 2)) (from version
s: 0.1a0, 0.1.1a0, 0.1.2b0, 0.1.4b0, 0.1.5b0, 0.1.7, 0.1.8, 0.2.0, 0.2.1, 0.2.2, 0.2.3, 0.3.0, 1.0.0, 1.1.0, 1.1.1, 1.2.0, 1.3.0, 1.3
.1, 1.3.2, 1.3.3, 1.3.4, 1.3.5, 1.3.6, 1.3.7, 1.3.8, 1.3.9, 1.4.0, 1.4.1, 2.0.0, 2.0.1, 2.0.2, 2.0.3, 2.0.4, 2.0.5, 2.0.6, 2.0.7, 2.0
.8, 2.0.9, 2.0.10, 2.0.11, 2.0.12, 2.1.0, 2.1.1, 3.0.0b1, 3.0.0b2, 3.0.0rc1, 3.0.0, 3.0.1)
No matching distribution found for charset-normalizer==3.3.2 (from -r requirements.txt (line 2))
Traceback (most recent call last):
File "cartogene_standalone.py", line 36, in
import pandas as pd
ModuleNotFoundError: No module named 'pandas'
Linkcomm Phase...
cp: cannot stat 'faceted_inact_node_network.tsv': No such file or directory
loading network from edgelist...
Traceback (most recent call last):
File "python/link_clustering.py", line 358, in
adj,edges = read_edgelist_unweighted(args[0], delimiter=delimiter)
File "python/link_clustering.py", line 210, in read_edgelist_unweighted
for line in open(filename, 'U'):
FileNotFoundError: [Errno 2] No such file or directory: 'faceted_inact_node_network.tsv'
Genebridge Phase...
cp: missing destination file operand after '../genebridge'
Try 'cp --help' for more information.
cp: missing destination file operand after '../genebridge'
Try 'cp --help' for more information.
cp: cannot stat 'interactionsCTD_chemical-protein.tsv': No such file or directory
Collecting asttokens==2.4.1 (from -r requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/45/86/4736ac618d82a20d87d2f92ae19441ebc7ac9e7a581d7e58bbe79233b24a/asttokens-2
.4.1-py2.py3-none-any.whl
Collecting certifi==2023.11.17 (from -r requirements.txt (line 2))
Using cached https://files.pythonhosted.org/packages/64/62/428ef076be88fa93716b576e4a01f919d25968913e817077a386fcbe4f42/certifi-202
3.11.17-py3-none-any.whl
Collecting charset-normalizer==3.3.2 (from -r requirements.txt (line 3))
Could not find a version that satisfies the requirement charset-normalizer==3.3.2 (from -r requirements.txt (line 3)) (from version
s: 0.1a0, 0.1.1a0, 0.1.2b0, 0.1.4b0, 0.1.5b0, 0.1.7, 0.1.8, 0.2.0, 0.2.1, 0.2.2, 0.2.3, 0.3.0, 1.0.0, 1.1.0, 1.1.1, 1.2.0, 1.3.0, 1.3
.1, 1.3.2, 1.3.3, 1.3.4, 1.3.5, 1.3.6, 1.3.7, 1.3.8, 1.3.9, 1.4.0, 1.4.1, 2.0.0, 2.0.1, 2.0.2, 2.0.3, 2.0.4, 2.0.5, 2.0.6, 2.0.7, 2.0
.8, 2.0.9, 2.0.10, 2.0.11, 2.0.12, 2.1.0, 2.1.1, 3.0.0b1, 3.0.0b2, 3.0.0rc1, 3.0.0, 3.0.1)
No matching distribution found for charset-normalizer==3.3.2 (from -r requirements.txt (line 3))
Traceback (most recent call last):
File "genebridge.py", line 33, in
import networkx as nx
ModuleNotFoundError: No module named 'networkx'
cp: cannot stat 'community': No such file or directory
cp: cannot stat 'Pyvis_Graph.html': No such file or directory
cp: cannot stat 'commMetrics.tsv': No such file or directory
cp: cannot stat 'nodeMetrics.tsv': No such file or directory
cp: missing destination file operand after '../edge2comm.txt'
Try 'cp --help' for more information.
Workflow complete!
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