samtools error with doctor.py

[gsk7757]

Hello, I tried installing and setting up the bioinfo environment as mentioned in the handbook. However, when I run doctor.py there were couple errors: samtools and fastq-dump. I tried installing samtools by using conda install -c bioconda samtools. But I have the same issue. Please help.

[ialbert]

it would be most curious to have samtools fail.

what happens when you run

micromamba install samtools

what message do you get?

[gsk7757]

I tried installing samtools again using

micromamba install samtools

micromamba install samtools
pkgs/main/noarch                                              No change
pkgs/r/osx-64                                                 No change
pkgs/r/noarch                                                 No change
pkgs/main/osx-64                                     5.1MB @   5.3MB/s  1.0s
bioconda/osx-64                                      4.2MB @   3.8MB/s  1.1s
bioconda/noarch                                      4.7MB @   3.3MB/s  1.2s
conda-forge/noarch                                  12.1MB @   8.1MB/s  1.3s
conda-forge/osx-64                                  26.3MB @  12.2MB/s  1.9s

Pinned packages:
  - python 3.8.*


Transaction

  Prefix: /Users/sgadila/micromamba/envs/bioinfo

  All requested packages already installed


Transaction starting

Transaction finished

To activate this environment, use:

    micromamba activate bioinfo

Or to execute a single command in this environment, use:

    micromamba run -n bioinfo mycommand

After running doctor.py, it still shows the same error as below

doctor.py

# Doctor! Doctor! Give me the news.
# Checking symptoms ...
# bwa           ... OK
# datamash      ... OK
# fastqc -h     ... OK
# hisat2        ... OK
# seqret -h     ... OK
# featureCounts ... OK
# efetch        ... OK
# esearch       ... OK
# samtools      --> ERROR
# fastq-dump    --> ERROR
# bowtie2       ... OK
# bcftools      ... OK
# seqtk         ... OK
# seqkit        ... OK
# bio           ... OK
# fastq-dump -X 1 -Z SRR1553591 --> ERROR
#
# Found some problems
#
# Unable to run: samtools, fastq-dump, fastq-dump -X 1 -Z SRR1553591
#
# Check the Biostar Handbook for installation help.
#

[ialbert]

if you just run samtools what happens?

samtools not working indicates some other problem - never seen such an error before - perhaps some sort of conflict with an existing installation

[ialbert]

See also the step-by-step instructions starting with step 5 as shown here:

https://www.biostarhandbook.com/step-by-step.html

[gsk7757]

Should I uninstall and reinstall everything from Step 1?

[gsk7757]

Here is the error message that popped up

samtools
dyld: Library not loaded: @rpath/libcurl.4.dylib
Referenced from: /Users/sgadila/micromamba/envs/bioinfo/bin/samtools
Reason: Incompatible library version: samtools requires version 13.0.0 or later, but libcurl.4.dylib provides version 11.0.0
Abort trap: 6

[ialbert]

that is one weird error for sure, never seen that one either,

try this, manually download the latest version

mkdir -p tmp
cd tmp
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-mac64.tar.gz
tar zxvf sratoolkit.current-mac64.tar.gz
sratoolkit.3.0.7-mac64/bin/fastq-dump

did the last command run?

[gsk7757]

Same error, when I ran the last command

sratoolkit.3.0.7-mac64/bin/fastq-dump
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
Referenced from: /Users/sgadila/tmp/sratoolkit.3.0.7-mac64/bin/fastq-dump (which was built for Mac OS X 12.6)
Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
Referenced from: /Users/sgadila/tmp/sratoolkit.3.0.7-mac64/bin/fastq-dump (which was built for Mac OS X 12.6)
Expected in: /usr/lib/libSystem.B.dylib

Abort trap: 6
(bioinfo)

[ialbert]

how up to date is your mac,

what version of MacOS do you have? Apple-> About this Mac

[gsk7757]

My MacOS version is 10.13.6.

[ialbert]

my guess is that might be the problem, would need to be updated to a newer version, that is a six year old operating system