Comments (3)
This does not seem to be problem with your sampleheet, from your log:
Command executed:
check_samplesheet.py \
samplesheet_with_rep.csv \
samplesheet.valid.csv
cat <<-END_VERSIONS > versions.yml
"NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK":
python: $(python --version | sed 's/Python //g')
END_VERSIONS
Command exit status:
127
Command output:
(empty)
Command error:
/bin/bash: .command.run: No such file or directory
Work dir:
/DATA/Meta_project/chip_MQ_decker/work/c0/d6c18165870c3b11e26e7d72f13381
This suggest to me that that your docker installation is not correctly mounting the host file system or a similar issue and thus, nextflow can not find .command.run
the script that actually takes care of running the nextflow process.
from chipseq.
This does not seem to be problem with your sampleheet, from your log:
Command executed: check_samplesheet.py \ samplesheet_with_rep.csv \ samplesheet.valid.csv cat <<-END_VERSIONS > versions.yml "NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK": python: $(python --version | sed 's/Python //g') END_VERSIONS Command exit status: 127 Command output: (empty) Command error: /bin/bash: .command.run: No such file or directory Work dir: /DATA/Meta_project/chip_MQ_decker/work/c0/d6c18165870c3b11e26e7d72f13381
This suggest to me that that your docker installation is not correctly mounting the host file system or a similar issue and thus, nextflow can not find
.command.run
the script that actually takes care of running the nextflow process.
Dear Jose,
Thanks for the response!
You are right, it seems there is a problem with Docker since the pipeline works well using "singularity". I think singularity offers several advantages compared to Docker in certain use cases. For e.g. singularity enables direct interaction with the host operating system, allowing users to access hardware resources and run applications with minimal performance overhead. This feature is particularly advantageous in high-performance computing (HPC) environments where tight integration with the underlying system is crucial.
from chipseq.
Since it worked I will close the issue now. Let us know if you have any further questions.
from chipseq.
Related Issues (20)
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from chipseq.