Closed
Description
openedon Sep 18, 2024
Description of the bug
I had successfully been running nf-pangenome on AWS EC2 using tibanna and a snakemake pipeline, but today I started getting this error irrespective of whether I set -profile to singularity, docker, or conda
I'm reading online that maybe ps needs to be explicitly installed into nf-pangenome's container. Can anyone help with this?
The command in the snakemake rule is
nextflow run nf-core/pangenome \
--input panSNCombined.fa.gz \
--n_haplotypes 14 \
--outdir <outdir> \
--communities true \
-profile singularity \
-c <customNfConfig.json> \
-process.echo
This is the error I get
ERROR ~ Error executing process > 'NFCORE_PANGENOME:PANGENOME:INPUT_CHECK:SAMTOOLS_FAIDX (panSNCombined.fa.gz)'
Caused by:
Process `NFCORE_PANGENOME:PANGENOME:INPUT_CHECK:SAMTOOLS_FAIDX (panSNCombined.fa.gz)` terminated with an error exit status (1)
Command executed:
samtools \
faidx \
panSNCombined.fa.gz \
cat <<-END_VERSIONS > versions.yml
"NFCORE_PANGENOME:PANGENOME:INPUT_CHECK:SAMTOOLS_FAIDX":
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
Command 'ps' required by nextflow to collect task metrics cannot be found
Command used and terminal output
No response
Relevant files
No response
System information
Docker version 23.0.3, build 3e7cbfd
Python 3.8.10
pip 20.0.2
tibanna awsf3 version 3.3.1
cwltool version 3.1.20211103193132
cromwell version 35 for WDL draft2
cromwell version 53.1 for WDL v1.0
singularity-ce version 3.10.4-focal
goofys version 0.24.0-45b8d78375af1b24604439d2e60c567654bcdf88
snakemake 7.28.3
nf-core/pangenome 1.1.2-gaf6d1dd
N E X T F L O W ~ version 24.04.4
r6a.32xlarge EC2 instance
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