Hi! I'm having issues with ampliseq on Dardel. I'm...
# helpdesk-hpc-swedenk
Karin Garefelt
03/27/2025, 10:48 AMHi! I'm having issues with ampliseq on Dardel. I'm using the pdc_kth profile, and loaded nextflow as a module. Would love any advice!
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ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:FASTQC (P34157-118-S18)'
Caused by:
Process `NFCORE_AMPLISEQ:AMPLISEQ:FASTQC (P34157-118-S18)` terminated with an error exit status (127)
Command executed:
printf "%s %s\n" P34157-118-S18_1.fastq.gz P34157-118-S18_1.gz P34157-118-S18_2.fastq.gz P34157-118-S18_2.gz | while read old_name new_name; do
[ -f "${new_name}" ] || ln -s $old_name $new_name
done
fastqc \
--quiet \
--threads 6 \
--memory 6144 \
P34157-118-S18_1.gz P34157-118-S18_2.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_AMPLISEQ:AMPLISEQ:FASTQC":
fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
END_VERSIONS
Command exit status:
127
Command output:
(empty)
Command error:
.command.sh: line 13: fastqc: command not found
Work dir:
/cfs/klemming/projects/supr/snic2020-6-126/projects/BB2560/VT-2025/ampliseq/work/0c/a29e8fbf5a8286aa9222087f5087c1
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>
-- Check '.nextflow.log' file for detailsm
Mahesh Binzer-Panchal
03/27/2025, 10:50 AMCan you post the command-line you used please? I don't think the
pdc_kthMahesh Binzer-Panchal
03/27/2025, 10:53 AMYour command-line instructions should look like:
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module load PDC apptainer
# then whatever you do to load Nextflow and the pipeline
nextflow run nf-core/ampliseq -profile pdc_kth -params-file params.yml ...m
Maxime Garcia
03/27/2025, 10:56 AMfastqc: command not foundk
Karin Garefelt
03/27/2025, 4:02 PMI restarted a new terminal with no additional modules and now it runs! Thank you for your quick help 🙂
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