Hi,
I use Illumina paired end libraries (10 GB per library) and I got an error in megahit. I executed nextflow run nf-core/mag --input samples.csv --outdir /home/s-junguy/magall -profile singularity -c ~/.nextflow/config --coassemble_group true --skip_spades true -resume and this is my custom config file:
ERROR ~ Error executing process > 'NFCORE_MAG:MAG:MEGAHIT (group-6)'
Caused by:
Process `NFCORE_MAG:MAG:MEGAHIT (group-6)` terminated with an error exit status (255)
Command executed:
## Check if we're in the same work directory as a previous failed MEGAHIT run
if [[ -d MEGAHIT ]]; then
rm -r MEGAHIT/
fi
megahit -t "256" -m 268435456000 -1 "P19752-128_run0_phix_removed.unmapped_1.fastq.gz,P19752-130_run0_phix_removed.unmapped_1.fastq.gz,P19752-129_run0_phix_removed.unmapped_1.fastq.gz,P19752-127_run0_phix_removed.unmapped_1.fastq.gz" -2 "P19752-128_run0_phix_removed.unmapped_2.fastq.gz,P19752-130_run0_phix_removed.unmapped_2.fastq.gz,P19752-129_run0_phix_removed.unmapped_2.fastq.gz,P19752-127_run0_phix_removed.unmapped_2.fastq.gz" -o MEGAHIT --out-prefix "MEGAHIT-group-6"
gzip -c "MEGAHIT/MEGAHIT-group-6.contigs.fa" > "MEGAHIT/MEGAHIT-group-6.contigs.fa.gz"
cat <<-END_VERSIONS > versions.yml
"NFCORE_MAG:MAG:MEGAHIT":
megahit: $(echo $(megahit -v 2>&1) | sed 's/MEGAHIT v//')
END_VERSIONS
Command exit status:
255
Command output:
(empty)
Command error:
WARNING: Could not lookup the current user's information: user: unknown userid 26972
FATAL: Couldn't determine user account information: user: unknown userid 26972
Work dir:
/home/user/magall/work/87/018acb711c5d5ab0d6c029fc9d746d
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
-- Check '.nextflow.log' file for details
What I do not understand is that megahit has run successfully before. I had to delete the directory /home/user/.nextflow/assets/nf-core/mag for an update because I had other issues with megahit before when I restarted the pipeline. The previous output is still in the directory but the pipeline had to start from the beginning because I deleted the directory /home/user/.nextflow/assets/nf-core/mag for an update.
Description of the bug
Hi, I use Illumina paired end libraries (10 GB per library) and I got an error in megahit. I executed
nextflow run nf-core/mag --input samples.csv --outdir /home/s-junguy/magall -profile singularity -c ~/.nextflow/config --coassemble_group true --skip_spades true -resume
and this is my custom config file:This is the error message:
What I do not understand is that megahit has run successfully before. I had to delete the directory /home/user/.nextflow/assets/nf-core/mag for an update because I had other issues with megahit before when I restarted the pipeline. The previous output is still in the directory but the pipeline had to start from the beginning because I deleted the directory /home/user/.nextflow/assets/nf-core/mag for an update.
Command used and terminal output
No response
Relevant files
No response
System information
No response