NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (MGUS_1) terminated with an error exit status (1) #1092
Comments
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Hi @rachidelfermi ! Did you manage to find a solution to this? It appears to be an issue with your HPC. Maybe the Will close this because it looks like an infra issue and not pipeline related. Please feel free to join the nf-core Slack Workspace for any future questions/issues. We have an #rnaseq channel where you can get more real-time help. |
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Hello, I seem to be having a similar problem, here is my error log that: nf-core/rnaseq execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:
Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (pituitary_stage3-1)'
Caused by:
Process `NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (pituitary_stage3-1)` terminated with an error exit status (1)
Command executed:
INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\.1.ht2$//'`
hisat2 \
-x $INDEX \
-1 pituitary_stage3-1_1_val_1.fq.gz \
-2 pituitary_stage3-1_2_val_2.fq.gz \
\
--known-splicesite-infile aaa_genomic.filtered.splice_sites.txt \
--summary-file pituitary_stage3-1.hisat2.summary.log \
--threads 8 \
--rg-id pituitary_stage3-1 --rg SM:pituitary_stage3-1 \
\
--no-mixed \
--no-discordant \
--met-stderr --new-summary --dta \
| samtools view -bS -F 4 -F 8 -F 256 - > pituitary_stage3-1.bam
if [ -f pituitary_stage3-1.unmapped.fastq.1.gz ]; then
mv pituitary_stage3-1.unmapped.fastq.1.gz pituitary_stage3-1.unmapped_1.fastq.gz
fi
if [ -f pituitary_stage3-1.unmapped.fastq.2.gz ]; then
mv pituitary_stage3-1.unmapped.fastq.2.gz pituitary_stage3-1.unmapped_2.fastq.gz
fi
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN":
hisat2: 2.2.1
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Skipping mount /usr/local/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
(ERR): mkfifo(/tmp/53.inpipe1) failed.
Exiting now ...
[main_samview] fail to read the header from "-".
Work dir:
~/project/work/f2/3c12bc9bf0e4ae9ae09f6ca2a68a96
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command lineI use an offline command line to execute the commands, here is my command line code： nextflow run -qs 8 -profile singularity -bg /home/huyan/software/nf-core/rnaseq/nf-core-rnaseq_3.14.0/3_14_0/ --email [email protected] --input ./samplesheet.csv --fasta /new_data/AcaLat_SV/assembly/aaa_genomic.fna --gtf /new_data/AcaLat_SV/assembly/aaa_genomic.gtf --aligner hisat2 --skip_qualimap --save_reference --outdir ./00_test --max_memory 40.GB --max_cpus 8Could you plz tell me what should I do next so that I can continue the pipeline with the -resume parameter as suggested without errors?☺ |
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Description of the bug
When running the nf-core i get to this step NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN process within the workflow, a critical error is encountered. The error occurs during the execution of the hisat2 command
Command used and terminal output
Relevant files
No response
System information
i working on HPC with node of 56 cpu and 180 GEGA o ram
i have a home directory of 100 G which 40 gega is free and the working dir is 20 Tera
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