NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (pituitary_stage3-1) terminated with an error exit status (1)

[hyBio]

Description of the bug

running rnaseq-pipeline locally and I'm having trouble with fail to read the header from "-".

Command used and terminal output

# my cmd
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 aaa_genomic.fna --gtf aaa_genomic.gtf --aligner hisat2 --skip_qualimap --save_reference --outdir ./00_test --max_memory 40.GB --max_cpus 8

# my error report
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 line

Relevant files

more detail

#1092 (comment)

System information

No response

[enriiquee]

Same issue here. Did you find a solution?

[merang2050]

It seems that there is a memory allocation issue with HiSAT2 aligner . Modify your config file based on the CPU and memory availability:

process {
executor = ‘local’
}

params {
max_cpus = 24
max_memory = 500.GB
max_time = 400.h
}

[drpatelh]

Seems to be a duplicate of #1288

[merang2050]

I still have same problem. Increasing the memory size did not solve the issue!!!

[pinin4fjords]

As in #1288, I think something is going wrong with the HISAT command, we're just seeing that manifest in the SAM error because of the pipe.

Since you said that you were running locally, I would suggest that you cd into the process directory.

 cd ~/project/work/f2/3c12bc9bf0e4ae9ae09f6ca2a68a96

Have a look at the .command.out, .command.err to see if there are any further clues as to what HISAT2 is throwing its tantrum about.

Failing that, edit the .command.sh to remove the pipe to samtools part:

\
      | samtools view -bS -F 4 -F 8 -F 256 -

and run manually:

bash .command.run

That should at least tell you exactly how HISAT2 is failing, without samtools intercepting anything.

[drpatelh]

Will close this for now as we are awaiting further information and testing. Please feel free to re-open if and when you can provide more details. Please feel to join the #rnaseq channel in the nf-core Slack Workspace for more real-time help.

Be great if we are able to get a set of files to be able to reproduce this issue. If you are able to reproduce using the comment above then the contents of the work directory should suffice.