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 aaa@mail.com --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!!!