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nf-core / rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
https://nf-co.re/rnaseq
MIT License
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NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (MGUS_1) terminated with an error exit status (1) #1092

Closed rachidelfermi closed 1 year ago

rachidelfermi commented 1 year ago

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

i used this script 
#!/bin/bash
#! How many whole nodes should be allocated?
#SBATCH --nodes=1
#! How many (MPI) tasks will there be in total? (<= nodes*56)
#SBATCH --ntasks=56
#! How much wallclock time will be required?
#SBATCH --time=36:00:00
#SBATCH --partition=compute
#SBATCH --account=omics_core-rqyo8fdrbpw-DEFAULT-CPU
eval "$(conda shell.bash hook)"

conda activate bioinfo
folder_out="$1"
path="$2"
$CACHE_DIR="/home/rachid.elfermi/lustre/omics_core-rqyo8fdrbpw/rachid.elfermi/singdir/job_$folder_out"
mkdir -p "$CACHE_DIR"
export NXF_SINGULARITY_CACHEDIR="$CACHE_DIR"

cd $path
echo $path

nextflow run nf-core/rnaseq -r 3.12.0 -name $folder_out -profile singularity -params-file nf-params.json

rm -rf "$CACHE_DIR"

the error was 

executor >  local (19)
[36/2b6a6d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[09/aa88ec] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[22/50b781] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[d8/8ed8d5] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[73/0e6c03] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[8e/338e3e] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[12/689d52] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -
[d7/4f39e0] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 3 of 3 ✔
[59/fbf824] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 3 of 3 ✔
[85/e510a8] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [  0%] 0 of 3
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:STRING... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR  -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -
[a2/41ccd0] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [ 66%] 2 of 3
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC   -
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (MGUS_1)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (MGUS_1)` terminated with an error exit status (1)

Command executed:

  INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\.1.ht2$//'`
  hisat2 \
      -x $INDEX \
      -1 MGUS_1_1_val_1.fq.gz \
      -2 MGUS_1_2_val_2.fq.gz \
       \
      --known-splicesite-infile genes.splice_sites.txt \
      --summary-file MGUS_1.hisat2.summary.log \
      --threads 12 \
      --rg-id MGUS_1 --rg SM:MGUS_1 \
       \
      --no-mixed \
      --no-discordant \
      --met-stderr --new-summary --dta \
      | samtools view -bS -F 4 -F 8 -F 256 - > MGUS_1.bam

  if [ -f MGUS_1.unmapped.fastq.1.gz ]; then
      mv MGUS_1.unmapped.fastq.1.gz MGUS_1.unmapped_1.fastq.gz
  fi
  if [ -f MGUS_1.unmapped.fastq.2.gz ]; then
      mv MGUS_1.unmapped.fastq.2.gz MGUS_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:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  WARNING: Skipping mount /var/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  (ERR): mkfifo(/tmp/45.inpipe1) failed.
  Exiting now ...
  [main_samview] fail to read the header from "-".

Work dir:
  /srv/lustre01/project/omics_core-rqyo8fdrbpw/rachid.elfermi/Test-RNA/split/batch_1/work/61/447cb638f20bd72b89552d923b98fa

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details

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

drpatelh commented 1 year ago

Hi @rachidelfermi ! Did you manage to find a solution to this? It appears to be an issue with your HPC. Maybe the tmp space on your cluster filled up?

  (ERR): mkfifo(/tmp/45.inpipe1) failed.

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.

hyBio commented 8 months ago

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 line

I 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 aaa@bbb.edu.cn --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 8

Could you plz tell me what should I do next so that I can continue the pipeline with the -resume parameter as suggested without errors?☺