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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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gtf2bed not staging with singularity on SGE HPC #901

Closed chriswyatt1 closed 1 year ago

chriswyatt1 commented 1 year ago

Description of the bug

This may just be me doing something silly, but the following breaks for me on HPC, sge. Singularity is not staging the bin scritps properly I think. So the gtf2bed script is not found. All the other modules work as expected, its just this one that breaks the pipeline.

Command used and terminal output

nextflow run -c ucl_cs5.config,rnaseq.config nf-core/rnaseq -r 3.9 -profile test --outdir Test_out -bg -resume -with-tower

Launching `https://github.com/nf-core/rnaseq` [ecstatic_lattes] DSL2 - revision: e049f51f02 [3.9]

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq v3.9
------------------------------------------------------
Core Nextflow options
  revision                  : 3.9
  runName                   : ecstatic_lattes
  containerEngine           : singularity
  launchDir                 : /home/cwyatt/Work/Test_nfcore_rnaseq
  workDir                   : /home/cwyatt/Work/Test_nfcore_rnaseq/work
  projectDir                : /home/cwyatt/.nextflow/assets/nf-core/rnaseq
  userName                  : cwyatt
  profile                   : test
  configFiles               : /home/cwyatt/.nextflow/assets/nf-core/rnaseq/nextflow.config, /home/cwyatt/Work/Test_nfcore_rnaseq/ucl_cs5.config, /home/cwyatt/Work/Test_nfcore_rnaseq/rnaseq.config

Input/output options
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.4/samplesheet_test.csv
  outdir                    : Test_out

UMI options
  umitools_bc_pattern       : NNNN
  umitools_bc_pattern2      : null
  umitools_umi_separator    : null

Read filtering options
  bbsplit_fasta_list        : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/bbsplit_fasta_list.txt
  skip_bbsplit              : false

Reference genome options
  fasta                     : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fasta
  gtf                       : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf.gz
  gff                       : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gff.gz
  transcript_fasta          : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/transcriptome.fasta
  additional_fasta          : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/gfp.fa.gz
  hisat2_index              : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/hisat2.tar.gz
  rsem_index                : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/rsem.tar.gz
  salmon_index              : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/salmon.tar.gz

Alignment options
  pseudo_aligner            : salmon

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: University College London Computer Science cluster
  config_profile_contact    : Chris Wyatt (ucbtcdr@ucl.ac.uk)
  config_profile_url        : https://www.rc.ucl.ac.uk/docs/Clusters/Myriad/

Max job request options
  max_cpus                  : 36
  max_memory                : 128 GB
  max_time                  : 3d

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/rnaseq for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.1400710

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md
------------------------------------------------------
WARN: =============================================================================
  Both '--gtf' and '--gff' parameters have been provided.
  Using GTF file as priority.
===================================================================================
WARN: =============================================================================
  '--transcript_fasta' parameter has been provided.
  Make sure transcript names in this file match those in the GFF/GTF file.

  Please see:
  https://github.com/nf-core/rnaseq/issues/753
===================================================================================
Monitor the execution with Nextflow Tower using this URL: https://tower.nf/user/chris-wyatt/watch/4eLEDcHwGJjsFy
[75/d93d30] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[34/bf9dfe] Submitted process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)
[fd/cf621c] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)
[0a/621ae4] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
Downloading plugin nf-amazon@1.11.1
[ca/6754b9] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA (gfp.fa)
Staging foreign file: s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357073_1.fastq.gz
[ae/83951d] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[bf/d02b98] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (genome_gfp.fasta)
[09/c0ef22] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
Staging foreign file: s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357072_1.fastq.gz
Staging foreign file: s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357072_2.fastq.gz
Pulling Singularity image https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0 [cache /SAN/biosciences/GotitsGenomes/.singularity/pull/depot.galaxyproject.org-singularity-trim-galore-0.6.7--hdfd78af_0.img]
[a0/0333d5] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
[01/f08953] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
[5e/838e6f] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)
Error executing process > 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)` terminated with an error exit status (255)

Command executed:

  gtf2bed \
      genome_gfp.gtf \
      > genome_gfp.bed

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED":
      perl: $(echo $(perl --version 2>&1) | sed 's/.*v\(.*\)) built.*/\1/')
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  WARNING: Skipping mount /var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  FATAL:   container creation failed: mount /tmp/9722333.1.cpu.q/nxf.rYnAzD0TZ3->/tmp/9722333.1.cpu.q/nxf.rYnAzD0TZ3 error: while mounting /tmp/9722333.1.cpu.q/nxf.rYnAzD0TZ3: destination /tmp/9722333.1.cpu.q/nxf.rYnAzD0TZ3 doesn't exist in container

Work dir:
  /home/cwyatt/Work/Test_nfcore_rnaseq/work/09/c0ef221f09c9c3c31d732000e6f15f

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Execution cancelled -- Finishing pending tasks before exit

Relevant files

No response

System information

HPC singularity SGE. 3.9 rnaseq Version: 22.10.3 build 5834 Created: 21-11-2022 21:37 UTC (21:37 BST) System: Linux 3.10.0-1160.49.1.el7.x86_64 Runtime: Groovy 3.0.13 on OpenJDK 64-Bit Server VM 17.0.1+12-39 Encoding: UTF-8 (UTF-8)

chriswyatt1 commented 1 year ago

I have changed where the bind mounts of singularity are, but still cannot work out whats going on. If you have any ideas, would be great to know what I am doing wrong. Thanks. I am using singularity v3.8.5-2.el7

chriswyatt1 commented 1 year ago

Here is my configuration file:

process {
  executor='sge'
  clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.bytes/task.cpus},tmem=${task.memory.bytes/task.cpus},tscratch=${task.memory.bytes/task.cpus}" }
  scratch = true
  penv = { task.cpus > 1 ? 'smp' : null }
}

params {
  // Defaults only, expecting to be overwritten
  max_memory = 128.GB
  max_cpus = 36
  max_time = 72.h
  // igenomes_base = 's3://ngi-igenomes/igenomes/'
}

// optional executor settings

executor {
  queueSize = 10
  submitRateLimit = '1 sec'
}

singularity {
    enabled = true
    autoMounts = true
}
drpatelh commented 1 year ago

Sorry for not replying Chris. Saw this and then forget to respond. How did you fix it?

nebo56 commented 6 months ago

I'm facing the same issue. How did you solve it? Cheers!