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nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data
https://nf-co.re/scrnaseq
MIT License
216 stars 172 forks source link

Pipeline competed with errors #192

Closed KeLi1018 closed 1 year ago

KeLi1018 commented 1 year ago

Description of the bug

Hi! I'm running nf-core/scrnaseq v.2.1.0 but I've had some issues.

Here is the samplesheet1.csv: sample,fastq_1,fastq_2 DP8400009886BL,DP8400009886BL_L01_7_1.fq.gz,DP8400009886BL_L01_7_2.fq.gz DP8400009886BL,DP8400009886BL_L01_9_1.fq.gz,DP8400009886BL_L01_9_2.fq.gz

The codes and output are in "Command used and terminal output"

Sorry, I couldn't work out how to fix this. Thanks, and its a very helpful pipeline.

Command used and terminal output

nextflow run nf-core/scrnaseq --input samplesheet1.csv --outdir 01.result_docker_sample1_pulled --fasta GCF_000003025.6_Sscrofa11.1_genomic.fna --gtf GCF_000003025.6_Sscrofa11.1_genomic.gtf -profile docker

N E X T F L O W  ~  version 22.10.4
Launching `https://github.com/nf-core/scrnaseq` [reverent_varahamihira] DSL2 - revision: c86646e4a8 [master]

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                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/scrnaseq v2.1.0
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Core Nextflow options
  revision        : master
  runName         : reverent_varahamihira
  containerEngine : docker
  launchDir       : /home/li/Data/ScRNA/00.nf-test
  workDir         : /home/li/Data/ScRNA/00.nf-test/work
  projectDir      : /home/li/.nextflow/assets/nf-core/scrnaseq
  userName        : li
  profile         : docker
  configFiles     : /home/li/.nextflow/assets/nf-core/scrnaseq/nextflow.config

Input/output options
  input           : samplesheet1.csv
  outdir          : 01.result_docker_sample1_pulled

Mandatory arguments
  protocol        : 10XV3

Reference genome options
  fasta           : GCF_000003025.6_Sscrofa11.1_genomic.fna
  gtf             : GCF_000003025.6_Sscrofa11.1_genomic.gtf

Kallisto/BUS Options
  bustools_correct: true

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

* The pipeline
  https://doi.org/10.5281/zenodo.3568187

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

* Software dependencies
  https://github.com/nf-core/scrnaseq/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (4)
[8c/ea2743] process > NFCORE_SCRNASEQ:SCRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet1.csv)                               [100%] 1 of 1 ✔
[64/eb72b2] process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (DP8400009886BL)                                           [  0%] 0 of 1
[70/a80a0c] process > NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER (GCF_000003025.6_Sscrofa11.1_genomic.fna)                      [100%] 1 of 1 ✔
[8e/7234ec] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SIMPLEAF_INDEX (GCF_000003025.6_Sscrofa11.1_genomic_genes.gtf) [  0%] 0 of 1
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SIMPLEAF_QUANT                                                 -
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:ALEVINQC                                                       -
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_H5AD                                                     -
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:CONCAT_H5AD                                                     -
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_SEURAT                                                   -
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS                                                    -
executor >  local (4)
[8c/ea2743] process > NFCORE_SCRNASEQ:SCRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet1.csv)                               [100%] 1 of 1 ✔
[64/eb72b2] process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (DP8400009886BL)                                           [  0%] 0 of 1
[70/a80a0c] process > NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER (GCF_000003025.6_Sscrofa11.1_genomic.fna)                      [100%] 1 of 1 ✔
[8e/7234ec] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SIMPLEAF_INDEX (GCF_000003025.6_Sscrofa11.1_genomic_genes.gtf) [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SIMPLEAF_QUANT                                                 -
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:ALEVINQC                                                       -
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_H5AD                                                     -
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:CONCAT_H5AD                                                     -
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_SEURAT                                                   -
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS                                                    -
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC                                                                        -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SIMPLEAF_INDEX (GCF_000003025.6_Sscrofa11.1_genomic_genes.gtf)'

Caused by:
  Process `NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SIMPLEAF_INDEX (GCF_000003025.6_Sscrofa11.1_genomic_genes.gtf)` terminated with an error exit status (1)

Command executed:

  # export required var
  export ALEVIN_FRY_HOME=.

  # prep simpleaf
  simpleaf set-paths

  # run simpleaf index
  simpleaf \
      index \
      --threads 6 \
      --fasta GCF_000003025.6_Sscrofa11.1_genomic.fna \
      --gtf GCF_000003025.6_Sscrofa11.1_genomic_genes.gtf \
      --rlen 91 \
      -o salmon

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SIMPLEAF_INDEX":
      simpleaf: $(simpleaf -V | tr -d '\n' | cut -d ' ' -f 2)
      salmon: $(salmon --version | sed -e "s/salmon //g")
  END_VERSIONS

Command exit status:
  1

Command output:
  found `salmon` in the PATH at /usr/local/bin/salmon
  found `alevin-fry` in the PATH at /usr/local/bin/alevin-fry
  found `pyroe` in the PATH at /usr/local/bin/pyroe

Command error:
  found `salmon` in the PATH at /usr/local/bin/salmon
  found `alevin-fry` in the PATH at /usr/local/bin/alevin-fry
  found `pyroe` in the PATH at /usr/local/bin/pyroe
  Error: pyroe failed to return succesfully ExitStatus(unix_wait_status(256))

Work dir:
  /home/li/Data/ScRNA/00.nf-test/work/8e/7234ec087a44bef4cf07b294f35a75

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

Relevant files

No response

System information

No response

rob-p commented 1 year ago

This suggests that one of the files passed to pyroe did not exist. ExitStatus(unix_wait_status(256)) is process failure for which that is the most common cause.

grst commented 1 year ago

Hi @rob-p,

any suspicion what could be the reason for that? The failure happens already during indexing, and according the the script section in the output, simpleaf index gets a valid filename for fasta and gtf file.

rob-p commented 1 year ago

Does this persist after the additions of @robsyme, @dongzehe and myself? If so, we should at least get much more informative output.

grst commented 1 year ago

Hi @KeLi1018,

could you please try to rerun the dev version of the workflow (nextflow run nf-core/scrnaseq [...] -r dev) and check if the error persists?

KeLi1018 commented 1 year ago

Thanks！ It works.