Error executing process > 'pipeline:report'

[DanilKrivonos]

Hello! I found a problem with the input file. If I give single fastq to --fastq parametr, I will see the error, but if I give directory with single fasta it worked. However, in in the documentation it is prepared that it is possible to transfer either a single fastq or directory.

(artic) krivonos_dv@r740gpu2:~/runs/PROJECTS/COVID$ nextflow run  epi2me-labs/wf-artic --fastq ./merged_reads/barcode01.fastq --scheme_version ARTIC/V4 --out_dir TEST_ASSAY/ --sample ./merged_reads/barcode01.fastq --scheme_name SARS-CoV-
2
N E X T F L O W  ~  version 22.04.0
Launching `https://github.com/epi2me-labs/wf-artic` [agitated_babbage] DSL2 - revision: 218aa1d6d0 [master]

WARN: Found unexpected parameters:
* --scheme_dir: primer_schemes
- Ignore this warning: params.schema_ignore_params = "scheme_dir"

Core Nextflow options
  revision       : master
  runName        : agitated_babbage
  containerEngine: docker
  launchDir      : /mnt/iscsidisk1/runs/runs-krivonos/PROJECTS/COVID
  workDir        : /mnt/iscsidisk1/runs/runs-krivonos/PROJECTS/COVID/work
  projectDir     : /home/krivonos_dv/.nextflow/assets/epi2me-labs/wf-artic
  userName       : krivonos_dv
  profile        : standard
  configFiles    : /home/krivonos_dv/.nextflow/assets/epi2me-labs/wf-artic/nextflow.config

Basic Input/Output Options
  out_dir        : TEST_ASSAY/
  fastq          : ./merged_reads/barcode01.fastq
  sample         : ./merged_reads/barcode01.fastq

Primer Scheme Selection
  scheme_version : ARTIC/V4

Advanced options
  normalise      : 200

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use epi2me-labs/wf-artic for your analysis please cite:

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

      ------------------------------------
      Available Primer Schemes:
      ------------------------------------

  Name          Version
  spike-seq     ONT/V4.1
  spike-seq     ONT/V1
  SARS-CoV-2    ARTIC/V3
  SARS-CoV-2    ARTIC/V4
  SARS-CoV-2    ARTIC/V2
  SARS-CoV-2    ARTIC/V4.1
  SARS-CoV-2    ARTIC/V1
  SARS-CoV-2    NEB-VarSkip/v2b
  SARS-CoV-2    NEB-VarSkip/v1a
  SARS-CoV-2    NEB-VarSkip/v1a-long
  SARS-CoV-2    NEB-VarSkip/v2
  SARS-CoV-2    Midnight-IDT/V1
  SARS-CoV-2    Midnight-ONT/V3
  SARS-CoV-2    Midnight-ONT/V2
  SARS-CoV-2    Midnight-ONT/V1

      ------------------------------------

WARN: Access to undefined parameter `detect_samples` -- Initialise it to a default value eg. `params.detect_samples = some_value`
Checking fastq input.
Single file input detected.
executor >  local (7)
executor >  local (7)
[aa/c51244] process > handleSingleFile (1)    [100%] 1 of 1 ✔
[81/b0891b] process > pipeline:getVersions    [100%] 1 of 1 ✔
[fb/4ddaed] process > pipeline:getParams      [100%] 1 of 1 ✔
[94/fbb340] process > pipeline:copySchemeDir  [100%] 1 of 1 ✔
[30/9a57a7] process > pipeline:preArticQC (1) [100%] 1 of 1, failed: 1 ✘
[-        ] process > pipeline:runArtic (1)   -
[-        ] process > pipeline:combineDepth   -
[-        ] process > pipeline:allConsensus   -
[-        ] process > pipeline:allVariants    -
[ba/d1ce66] process > pipeline:prep_nextclade [100%] 1 of 1 ✔
[-        ] process > pipeline:nextclade      -
[-        ] process > pipeline:pangolin       -
[-        ] process > pipeline:telemetry      -
[-        ] process > pipeline:report         -
[-        ] process > output                  -
Error executing process > 'pipeline:preArticQC (1)'

Caused by:
  Process `pipeline:preArticQC (1)` terminated with an error exit status (139)

Command executed:

  fastcat -s ./merged_reads/barcode01.fastq -r ./merged_reads/barcode01.fastq.stats -x barcode01 > /dev/null

Command exit status:
  139

Command output:
  (empty)

Command error:
  .command.sh: line 2:    27 Segmentation fault      (core dumped) fastcat -s ./merged_reads/barcode01.fastq -r ./merged_reads/barcode01.fastq.stats -x barcode01 > /dev/null

Work dir:
  /mnt/iscsidisk1/runs/runs-krivonos/PROJECTS/COVID/work/30/9a57a7079be8610757a592f2a02807

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

[mattdmem]

Thanks for this. I will take a look.