column "runid" not existed in file: fastcat_stats/per-read-stats.tsv.gz

[yanchunzhang]

Operating System

CentOS 7

Other Linux

No response

Workflow Version

v1.1.3

Workflow Execution

Command line (Cluster)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-16s --fastq wf-16s-demo/test_data/ -profile standard -without-docker

Workflow Execution - CLI Execution Profile

None

What happened?

Hi, I'm trying to run it on both my own data and the demo data, always got the error saying "nextflow run epi2me-labs/wf-16s --fastq wf-16s-demo/test_data/ -profile standard -without-docker". Could you please take a lookt on it? Thanks, Yanchun

Relevant log output

[skipped  ] process > prepare_databases:download_unpack_taxonomy     [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > prepare_databases:download_reference_ref2taxid [100%] 1 of 1, stored: 1 ✔
[55/e22251] process > fastcat (2)                                    [ 66%] 2 of 3, failed: 2
[c6/79f7ae] process > minimap_pipeline:run_common:getVersions        [  0%] 0 of 1
[f6/ad71b8] process > minimap_pipeline:run_common:getParams          [100%] 1 of 1 ✔
[-        ] process > minimap_pipeline:minimap                       -
[-        ] process > minimap_pipeline:createAbundanceTables         -
[-        ] process > minimap_pipeline:makeReport                    -
[3b/3cbbcc] process > minimap_pipeline:output (1)                    [100%] 1 of 1
Using a default database.
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
[skipping] Stored process > prepare_databases:download_reference_ref2taxid
[skipping] Stored process > prepare_databases:download_unpack_taxonomy
Error executing process > 'fastcat (3)'

Caused by:
  Process `fastcat (3)` terminated with an error exit status (255)

Command executed:

  mkdir fastcat_stats
  fastcat             -s barcode03             -r >(bgzip -c > fastcat_stats/per-read-stats.tsv.gz)             -f fastcat_stats/per-file-stats.tsv             -a 800 -b 2000             input             | bgzip > seqs.fastq.gz

  # extract the run IDs from the per-read stats
  csvtk cut -tf runid fastcat_stats/per-read-stats.tsv.gz         | csvtk del-header | sort | uniq > fastcat_stats/run_ids

Command exit status:
  255

Command output:
  (empty)

Command error:
  [ERRO] column "runid" not existed in file: fastcat_stats/per-read-stats.tsv.gz
  [ERRO] empty file: -

Work dir:
  /sc/arion/projects/schzrnas/zhangy40/intratumor_bacteria/010324_16s/processed/demulti_trim/work/65/3534051a368bb58b65c852b2400f09

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

WARN: Killing running tasks (2)

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

no

Other demo data information

No response

[yanchunzhang]

Figured it out to be the fastcat version issue. Updated and it worked.