Invalid sample sheet: values in 'barcode' column are incorrect format

[katievigil]

Operating System

Windows 11

Other Linux

No response

Workflow Version

v23.04.2

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

v2.12.1

CLI command run

/mnt/c/Users/kvigil/AppData/Local/EPI2ME/app-5.2.2/resources/nextflow-all -log /mnt/c/Users/kvigil/epi2melabs/instances/wf-metagenomics_01JFQB77HVY9QGQK6HPQVH7A4V/nextflow.log run /mnt/c/Users/kvigil/epi2melabs/workflows/epi2me-labs/wf-metagenomics/main.nf -params-file /mnt/c/Users/kvigil/epi2melabs/instances/wf-metagenomics_01JFQB77HVY9QGQK6HPQVH7A4V/params.json -w /mnt/c/Users/kvigil/epi2melabs/instances/wf-metagenomics_01JFQB77HVY9QGQK6HPQVH7A4V/work -ansi-log false -offline -profile standard -with-weblog 'http://10.255.255.254:53250' -name ONR_viral

Workflow Execution - CLI Execution Profile

custom

What happened?

Invalid sample sheet: values in 'barcode' column are incorrect format.

EPI2ME desktop log:
EPI2ME_issue_export.tar.gz

Sample-sheet:
sample_sheet.csv

Example of file format:
Each concatenated .fastq barcode is in separate directories, but the directories are not labeled "barcode01, barcode02 etc." They have more information then this, because I used Dorado to basecall.

Relevant log output

N E X T F L O W  ~  version 23.04.2
Launching `/mnt/c/Users/kvigil/epi2melabs/workflows/epi2me-labs/wf-metagenomics/main.nf` [ONR_viral] DSL2 - revision: 61b39c3366
WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-metagenomics v2.12.1
--------------------------------------------------------------------------------
Core Nextflow options
  runName                 : ONR_viral
  containerEngine         : docker
  launchDir               : /mnt/c/Users/kvigil/epi2melabs/instances/wf-metagenomics_01JFQB77HVY9QGQK6HPQVH7A4V
  workDir                 : /mnt/c/Users/kvigil/epi2melabs/instances/wf-metagenomics_01JFQB77HVY9QGQK6HPQVH7A4V/work
  projectDir              : /mnt/c/Users/kvigil/epi2melabs/workflows/epi2me-labs/wf-metagenomics
  userName                : epi2mewsl
  profile                 : standard
  configFiles             : /mnt/c/Users/kvigil/epi2melabs/workflows/epi2me-labs/wf-metagenomics/nextflow.config
Input Options
  fastq                   : /mnt/c/Users/kvigil/OneDrive - Oxford Nanopore Technologies/results/katie/fastq_all_raw
  classifier              : minimap2
  exclude_host            : /mnt/c/Users/kvigil/Desktop/viral_reference/blanks_concatenated.fasta
Sample Options
  sample_sheet            : /mnt/c/Users/kvigil/OneDrive - Oxford Nanopore Technologies/results/katie/sample_sheet.csv
Reference Options
  store_dir               : /mnt/c/Users/kvigil/epi2melabs/data
  taxonomy                : /mnt/c/Users/kvigil/Desktop/viral_reference/NCBI_taxdump
  reference               : /mnt/c/Users/kvigil/Desktop/viral_reference/viral.1.1.genomic.fna
  ref2taxid               : /mnt/c/Users/kvigil/Desktop/viral_reference/ref2taxid.targloci.tsv
Minimap2 Options
  minimap2_by_reference   : true
Report Options
  n_taxa_barplot          : 20
Output Options
  out_dir                 : /mnt/c/Users/kvigil/epi2melabs/instances/wf-metagenomics_01JFQB77HVY9QGQK6HPQVH7A4V/output
  igv                     : true
  include_read_assignments: true
Advanced Options
  min_len                 : 200
  min_read_qual           : 15
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-metagenomics for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-metagenomics v2.12.1.
--------------------------------------------------------------------------------
Checking inputs.
Note: Reference/Database are custom.
Note: Memory available to the workflow must be slightly higher than size of the database custom index.
Note: Taxonomy database is custom.
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Note: Empty files or those files whose reads have been discarded after filtering based on read length and/or read quality will not appear in the report and will be excluded from subsequent analysis.
Minimap2 pipeline.
Preparing databases.
Checking custom taxonomy mapping exists
Checking custom reference exists
Checking custom ref2taxid mapping exists
[be/feb1f0] Submitted process > minimap_pipeline:run_common:getVersions
[1c/74cb44] Submitted process > prepare_databases:check_reference_ref2taxid
[d9/037e1d] Submitted process > validate_sample_sheet
[2a/9d558f] Submitted process > minimap_pipeline:run_common:getParams
Invalid sample sheet: values in 'barcode' column are incorrect format.
WARN: Killing running tasks (3)

Application activity log entry

Nextflow workflow report
[ONR_viral]
Workflow execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: null.

The full error message was:

Invalid sample sheet: values in 'barcode' column are incorrect format.
Run times
22-Dec-2024 14:09:41 - 22-Dec-2024 14:10:01 (duration: 19.4s)
  1 succeeded  
Nextflow command
/mnt/c/Users/kvigil/AppData/Local/EPI2ME/app-5.2.2/resources/nextflow-all -log /mnt/c/Users/kvigil/epi2melabs/instances/wf-metagenomics_01JFQB77HVY9QGQK6HPQVH7A4V/nextflow.log run /mnt/c/Users/kvigil/epi2melabs/workflows/epi2me-labs/wf-metagenomics/main.nf -params-file /mnt/c/Users/kvigil/epi2melabs/instances/wf-metagenomics_01JFQB77HVY9QGQK6HPQVH7A4V/params.json -w /mnt/c/Users/kvigil/epi2melabs/instances/wf-metagenomics_01JFQB77HVY9QGQK6HPQVH7A4V/work -ansi-log false -offline -profile standard -with-weblog 'http://10.255.255.254:53250' -name ONR_viral
CPU-Hours
(a few seconds)
Launch directory
/mnt/c/Users/kvigil/epi2melabs/instances/wf-metagenomics_01JFQB77HVY9QGQK6HPQVH7A4V
Work directory
/mnt/c/Users/kvigil/epi2melabs/instances/wf-metagenomics_01JFQB77HVY9QGQK6HPQVH7A4V/work
Project directory
/mnt/c/Users/kvigil/epi2melabs/workflows/epi2me-labs/wf-metagenomics
Script name
main.nf
Script ID
61b39c3366e09dc494dbb60e5f0eb325
Workflow session
e695f6b1-9356-4cc7-a45e-c2b751129ed0
Workflow profile
standard
Nextflow version
version 23.04.2, build 5871 (08-06-2023 09:33 UTC)

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

yes

Other demo data information

No response

[katievigil]

slurm-2647349.out-cypress01-121.txt

Update: looks like without using my blanks_concatenated.fasta and the sample sheet. I was able to complete the minimap run using commandline on HPC.

[nggvs]

Hi @katievigil
Thank you for using the workflow. If you use a sample_sheet with different barcodes, the barcodes must be named as barcode01 and so on. From your last message, should be working regardless the pipeline as you're not using a sample_sheet.

[katievigil]

@nggvs Thanks for your response. So just to clarify, my file names have to have a generic name like "barcode01, barcode02, barcode03 etc." They can't have a different type of name, like the names I designated when running Dorado standalone?