Empty file for workflow (even on demo)

[nikelau]

Operating System

Windows 11

Other Linux

No response

Workflow Version

1.1.3

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

EPI2ME V5.1.10

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

when running the workflow it does not recognise the input files (even in the demo data) and prematurely terminated workflow

Relevant log output

N E X T F L O W  ~  version 23.04.2
Launching `/mnt/d/epi2melabs/workflows/epi2me-labs/wf-16s/main.nf` [clever_hermann] DSL2 - revision: 8363748886
WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
WARN: Found unexpected parameters:
* --client_fields: D:\epi2melabs\instances\wf-16s_01HW1YTQ2S3VY4VKAE9G3PF3Y4\client_fields.json
- Ignore this warning: params.schema_ignore_params = "client_fields" 
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-16s v1.1.3
--------------------------------------------------------------------------------
Core Nextflow options
  runName              : clever_hermann
  containerEngine      : docker
  launchDir            : /mnt/d/epi2melabs/instances/wf-16s_01HW1YTQ2S3VY4VKAE9G3PF3Y4
  workDir              : /mnt/d/epi2melabs/instances/wf-16s_01HW1YTQ2S3VY4VKAE9G3PF3Y4/work
  projectDir           : /mnt/d/epi2melabs/workflows/epi2me-labs/wf-16s
  userName             : epi2mewsl
  profile              : standard
  configFiles          : /mnt/d/epi2melabs/workflows/epi2me-labs/wf-16s/nextflow.config, /mnt/d/epi2melabs/instances/wf-16s_01HW1YTQ2S3VY4VKAE9G3PF3Y4/demo.config
Input Options
  fastq                : /mnt/d/epi2melabs/demo/epi2me-labs/wf-16s/4a8184a7051ee15baf45371c909b9aac924a3a81/wf-16s-demo/test_data
Reference Options
  store_dir            : /mnt/d/epi2melabs/data
  database_sets        : [ncbi_16s_18s:[reference:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_16s_18s.fna, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_kraken2.tar.gz, ref2taxid:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ref2taxid.targloci.tsv, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-01-01.zip], ncbi_16s_18s_28s_ITS:[reference:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS.fna, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS_kraken2.tar.gz, ref2taxid:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ref2taxid.ncbi_16s_18s_28s_ITS.tsv, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-01-01.zip], SILVA_138_1:[database:null]]
Minimap2 Options
  minimap2_by_reference: true
Output Options
  out_dir              : /mnt/d/epi2melabs/instances/wf-16s_01HW1YTQ2S3VY4VKAE9G3PF3Y4/output
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-16s for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-16s v1.1.3.
--------------------------------------------------------------------------------
Checking inputs.
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.
Using default taxonomy database.
Using a default database.
[skipping] Stored process > prepare_databases:download_unpack_taxonomy
[skipping] Stored process > prepare_databases:download_reference_ref2taxid
[2d/a70a80] Submitted process > minimap_pipeline:run_common:getVersions
[7c/dc83b2] Submitted process > fastcat (1)
[86/d759dc] Submitted process > fastcat (3)
[64/727c39] Submitted process > minimap_pipeline:run_common:getParams
[19/e23a65] Submitted process > minimap_pipeline:output (1)
[dc/c5fd6d] Submitted process > fastcat (2)
WARN: Found empty file for sample 'barcode03'.
WARN: Found empty file for sample 'barcode01'.
WARN: Found empty file for sample 'barcode02'.
[2a/a4b1fe] Submitted process > minimap_pipeline:output (2)

Application activity log entry

{
  "name": "Launcher tests",
  "description": "Perform all launcher setup tests",
  "updates": [
    {
      "message": "Initialising"
    },
    {
      "message": "Checking Windows version"
    },
    {
      "message": "WSL command exists, checking status"
    },
    {
      "message": "WSL is installed, checking version"
    },
    {
      "message": "Checking for updates to the EPI2ME distribution"
    },
    {
      "message": "The EPI2ME distribution is not online, starting."
    },
    {
      "message": "WSL is ready to use."
    },
    {
      "message": "Checking Nextflow initialises"
    },
    {
      "message": "Nextflow is ready to use."
    },
    {
      "message": "All Setup tests are passing"
    }
  ],
  "id": "01HW1Z26KW71DJXR5X9M25A9HD",
  "percentage": 100,
  "status": "COMPLETED",
  "createdAt": "2024-04-22T03:54:43.708Z",
  "updatedAt": "2024-04-22T03:55:16.318Z",
  "metadata": {
    "trace": {
      "nxfCmd": "wsl",
      "nxfArgs": [
        "-d",
        "epi2me",
        "/mnt/c/Users/User/AppData/Local/EPI2ME/app-5.1.10/resources/nextflow-all",
        "-h"
      ],
      "nxfExitCode": "0"
    },
    "track": {
      "windowsVersion": [
        "10",
        "0",
        "22621"
      ],
      "windowsRelease": 2009,
      "wslVersion": "2.0.14"
    }
  }
}

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

no

Other demo data information

No response

[nikelau]

And surely there are files in my initial directory or this demo folder:

nanopore@DESKTOP-A94RLAE:/mnt/d/epi2melabs/demo/epi2me-labs/wf-16s/4a8184a7051ee15baf45371c909b9aac924a3a81/wf-16s-demo/test_data/barcode01$ ls
reads1_subset.fastq.gz  reads2_subset.fastq.gz

[nikelau]

As with the other issue seems reinstalling the workflow solved the problem.