Error running wf-alignment: pipeline:bamstats or publish

[XzeatX]

Operating System

Windows 10

Other Linux

No response

Workflow Version

v1.2.2

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

v5.2.2

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

I am unable to align my sequences to the reference genome using wf-alignment. It completes up to the pipeline:alignReads, but then starts the pipeline:bamstats and publish, where it halts.

The report states:

/mnt/d/basecalleo SUPerior/instances/wf-alignment_01JG4VRTADFYESNM5KDZD3ZCX9/work/tmp/27/950dcac414c64c9789c209cf6c886e/collect-file.data: Operation not permitted

When I run the demo, it completes 100%.

Any help would be greatly appreciated.

Relevant log output

N E X T F L O W  ~  version 23.04.2
Launching `/mnt/d/basecalleo SUPerior/workflows/epi2me-labs/wf-alignment/main.nf` [dreamy_alder] DSL2 - revision: 520ff1f043
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-alignment v1.2.2
--------------------------------------------------------------------------------
Core Nextflow options
  runName        : dreamy_alder
  containerEngine: docker
  launchDir      : /mnt/d/basecalleo SUPerior/instances/wf-alignment_01JG4VRTADFYESNM5KDZD3ZCX9
  workDir        : /mnt/d/basecalleo SUPerior/instances/wf-alignment_01JG4VRTADFYESNM5KDZD3ZCX9/work
  projectDir     : /mnt/d/basecalleo SUPerior/workflows/epi2me-labs/wf-alignment
  userName       : epi2mewsl
  profile        : standard
  configFiles    : /mnt/d/basecalleo SUPerior/workflows/epi2me-labs/wf-alignment/nextflow.config
Input Options
  fastq          : /mnt/d/basecalleo SUPerior/pass
  references     : /mnt/d/basecalleo SUPerior/epi2mewf/hgenome/ncbi_dataset/data/GCF_000001405.40
Output Options
  out_dir        : /mnt/d/basecalleo SUPerior/instances/wf-alignment_01JG4VRTADFYESNM5KDZD3ZCX9/output
  igv            : true
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-alignment for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-alignment v1.2.2.
--------------------------------------------------------------------------------
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
[64/ce9770] Submitted process > pipeline:getVersions
[5e/792773] Submitted process > pipeline:process_references:combine
[13/3ef913] Submitted process > pipeline:getParams
[b0/b532fb] Submitted process > pipeline:process_references:fx2tab (1)
[44/bd937f] Submitted process > fastcat (1)
[18/d60a22] Submitted process > fastcat (2)
[5d/17d139] Submitted process > fastcat (3)
[94/30607c] Submitted process > fastcat (4)
[4f/f4ec25] Submitted process > fastcat (5)
[f9/e283d3] Submitted process > fastcat (6)
[97/9f6e1f] Submitted process > fastcat (7)
[c9/14f8d2] Submitted process > fastcat (8)
[fd/3ad8f9] Submitted process > pipeline:addStepsColumn
[6f/4a0d40] Submitted process > fastcat (9)
[4d/0ede00] Submitted process > fastcat (10)
[e7/1fb1bd] Submitted process > fastcat (11)
[7d/6a8333] Submitted process > fastcat (12)
[e9/dfda6f] Submitted process > pipeline:makeMMIndex
[97/df4bf6] Submitted process > pipeline:alignReads (1)
[20/40611f] Submitted process > pipeline:alignReads (8)
[07/dc8c02] Submitted process > pipeline:alignReads (4)
[30/344d39] Submitted process > pipeline:alignReads (11)
[20/e35ba9] Submitted process > pipeline:alignReads (10)
[06/ce1b4b] Submitted process > pipeline:alignReads (2)
[37/60a395] Submitted process > pipeline:alignReads (9)
[83/7edccf] Submitted process > pipeline:alignReads (12)
[ea/a6fd5a] Submitted process > pipeline:alignReads (6)
[c1/3b7619] Submitted process > pipeline:alignReads (5)
[c8/0f1031] Submitted process > pipeline:alignReads (3)
[ca/21737d] Submitted process > pipeline:alignReads (7)
[00/c70605] Submitted process > pipeline:bamstats (1)
[c4/fb1480] Submitted process > publish (1)
ERROR ~ /mnt/d/basecalleo SUPerior/instances/wf-alignment_01JG4VRTADFYESNM5KDZD3ZCX9/work/tmp/27/950dcac414c64c9789c209cf6c886e/collect-file.data: Operation not permitted
 -- Check '/mnt/d/basecalleo SUPerior/instances/wf-alignment_01JG4VRTADFYESNM5KDZD3ZCX9/nextflow.log' file for details
[f0/335fc2] Submitted process > publish (2)
WARN: Killing running tasks (3)

Application activity log entry

No response

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

yes

Other demo data information

No response