[Bug]: fastcat Command error: touch: cannot touch '.command.trace': Permission denied

[AngusNano]

What happened?

Hi,

I'm having difficulties getting wf-transcriptomes to work. When I initiate the 'Use demo data', the workflow stops with a Command error: touch: cannot touch '.command.trace': Permission denied

I get the same error if I try to run my own data.

The problem appears to be when the workflow tries to execute the fastcat command.

Any help would be appreciated.

Cheers,

Angus report.html.zip

Operating System

ubuntu 20.04

Workflow Execution

EPI2ME Labs desktop application

Workflow Execution - EPI2ME Labs Versions

V4.1.2

Workflow Execution - CLI Execution Profile

Docker

Workflow Version

v0.1.9

Relevant log output

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'pipeline:summariseConcatReads (6)'

Caused by:
  Process `pipeline:summariseConcatReads (6)` terminated with an error exit status (1)

Command executed:

  fastcat -s barcode02 -r barcode02.stats -x barcode02 >  barcode02.fastq

Command exit status:
  1

Command output:
  (empty)

Command error:
  touch: cannot touch '.command.trace': Permission denied

Work dir:
  /home/angus/epi2melabs/instances/wf-transcriptomes_dc344fc2-073d-415f-be83-8bbcb7309c1b/work/e9/6d16b1b7bea22a46f90bed4c0a2309

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

[FankangMeng]

@AngusNano Hi 'm having difficulties the same as you. I have tried all the workflows in epi2melabs but none of them work and most of them has this error ' touch: cannot touch '.command.trace': Permission denied'. Do you have any updates on this?

[aw1231]

I am also encountering this issue on the latest version 0.1.12. The demo dataset also doesn't run and encounters the same error.

[cjw85]

Our current understanding of this issue is that it stems from mal-installation of Docker Desktop. The resolution appears to be to delete the folder ~/.docker.

We haven't had reports of this symptom when not using Docker Desktop to install docker (i.e. using the more vanilla docker.io).

https://github.com/epi2me-labs/wf-metagenomics/issues/43

Before deleting ~/.docker it might be useful if your could poke around and post copies of the files you find there so we can better understand how to implement an automatic and less drastic approach that completely deleting the directory.

[cjw85]

Currently the EPI2ME application points users to install Docker Desktop regardless of OS. The intention here was that it was more in keeping with the nature of the EPI2ME application (desktop bioinformatics for non-specialists).

Given this appears to complicate the process of using docker, we are going to make a change to point people to installing docker through their system pacakge manager in a more traditional way (e.g. apt install docker.io on Ubuntu).

I will close this issue as I believe it is now understood and can either be worked around in the case of users explicitely wanting to use Docker Desktop.