MacOS M1 chip, sed making tmp file with wrong permissions and failure to export issue

[rebeelouise]

Operating System

macOS

Other Linux

No response

Workflow Version

v0.3.31

Workflow Execution

EPI2ME Desktop application

EPI2ME Version

No response

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

Trying to get the pipeline up on running on my macbook (p.s. I wish this was a thing when I first started sequencing!!!).

It works fine up until pipeline:runArtic nextflow.log

It looks like sed is making a tmp file with weird permissions and then kills the workflow.

I have tried installing sed with brew install gnu-sed as apparently later versions have fixed this bug, but still getting the same error.

Also tried to export the issue and having the same problem...

{ "name": "Export issue", "description": "Export relevant files to report an issue with the app", "updates": [ { "message": "Checking paths" }, { "message": "Adding path main.log" }, { "message": "Archiving files" }, { "message": "Non-zero exit status" }, { "message": "Failed to export" } ], "id": "01HDNJY867JKD73V4DFWJH9BTK", "percentage": 27, "status": "STOPPED_WITH_ERROR", "createdAt": "2023-10-26T08:52:12.615Z", "updatedAt": "2023-10-26T08:52:12.651Z", "metadata": { "trace": { "resultTarArgs": [ "-czvf", "'/Users/rebee/epi2melabs/exports/EPI2ME_issue_export.tar.gz'", "-C", "'/Users/rebee/epi2melabs/exports/archive'", "." ], "resultTarStdout": "", "resultTarStderr": "tar: Failed to open ''/Users/rebee/epi2melabs/exports/EPI2ME_issue_export.tar.gz''\n" } } }

Relevant log output

sed: couldn't open temporary file ./sedN5Vr2m: Permission denied
Work dir:
  /Users/rebee/epi2melabs/instances/wf-artic_01HDKZMQ3AWM3GF9CVJ49BW293/work/da/5e2dee458ca7c27baf9ac0183cbe1d
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
 -- Check '/Users/rebee/epi2melabs/instances/wf-artic_01HDKZMQ3AWM3GF9CVJ49BW293/nextflow.log' file for details
WARN: Killing running tasks (1)

Application activity log entry

No response

[mattdmem]

Hey @rebeelouise - I have a fix in the works for this. Hang tight. (Although the workflow isn't optimised for M1 (ARM) macs at the moment)

Matt

[rebeelouise]

p.s. wf-transcriptome pipeline ran fine with no errors on the demo data. was using the demo data for artic

[rebeelouise]

Hey @rebeelouise - I have a fix in the works for this. Hang tight. (Although the workflow isn't optimised for M1 (ARM) macs at the moment)

Matt

Speedy!! No problemo! If it's just a Mac problem I am cool with that - I just want to demo it for a student who is on windows and doesn't have a background in informatics.

[mattdmem]

It's a general problem with sed - but I just wanted to point out that we haven't built wf-artic for mac ARM yet! Windows will be fine.

[mattdmem]

v0.3.32 is just releasing now - should be here soon!