MacOS M1 chip, sed making tmp file with wrong permissions and failure to export issue
rebeelouise opened this issue · 5 comments
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
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
p.s. wf-transcriptome pipeline ran fine with no errors on the demo data.
was using the demo data for artic
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.
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.
v0.3.32 is just releasing now - should be here soon!