Comments (7)
Hi @Bioloko ,
could you maybe share the .nextflow.log
and the .command.log
file from artic_medaka
's work directory?
@hoelzer also had problems on a Mac (#240), but I don't know if it is the same error.
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Hi Marie,
Thank you for your mail. Im searching in the work folder of the failed process (77/71e0b6] process > artic_ncov_wf:artic_medaka (1) [100%] 1 of 1, failed: 1) and i cant see any .nextflow.log or .command.log i only see in addition of more files two logs (minion.log.txt) and vcfcheck.log). I attach you these files.
817747.vcfcheck.log
817747.minion.log.txt
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I can't see something suspicious in minion.log.txt
and vcfcheck.log
.
.nextflow.log
and .command.log
are hidden files - maybe you have to change a setting in you file browser (on Mac Shift + Command + period
should do it).
.command.log
should be in the same directory as minion.log.txt
and vcfcheck.log
; .nextflow.log
in the folder where you started the pipeline from
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Hi Marie,
Thank you for your mail. Finally i found the nextflow.log and command.log following your instructions. Please find attached the files.
Best
command_log.txt
nextflow_log.txt
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Hi @Bioloko , thanks for sharing!
From the log files, I'd say this issue is not related to #240 .
The error is a permission problem (last line of .command.log
): sed: couldn't open temporary file ./sedi4f8Y8: Permission denied
Permission problems are often connected to Docker - would you be able to try it with Singularity (-profile local,singularity
)?
Else, I found this note for Docker usage on Mac, referencing this tutorial
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Hi @Bioloko ,
It's nice to hear that it worked with Singularity.
Since I'm a Linux user, I can't offer you much support :/
I'd close the ticket as this is not a general issue, but feel free to discuss below (or reopen)!
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Related Issues (20)
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- summary_report.py fails HOT 7
- publish primersitereport from medaka output
- VarSkipV2b primer does not work as expected HOT 7
- Update Medaka to support R10.4.1 models HOT 14
- Update --help to list up-to-date primer schemes that are supported
- MinKNOW/Guppy update needs new model for R10.4.1 5 kHz HOT 6
- Warning when execution report and timeline already exists HOT 1
- new pangolin table columns HOT 1
- CovarPlot fails w/ custom BED HOT 5
- Process retry in slurm profile HOT 1
- Publish VCF files HOT 2
- Update medaka to get the latest models HOT 1
- Test Freyja Update function HOT 11
- [Question] CI for Variant Calling HOT 5
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