The pipeline fails in artic_ncov_wf_artic_medaka

[Bioloko]

The pipeline fails when starts runing artic_ncov_wf:artic_medaka, just jump these steps and finish the analysis without generating consensus sequences. But no error is shown in the console. im using a Mac (3,2 GHz Intel Xeon W 16 nucleus, 192 GB RAM)

Command used

nextflow run replikation/poreCov -profile local,docker -r 1.8.3 --fastq '/Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/catted_files/*.fastq.gz' --primerV V1200 --output /Users/agaliana/artic-ncov2019_poreCoV/CORONA_230928_test --cores 16 --memory 180 --update --rapid --medaka_model r1041_e82_400bps_fast_g632 --samples /Users/agaliana/artic-ncov2019_poreCoV/CORONA_230928_test/148_sec_pend.txt

[MarieLataretu]

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 (https://github.com/replikation/poreCov/issues/240), but I don't know if it is the same error.

[Bioloko]

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

[MarieLataretu]

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

[Bioloko]

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

[MarieLataretu]

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

[Bioloko]

Hi Marie,

Thank you for your time. Yesterday I was doing some tests with an ubuntu installed virtual machine with the singularity profile and the analysis was performed successfully. I prefer to work with the Mac instead of te virtual machine, so maybe I have to try something related with permissions im going to check the links and see if I have any idea about.

Best

El 5 oct 2023, a las 12:00, MarieLataretu @.***> escribió:

Hi @Bioloko https://github.com/Bioloko , thanks for sharing!

From the log files, I'd say this issue is not related to #240 https://github.com/replikation/poreCov/issues/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 https://www.nextflow.io/docs/latest/container.html#id3 for Docker usage on Mac, referencing this tutorial https://www.viget.com/articles/how-to-use-docker-on-os-x-the-missing-guide/ — Reply to this email directly, view it on GitHub https://github.com/replikation/poreCov/issues/259#issuecomment-1748526967, or unsubscribe https://github.com/notifications/unsubscribe-auth/BDAHIBUQ6DJ7K4BBTJRHYXTX52ANJAVCNFSM6AAAAAA5Q26X5SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBYGUZDMOJWG4. You are receiving this because you were mentioned.

[MarieLataretu]

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)!