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CDCgov / mycosnp-nf

CDCgov/mycosnp-nf
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Issue with masking step #49

Open urbagal opened 2 years ago

urbagal commented 2 years ago

Describe the bug Used another Pathogen for testing. The next flow run stops at the masking step. Gets an error:

-[CDCgov/mycosnp-nf] Pipeline completed with errors- Error executing process > 'NFCORE_MYCOSNP:MYCOSNP:BWA_REFERENCE:NUCMER (reference)'

Caused by: Process NFCORE_MYCOSNP:MYCOSNP:BWA_REFERENCE:NUCMER (reference) terminated with an error exit status (140)

Impact Pipeline completed with error.

To Reproduce ran mycosnp command: nextflow run CDCgov/mycosnp-nf --custom_config_base /scicomp/groups/OID/NCEZID/DFWED/MDB/nf-core-custom -profile singularity,sge --input All_input.csv --fasta GCF_000003855.fasta

Expected behavior completed the nextflow run without any error.

Logs If applicable, please attach logs to help describe your problem.

Execution cancelled -- Finishing pending tasks before exit -[CDCgov/mycosnp-nf] Pipeline completed with errors- Error executing process > 'NFCORE_MYCOSNP:MYCOSNP:BWA_REFERENCE:NUCMER (reference)'

Caused by: Process NFCORE_MYCOSNP:MYCOSNP:BWA_REFERENCE:NUCMER (reference) terminated with an error exit status (140)

mciprianoCDC commented 2 years ago

This issue is happening for runs which the masking step is taking a long time (large genomes)

sateeshperi commented 2 years ago

is this still an issue @urbagal @mciprianoCDC

urbagal commented 2 years ago

I never heard from Michael it has been resolved. Let me check . - U

From: Sateesh Peri @.> Sent: Wednesday, May 11, 2022 9:47 PM To: CDCgov/mycosnp-nf @.> Cc: Bagal, Ujwal (CDC/DDID/NCEZID/DFWED) (CTR) @.>; Mention @.> Subject: Re: [CDCgov/mycosnp-nf] Issue with masking step (Issue #49)

is this still an issue @urbagalhttps://github.com/urbagal @mciprianoCDChttps://github.com/mciprianoCDC

— Reply to this email directly, view it on GitHubhttps://github.com/CDCgov/mycosnp-nf/issues/49#issuecomment-1124447746, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATFR55MQIO3LCFY3MEZLZBTVJRPI5ANCNFSM5UJH4BIQ. You are receiving this because you were mentioned.Message ID: @.***>

urbagal commented 2 years ago

Looks like it is still an issue. The run did not completed.

From: Sateesh Peri @.> Sent: Wednesday, May 11, 2022 9:47 PM To: CDCgov/mycosnp-nf @.> Cc: Bagal, Ujwal (CDC/DDID/NCEZID/DFWED) (CTR) @.>; Mention @.> Subject: Re: [CDCgov/mycosnp-nf] Issue with masking step (Issue #49)

is this still an issue @urbagalhttps://github.com/urbagal @mciprianoCDChttps://github.com/mciprianoCDC

— Reply to this email directly, view it on GitHubhttps://github.com/CDCgov/mycosnp-nf/issues/49#issuecomment-1124447746, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATFR55MQIO3LCFY3MEZLZBTVJRPI5ANCNFSM5UJH4BIQ. You are receiving this because you were mentioned.Message ID: @.***>