Issue with masking step

[urbagal]

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]

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

[sateeshperi]

is this still an issue @urbagal @mciprianoCDC

[urbagal]

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 @urbagal<https://github.com/urbagal> @mciprianoCDC<https://github.com/mciprianoCDC> — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATFR55MQIO3LCFY3MEZLZBTVJRPI5ANCNFSM5UJH4BIQ>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[urbagal]

Looks like it is still an issue. The run did not completed. * 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 @urbagal<https://github.com/urbagal> @mciprianoCDC<https://github.com/mciprianoCDC> — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATFR55MQIO3LCFY3MEZLZBTVJRPI5ANCNFSM5UJH4BIQ>. You are receiving this because you were mentioned.Message ID: ***@***.***>