MLST db error

[AmyR05]

Describe the bug Error received during the PHOENIX:PHOENIX_EXTERNAL:DO_MLST:MLST process:

Impact Cannot complete pipeline

To Reproduce Steps to reproduce the behavior:

• HPC environment/singularity
• v2.0.1 -nextflow run cdcgov/phoenix -r v2.0.1 -entry PHOENIX -profile singularity,unlhcc --input /lustre/work/nphl/amyrod/CRE/AR230147/HAISAMPLESHEET.csv --kraken2db /work/HCC/BCRF/app_specific/phoenix-minikraken2db/06052023/ --outdir $PWD/Results
• Custom config: process { executor = 'slurm' cpus = 2 memory = '10 GB' time = '1 hour' queueSize = 10 submitRateLimit = '10 min' queue = 'batch'
• container creation failed: mount hook function failure: mount /$PATH/new_DBS_20230502/20230504/MLST/db->/mlst-2.23.0/db error: while mounting /$PATH/new_DBS_20230502/20230504/MLST/db: mount source /$PATH/new_DBS_20230502/20230504/MLST/db doesn't exist
• Include the files that caused the error
  • (if the file(s) contains something you don't want public open an issue with a brief description AND then email HAISeq@cdc.gov with the title QH ISSUE # so we can track the problem. DO NOT send PII!

execution_trace_2023-07-27_14-06-58.txt

[jvhagey]

Hi @AmyR05, unfortunately you have discovered a VERY bad 🐛 . A path was hard coded that shouldn't be (YIKES). So this is a "its not you, its us" situation. We realized this yesterday and have been working on a fix. There will be a v2.0.2 release to address this and are trying to get something sorted ASAP. Until its resolved please continue using the older version.

Are you using Docker or Singularity?

Thanks for reporting this and I appreciate the patience as we work on a fix.

[mollymitchell70]

Hi Jill, we are also seeing this error within the SE BRR region - just leaving this comment here so I get a notification if updates on a fix come through! Thanks for your help :)

[jvhagey]

A new release #116 has been created to address this. Let me know if this resolves the issue.

[AmyR05]

I have completed this updated version of Phoenix with no further issues. Thank you Jill!

From: Jill V. Hagey, PhD @.> Sent: Thursday, August 3, 2023 2:58 PM To: CDCgov/phoenix @.> Cc: Roden, Amy E @.>; Mention @.> Subject: Re: [CDCgov/phoenix] MLST db error (Issue #115)

Non-UNMC email A new release #116 [github. com] has been created to address this. Let me know if this resolves the issue. — Reply to this email directly, view it on GitHub [github. com], or unsubscribe [github. com]. You are receiving this because you

A new release #116 [github.com]https://urldefense.com/v3/__https:/github.com/CDCgov/phoenix/releases/tag/v2.0.2__;!!JkUDQA!JpX5Vo0OOFE6TOAzIxylqrGrQoPo6PIV17tkt-a2xS7rAYeL59SvGJvpPwTjIf4RF45pSMaOYM6KZAU572VBOJiLYQ$ has been created to address this. Let me know if this resolves the issue.

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