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CDCgov / phoenix

🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens
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Phoenix 2.1.0 MultiQC #142

Closed AmyR05 closed 4 months ago

AmyR05 commented 5 months ago

While running Phoenix 2.1.0 "Pipeline completed successfully" message appears and pipeline terminates with no errors, however not all processes are actually ran and final results/reports are not available.

execution_trace_2024-02-13_11-50-23.txt .nextflow.log.log PHX 2 0 2 Not completing processes unlhcc.config.txt

jvhagey commented 5 months ago

Hi @AmyR05, it looks like the GRiPHin step finished is there not a GRiPHin file produced? If so can you provide it? This sample is failing the corruption check we added with this version of phoenix, so something is up with those files either file integrity wise or some other bug. What is the extension on these files? Does it happen to be .fq.gz?

AmyR05 commented 5 months ago

Good morning,

The GriPHin summary generated is attached. I have also attached the file_integrity summary generated from the pipeline. Our inputs are .fastq.gz, which is what we have used for the previous versions of Phoenix.

Thanks! Amy

From: Jill V. Hagey, PhD @.> Sent: Tuesday, February 20, 2024 7:38 AM To: CDCgov/phoenix @.> Cc: Roden, Amy E @.>; Mention @.> Subject: Re: [CDCgov/phoenix] Phoenix 2.1.0 MultiQC (Issue #142)

Non-UNMC email Hi @AmyR05 [github. com], it looks like the GRiPHin step finished is there not a GRiPHin file produced? If so can you provide it? This sample is failing the corruption check we added with this version of phoenix, so something is up with those

Hi @AmyR05 [github.com]https://urldefense.com/v3/__https:/github.com/AmyR05__;!!JkUDQA!LWbP8TJZ3Q7J4Bj7NC8tJFMsnph8RbgKfx9ix2VhMWmH0jnEvR3-FNqFN_IueZXWgLFh_5gqiHaROVNeE_wbVhDTig$, it looks like the GRiPHin step finished is there not a GRiPHin file produced? If so can you provide it? This sample is failing the corruption check we added with this version of phoenix, so something is up with those files either file integrity wise or some other bug. What is the extension on these files? Does it happen to be .fq.gz?

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PASSED: File AR240052_R2 R1 is not corrupt. PASSED: File AR240052_R2 R2 is not corrupt.

jvhagey commented 5 months ago

Hi @AmyR05, you need to attach the files to the github discussion. They don't show up if you send them in back via email.

AmyR05 commented 5 months ago

AR240052_summary.txt Results_GRiPHin_Summary.xlsx

jvhagey commented 5 months ago

Hey, @AmyR05 I just realized that the.nextflow.log you sent is for a different sample and is the older v2.0.2 of phx. Can you send the one for the failed sample? Also, are these AR Bank samples? I want to run it on my side to see what is going on. If the raw sequences aren't public you can email HAISeq@cdc.gov for me to get access to.

AmyR05 commented 5 months ago

v2.1.0.nextflow.log This should be the correct log. This is an AR Bank sample, however it was not loaded to NCBI per ARLRN guidelines as it is KPC+. My colleague will email the fastq files to the designated email for troubleshooting. I had this same issue with all samples I have attempted on this version of Phoenix though.

jvhagey commented 5 months ago

ok, this is a file name parsing issue. Things got messed up as there was multiple instance of "R2" in the full file name, which is usually what we use for telling reverse from forward reads. I have a fix and will get a patch sorted out in the next week. Thanks for bringing this to our attention.