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CDCgov / phoenix

🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens
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MLST_Check_error #106

Closed fnindo closed 1 year ago

fnindo commented 1 year ago

I ran into this error at MLST check step for one of the samples, and I am not sure if there is fix for this: phoenix.log

jvhagey commented 1 year ago

Hi @fnindo thanks for reporting this. Can you fill out the rest the the issue template. i.e. please provide the command you used to run PHoeNIx and the system time you are working on.

fnindo commented 1 year ago

Hi @jvhagey I ran phoenix using this command: nextflow run $phoenix_path -profile singularity -entry PHOENIX --input $manifest --kraken2db $kraken2db --outdir $outdir/phoenix --max_cpus $threads --max_memory $memory

jvhagey commented 1 year ago

Did you run this today or was it by chance earlier in the week? PubMLST.org has been down and some files weren't being pulled because of it.... just want to confirm when the problem came up.

fnindo commented 1 year ago

I just ran it today

fnindo commented 1 year ago

Hi Jill, It appears that the error was associated with Pubmlst.org Acinobacter baumanii db being down as my colleague Jared was able to run that sample successfully this morning.

jvhagey commented 1 year ago

oh good, because just retrying it was going to be my suggestion. We are working on adding in some handling for when pubMLST goes does as it seems to happen with some regularity.