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FDA-ARGOS / data.argosdb

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HIVE3 Salmonella Computations getting killed #498

Open cwoodside1278 opened 2 weeks ago

cwoodside1278 commented 2 weeks ago

Some Salmonella enterica computations are not running. They complete all of the downloads and steps and then are Killed at 30% in the ARGOS-QC Post Alignment Quality step.

Reilan has also experienced this issue and another with her computations. Some say p_ref_downloader error. She checks the genomes to make sure that there is chromosome information and refseq and they are both there. No reason as to why it will not download the references.

table 1

The first three in this acinebacter pitti failed

table 2 second in this spreadsheet acinebacter ursingii failed

kee007ney commented 1 week ago

@cwoodside1278 Please share a few example failed computations with me.

cwoodside1278 commented 1 week ago

I am sharing a folder (obj 48900) that has one fialed and one killed salmonella computation @kee007ney

cwoodside1278 commented 1 week ago

Also 47569 is another folder with some failed, some killed, and some successful @kee007ney

kee007ney commented 1 week ago

Error says data error detected. May just be poor quality files. Christie to evaluate the quality of all input files separately.