intermittent 1;31m*** ERROR *** #123
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Hello @evolarjun, Thank you. I updated the software and database and ended up getting the same error with a different sample. I attached the contig file but I had to change the file extension to .txt to attach. BWH_9_K_pne_rex_2022_04_06_contigs.txt amrfinder --plus -n /ncache0/2442154.1.all.q/tmpedMqvC/stg6927d039-7140-48ea-a78c-e54b6d224a1a/contigs.fasta --database /data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/share/amrfinderplus/data/2023-04-17.1 --organism Klebsiella > /ncache0/2442154.1.all.q/tmpuOHvtz/BWH_9_K_pne_rex_2022_04_06_amrfindplus.tsv �[1;31m*** ERROR ***�[0m HOSTNAME: ? |
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There is no organism "Klebsiella". Please see the list of possible organisms:
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Hi @taffners, Sorry, I had written a response, but it seems to have disappeared. In more recent releases of the databases the organism-specific data for Klebsiella was split. See our documentation of the Let us know if you are still having issues. |
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Thank you. It looks like it has worked.
…On Thu, May 18, 2023 at 7:39 AM Arjun Prasad ***@***.***> wrote:
Hi @taffners <https://github.com/taffners>,
Sorry, I had written a response, but it seems to have disappeared.
In more recent releases of the databases the organism-specific data for
Klebsiella was split. See our documentation of the --organism option
<https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus#--organism-option>
for details on the current options. I think this is a different error from
the first and hopefully the intermittent error you were seeing before
doesn't rear its head again.
Let us know if you are still having issues.
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Hello @evolarjun and/or @vbrover , I'm getting an error again which is intermittent. The other 20 samples on the plate ran without error. However, one sample got the error below: |
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The failing command is Is the crash reproducible? Could you post the |
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What is the size and version of |
evolarjun
added
bug
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For a few months now I have not seen this error message but I now have a problematic sample again. This sample was a nanopore long reads assembled by flye. Previously we have only been using MiSeq short reads assemblied by spades. I'm unsure if this is the difference but I doubt it. AMRFinder has been able to successfully run on about 50 other nanopore long read samples assebmled by flye but it does appear to have more difficultly with Klebsiella_oxytoca samples. My worst Klebsiella_oxytoca sample is attached and amrfinder works sometimes but 95% of the time it errors out. I have two example runs below one of when it failed and one when it passed. If I remove the --organism Klebsiella_oxytoca it runs without error. I recently updated amrfinder and the database to see if this would solve the problem but the error still occurs. The size of the new database is 219M and the version is 2023-08-08.2 I attached the contig file but changed the extension to .txt so it would upload ################### Here's an example of when the sample worked################## $ amrfinder --plus -n /data1/Samantha_Test/results/tmp/dev/long_reads/2023_08_01_X1_8/NBWH_1401_K_oxy_2023_08_01_X1/contigs.fasta --database /data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/share/amrfinderplus/data/2023-08-08.2 --organism Klebsiella_oxytoca > /data1/Samantha_Test/results/tmp/dev/long_reads/2023_08_01_X1_8/NBWH_1401_K_oxy_2023_08_01_X1/amrfindplus_1.tsv ################### Here's an example of when the sample failed################## *** ERROR *** HOSTNAME: ? Thank you. Have a good weekend. |
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I am away from my desk until 9/6/2023, but it looks like it is a |
Hello,
I have been getting an intermittent 1;31m*** ERROR ***. I'm unsure what is causing it. When I rerun the sample amrfinder works perfectly fine and all the rest of the samples in the run mentioned below ran successfully. What could be causing this error? Thank you.
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