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AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/
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intermittent 1;31m*** ERROR *** #123

Open taffners opened 1 year ago

taffners commented 1 year ago

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.

Running: amrfinder --plus -n /ncache0/2435308.1.all.q/tmpVAYFMs/stg5d37a3a6-8158-4a45-8cad-1d6a06a80879/contigs.fasta --database /data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder/share/amrfinderplus/data/2021-09-30.1 --organism Escherichia
Software directory: '/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder/bin/'
Software version: 3.10.16
Database directory: '/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder/share/amrfinderplus/data/2021-09-30.1'
Database version: 2021-09-30.1
AMRFinder translated nucleotide and mutation search
Running tblastn...
Running blastn...

*** ERROR ***

HOSTNAME: ?
SHELL: ?
PWD: /ncache0/2435308.1.all.q/tmpGjXisp
Progam name:  amrfinder
Command line: amrfinder --plus -n /ncache0/2435308.1.all.q/tmpVAYFMs/stg5d37a3a6-8158-4a45-8cad-1d6a06a80879/contigs.fasta --database /data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder/share/amrfinderplus/data/2021-09-30.1 --organism Escherichia
evolarjun commented 1 year ago

Hi @taffners,

That's very strange. Could you attach the contigs.fasta file that isn't working?

You're also using a very old version of the software and database. Could you try upgrading the software and updating the database and see if you are still getting the error.?

taffners commented 1 year ago

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 Running: 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 Software directory: '/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/bin/' Software version: 3.11.14 Database directory: '/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/share/amrfinderplus/data/2023-04-17.1' Database version: 2023-04-17.1 AMRFinder translated nucleotide and mutation search

 ERROR  Possible organisms: Acinetobacter_baumannii, Burkholderia_cepacia, Burkholderia_pseudomallei, Campylobacter, Citrobacter_freundii, Clostridioides_difficile, Enterobacter_cloacae, Enterococcus_faecalis, Enterococcus_faecium, Escherichia, Klebsiella_aerogenes, Klebsiella_oxytoca, Klebsiella_pneumoniae, Neisseria_gonorrhoeae, Neisseria_meningitidis, Pseudomonas_aeruginosa, Salmonella, Serratia_marcescens, Staphylococcus_aureus, Staphylococcus_pseudintermedius, Streptococcus_agalactiae, Streptococcus_pneumoniae, Streptococcus_pyogenes, Vibrio_cholerae

HOSTNAME: ? SHELL: ? PWD: /ncache0/2442154.1.all.q/tmpuOHvtz PATH: /data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/bin:/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/condabin:/apps/R/3.6.1/bin:/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/micro_pipeline_3_7/bin:/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/condabin:/ncache0/2442154.1.all.q:/usr/local/bin:/bin:/usr/bin Progam name: amrfinder Command line: 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

vbrover commented 1 year ago

There is no organism "Klebsiella".

Please see the list of possible organisms:

Possible organisms: Acinetobacter_baumannii, Burkholderia_cepacia, Burkholderia_pseudomallei, Campylobacter, Citrobacter_freundii, Clostridioides_difficile, Enterobacter_cloacae, Enterococcus_faecalis, Enterococcus_faecium, Escherichia, Klebsiella_aerogenes, Klebsiella_oxytoca, Klebsiella_pneumoniae, Neisseria_gonorrhoeae, Neisseria_meningitidis, Pseudomonas_aeruginosa, Salmonella, Serratia_marcescens, Staphylococcus_aureus, Staphylococcus_pseudintermedius, Streptococcus_agalactiae, Streptococcus_pneumoniae, Streptococcus_pyogenes, Vibrio_cholerae

evolarjun commented 1 year ago

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 --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.

taffners commented 1 year ago

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.

— Reply to this email directly, view it on GitHub https://github.com/ncbi/amr/issues/123#issuecomment-1552931012, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALZ52KKJ76WOIFKAKSEVLQTXGYC75ANCNFSM6AAAAAAYD24XGM . You are receiving this because you were mentioned.Message ID: @.***>

taffners commented 1 year ago

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:

amrfinder --plus -n /ncache0/2457651.1.all.q/tmpptTMlr/stgedcb6672-106d-4fd5-80e7-891c670ce086/contigs.fasta --database /data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/share/amrfinderplus/data/2023-04-17.1 --organism Escherichia > /ncache0/2457651.1.all.q/tmpR0Hfur/BWH_263_E_col_2022_05_13_amrfindplus.tsv
Running: amrfinder --plus -n /ncache0/2457651.1.all.q/tmpptTMlr/stgedcb6672-106d-4fd5-80e7-891c670ce086/contigs.fasta --database /data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/share/amrfinderplus/data/2023-04-17.1 --organism Escherichia
Software directory: '/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/bin/'
Software version: 3.11.14
Database directory: '/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/share/amrfinderplus/data/2023-04-17.1'
Database version: 2023-04-17.1
AMRFinder translated nucleotide and mutation search
Running tblastn
Running blastn

*** ERROR ***
'/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/bin/blastn'  -query '/ncache0/2457651.1.all.q/tmpptTMlr/stgedcb6672-106d-4fd5-80e7-891c670ce086/contigs.fasta' -db /ncache0/2457651.1.all.q/tmpViI0dD/amrfinder.iRb6rR/db/AMR_DNA-Escherichia -evalue 1e-20  -dust no  -max_target_seqs 10000    -num_threads 2  -mt_mode 1 -outfmt '6 qseqid sseqid qstart qend qlen sstart send slen qseq sseq' -out /ncache0/2457651.1.all.q/tmpViI0dD/amrfinder.iRb6rR/blastn > /ncache0/2457651.1.all.q/tmpViI0dD/amrfinder.iRb6rR/log 2> /ncache0/2457651.1.all.q/tmpViI0dD/amrfinder.iRb6rR/blastn-err
status = 35584
Segmentation fault (core dumped)

HOSTNAME: ?
SHELL: ?
PWD: /ncache0/2457651.1.all.q/tmpR0Hfur
PATH: /data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/bin:/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/condabin:/apps/R/3.6.1/bin:/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/micro_pipeline_3_7/bin:/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/condabin:/ncache0/2457651.1.all.q:/usr/local/bin:/bin:/usr/bin
Progam name:  amrfinder
Command line: amrfinder --plus -n /ncache0/2457651.1.all.q/tmpptTMlr/stgedcb6672-106d-4fd5-80e7-891c670ce086/contigs.fasta --database /data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/share/amrfinderplus/data/2023-04-17.1 --organism Escherichia
vbrover commented 1 year ago

The failing command is

/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/bin/blastn  -query '/ncache0/2457651.1.all.q/tmpptTMlr/stgedcb6672-106d-4fd5-80e7-891c670ce086/contigs.fasta' -db /ncache0/2457651.1.all.q/tmpViI0dD/amrfinder.iRb6rR/db/AMR_DNA-Escherichia -evalue 1e-20  -dust no  -max_target_seqs 10000    -num_threads 2  -mt_mode 1 -outfmt '6 qseqid sseqid qstart qend qlen sstart send slen qseq sseq' -out /ncache0/2457651.1.all.q/tmpViI0dD/amrfinder.iRb6rR/blastn > /ncache0/2457651.1.all.q/tmpViI0dD/amrfinder.iRb6rR/log 2> /ncache0/2457651.1.all.q/tmpViI0dD/amrfinder.iRb6rR/blastn-err

Is the crash reproducible? What is the contents of these files?

/ncache0/2457651.1.all.q/tmpViI0dD/amrfinder.iRb6rR/blastn
/ncache0/2457651.1.all.q/tmpViI0dD/amrfinder.iRb6rR/log
/ncache0/2457651.1.all.q/tmpViI0dD/amrfinder.iRb6rR/blastn-err

Could you post the blastn input file?

/ncache0/2457651.1.all.q/tmpptTMlr/stgedcb6672-106d-4fd5-80e7-891c670ce086/contigs.fasta
vbrover commented 1 year ago

What is the size and version of /data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/bin/blastn?

taffners commented 1 year ago

@vbrover @evolarjun

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

$ cd /data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/share/amrfinderplus/data
$ $ du -h 2023-08-08.2
219M    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 Running: 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 Software directory: '/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/bin/' Software version: 3.11.18 Database directory: '/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/share/amrfinderplus/data/2023-08-08.2' Database version: 2023-08-08.2 AMRFinder translated nucleotide and mutation search Running tblastn Running blastn Making report AMRFinder took 160 seconds to complete

###################

Here's an example of when the sample failed

################## $ 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_2.tsv Running: 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 Software directory: '/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/bin/' Software version: 3.11.18 Database directory: '/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/share/amrfinderplus/data/2023-08-08.2' Database version: 2023-08-08.2 AMRFinder translated nucleotide and mutation search Running tblastn Running blastn

ERROR '/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/bin/blastn' -query '/data1/Samantha_Test/results/tmp/dev/long_reads/2023_08_01_X1_8/NBWH_1401_K_oxy_2023_08_01_X1/contigs.fasta' -db /ncache0/2643518.1.all.q/amrfinder.cNvp4c/db/AMR_DNA-Klebsiella_oxytoca -evalue 1e-20 -dust no -max_target_seqs 10000 -num_threads 2 -mt_mode 1 -outfmt '6 qseqid sseqid qstart qend qlen sstart send slen qseq sseq' -out /ncache0/2643518.1.all.q/amrfinder.cNvp4c/blastn > /ncache0/2643518.1.all.q/amrfinder.cNvp4c/log 2> /ncache0/2643518.1.all.q/amrfinder.cNvp4c/blastn-err status = 35584 Segmentation fault (core dumped)

HOSTNAME: ? SHELL: /bin/bash PWD: /data1/Samantha_Test/results/tmp/dev/long_reads/2023_08_01_X1_8/NBWH_1401_K_oxy_2023_08_01_X1 PATH: /data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/amrfinder_3_11/bin:/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/condabin:/apps/spack/bin:/apps/R/2.15.1/bin:/bin:/usr/bin:/snap/bin:/opt/sge/bin/lx-amd64 Progam name: amrfinder Command line: 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

Thank you. Have a good weekend. Samantha contigs.txt

vbrover commented 1 year ago

I am away from my desk until 9/6/2023, but it looks like it is a blast problem. We do not maintain blast at conda. Could you install NCBI blast form https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ into the directory named, for example, BLAST, and then run amrfinder with the option --blast_bin BLAST?