intermittent 1;31m*** ERROR ***

[taffners]

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...

�[1;31m*** ERROR ***�[0m


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]

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]

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

�[1;31m*** ERROR ***�[0m
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]

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]

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]

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 <#123 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALZ52KKJ76WOIFKAKSEVLQTXGYC75ANCNFSM6AAAAAAYD24XGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[taffners]

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
�[36mRunning tblastn�[0m
�[36mRunning blastn�[0m

�[1;31m*** ERROR ***�[0m
'/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]

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]

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

[taffners]

@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]

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?