Closed SeanSierra-Patev closed 3 months ago
I think this is a resource problem like this? #143 can you up the resources and let me know what level works?
overall, with --max_memory / --max_cpus or in the conf for this tool specifically? Because I thought the default was 128G which is all I've got
No, the steps are individually set to not over use resources. For AMRFinder the defaults is 4GB can you up in this section of the code and see if it resolves? It is set to try again and double the memory if it runs out, but maybe something about how AMRFinder is failing its not seeing it as a memory problem? If its a sample specific issue I can also try running it and debugging if you send it to HAISeq@cdc.gov
Ok sure, I'll give that a go and get back to you. I have something else running at the moment but I will give it a try first thing in the AM
increasing to 8 and then 16 did not resolve the core dump unfortunately
Updating the issue:
@SeanSierra-Patev sent me the files and they ran to completion just fine and it doesn't seem that lack of memory would be the issue here.
The only reference I can find is this recent issue https://github.com/ncbi/amr/issues/118 which points to the sequence line length being a possible issue.
Can you try running phx v2.1.1-dev
, it has an updated amrfinder container, but the blastn isn't a different version? I don't actually know if this is phx specific or an amrfinder/blastn issue. So can you also try running amrfinder outside of the pipeline?
Hi I encountered the same issue,
*** ERROR ***
'/ncbi-blast-2.13.0+/bin/blastn' -query 'AR-0074.filtered.scaffolds.fa' -db /tmp/amrfinder.hRw81Y/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 /tmp/amrfinder.hRw81Y/blastn > /tmp/amrfinder.hRw81Y/log 2> /tmp/amrfinder.hRw81Y/blastn-err
status = 35584
Segmentation fault (core dumped)
HOSTNAME: 98e20ea005df
SHELL: ?
PWD: /scratch/zl7w2/tools/phoenix/work/fb/1255d78d434d0186df9a7d889b8517
PATH: /amrfinder:/ncbi-blast-2.13.0+/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/scratch/zl7w2/tools/phoenix/bin
Progam name: amrfinder
Command line: amrfinder --nucleotide AR-0074.filtered.scaffolds.fa --protein AR-0074.faa --gff AR-0074.gff --annotation_format prokka --mutation_all AR-0074_all_mutations.tsv --organism Klebsiella_oxytoca --plus --database amrfinderdb_v3.11_20230417.1 --threads 6
Work dir:
/scratch/zl7w2/tools/phoenix/work/fb/1255d78d434d0186df9a7d889b8517
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '.nextflow.log' file for details
How can I test the data with the phoenix dev version?
@tang27abu, can you provide more detail on this sample? Is it an AR Bank sample?
Here is the command:
nextflow run cdcgov/phoenix -r v2.1.1-dev -latest -profile singularity -entry PHOENIX --input samplesheet.csv --kraken2db $kraken2db
@tang27abu, can you provide more detail on this sample? Is it an AR Bank sample?
Here is the command:
nextflow run cdcgov/phoenix -r v2.1.1-dev -latest -profile singularity -entry PHOENIX --input samplesheet.csv --kraken2db $kraken2db
I was trying to run with this command nextflow run cdcgov/phoenix -r v2.1.1-dev /scratch/zl7w2/tools/phoenix/main.nf -profile docker -entry PHOENIX --input /scratch/zl7w2/Matt/MUCRO4/reads/metadata.csv --kraken2db /scratch/zl7w2/tools/phoenix/k2db
And get the error below:
[50/44fca7] process > PHOENIX:PHOENIX_EXTERNAL:GET_TAXA_FOR_AMRFINDER (AR-0074) [100%] 4 of 4
[66/48cce1] process > PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN (AR-0074) [100%] 4 of 4, failed: 1
[9d/a4abd0] process > PHOENIX:PHOENIX_EXTERNAL:CALCULATE_ASSEMBLY_RATIO (AR-0074) [100%] 4 of 4
[e6/2af222] process > PHOENIX:PHOENIX_EXTERNAL:GENERATE_PIPELINE_STATS_WF:GENERATE_PIPELINE_STATS (AR-0034) [100%] 3 of 3
[f2/01cce4] process > PHOENIX:PHOENIX_EXTERNAL:CREATE_SUMMARY_LINE (AR-0034) [100%] 3 of 3
[- ] process > PHOENIX:PHOENIX_EXTERNAL:FETCH_FAILED_SUMMARIES -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:GATHER_SUMMARY_LINES -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:GRIPHIN -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:MULTIQC -
-[cdcgov/phoenix] Pipeline completed with errors-
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN (AR-0074)'
Caused by:
Process `PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN (AR-0074)` terminated with an error exit status (1)
Command executed:
#adding python path for running srst2 on terra
if [[ AR-0074.filtered.scaffolds.fa.gz = *.gz ]]; then
NUC_FNAME=$(basename AR-0074.filtered.scaffolds.fa.gz .gz)
gzip -c -d AR-0074.filtered.scaffolds.fa.gz > $NUC_FNAME
else
NUC_FNAME = AR-0074.filtered.scaffolds.fa.gz
fi
# decompress the amrfinder database
tar xzvf amrfinderdb_v3.11_20231115.1.tar.gz
amrfinder \
--nucleotide $NUC_FNAME \
--protein AR-0074.faa \
--gff AR-0074.gff \
--annotation_format prokka \
--mutation_all AR-0074_all_mutations.tsv \
--organism Klebsiella_oxytoca \
--plus \
--database amrfinderdb_v3.11_20231115.1 \
--threads 6 > AR-0074_all_genes.tsv
sed -i '1s/ /_/g' AR-0074_all_genes.tsv
cat <<-END_VERSIONS > versions.yml
"PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN":
amrfinderplus: $(amrfinder --version)
amrfinderplus_db_version: $(head amrfinderdb_v3.11_20231115.1/version.txt)
amrfinderplus_container: sha256:2311400ff8576f04e77a250e0665daa05f11b67f6a5901c8eac267378dccc932
END_VERSIONS
#revert python path back to main envs for running on terra
Command exit status:
1
Command output:
amrfinderdb_v3.11_20231115.1/AMR_CDS.ndb
amrfinderdb_v3.11_20231115.1/AMRProt.ptf
amrfinderdb_v3.11_20231115.1/AMRProt.psq
amrfinderdb_v3.11_20231115.1/AMR_DNA-Escherichia.nto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.tab
amrfinderdb_v3.11_20231115.1/AMR_DNA-Streptococcus_pneumoniae.nto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Salmonella.njs
amrfinderdb_v3.11_20231115.1/AMR_DNA-Klebsiella_oxytoca.tab
amrfinderdb_v3.11_20231115.1/AMR_DNA-Salmonella.nto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Campylobacter.not
amrfinderdb_v3.11_20231115.1/AMRProt
amrfinderdb_v3.11_20231115.1/AMR_DNA-Acinetobacter_baumannii.nhr
amrfinderdb_v3.11_20231115.1/AMRProt.phr
amrfinderdb_v3.11_20231115.1/AMR.LIB.h3p
amrfinderdb_v3.11_20231115.1/AMR_DNA-Escherichia.njs
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecalis.nhr
amrfinderdb_v3.11_20231115.1/AMR_DNA-Campylobacter.nto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.nsq
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.nhr
amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.not
amrfinderdb_v3.11_20231115.1/AMR_DNA-Escherichia.ntf
amrfinderdb_v3.11_20231115.1/AMR_DNA-Neisseria_gonorrhoeae.njs
amrfinderdb_v3.11_20231115.1/AMR_CDS.nsq
amrfinderdb_v3.11_20231115.1/AMRProt.pto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Streptococcus_pneumoniae.ndb
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.nin
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.nsq
amrfinderdb_v3.11_20231115.1/ReferenceGeneCatalog.txt
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.ntf
amrfinderdb_v3.11_20231115.1/AMR_DNA-Staphylococcus_aureus.tab
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.nto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Neisseria_gonorrhoeae.tab
amrfinderdb_v3.11_20231115.1/AMRProt.pjs
amrfinderdb_v3.11_20231115.1/AMR_DNA-Campylobacter.ndb
amrfinderdb_v3.11_20231115.1/AMR_DNA-Campylobacter.tab
amrfinderdb_v3.11_20231115.1/AMR_CDS.nto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Staphylococcus_aureus.not
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecalis.ndb
amrfinderdb_v3.11_20231115.1/AMRProt.pin
amrfinderdb_v3.11_20231115.1/AMR_DNA-Klebsiella_oxytoca.nhr
amrfinderdb_v3.11_20231115.1/AMR_CDS.nhr
amrfinderdb_v3.11_20231115.1/AMR_DNA-Streptococcus_pneumoniae.njs
amrfinderdb_v3.11_20231115.1/AMR_DNA-Acinetobacter_baumannii.nin
amrfinderdb_v3.11_20231115.1/AMR.LIB.h3m
amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.tab
amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.nhr
amrfinderdb_v3.11_20231115.1/AMR_DNA-Streptococcus_pneumoniae.nin
amrfinderdb_v3.11_20231115.1/AMR.LIB
amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.ndb
amrfinderdb_v3.11_20231115.1/AMR_DNA-Neisseria_gonorrhoeae.nsq
Command error:
Running: amrfinder --nucleotide AR-0074.filtered.scaffolds.fa --protein AR-0074.faa --gff AR-0074.gff --annotation_format prokka --mutation_all AR-0074_all_mutations.tsv --organism Klebsiella_oxytoca --plus --database amrfinderdb_v3.11_20231115.1 --threads 6
Software directory: '/amrfinder/'
Software version: 3.11.26
Database directory: 'amrfinderdb_v3.11_20231115.1'
Database version: 2023-11-15.1
AMRFinder combined translated and protein and mutation search
Running blastp
Running hmmsearch
Running tblastn
Running blastn
*** ERROR ***
'/ncbi-blast-2.14.0+/bin/blastn' -query 'AR-0074.filtered.scaffolds.fa' -db /tmp/amrfinder.tXGtz7/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 /tmp/amrfinder.tXGtz7/blastn > /tmp/amrfinder.tXGtz7/log 2> /tmp/amrfinder.tXGtz7/blastn-err
status = 35584
Segmentation fault (core dumped)
HOSTNAME: 1dcd48de1792
SHELL: ?
PWD: /scratch/zl7w2/tools/phoenix/assets/databases/work/66/48cce13659da4d61b03151dcf8ebc0
PATH: /home/zl7w2/.nextflow/assets/cdcgov/phoenix/bin:/amrfinder:/ncbi-blast-2.14.0+/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
Progam name: amrfinder
Command line: amrfinder --nucleotide AR-0074.filtered.scaffolds.fa --protein AR-0074.faa --gff AR-0074.gff --annotation_format prokka --mutation_all AR-0074_all_mutations.tsv --organism Klebsiella_oxytoca --plus --database amrfinderdb_v3.11_20231115.1 --threads 6
Work dir:
/scratch/zl7w2/tools/phoenix/assets/databases/work/66/48cce13659da4d61b03151dcf8ebc0
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
Is there anything else in the .command.err
or .command.out
files that are in the work dir listed? Is this a public sample I could try and run on my end to see if I can reproduce the problem?
@tang27abu, can you provide more detail on this sample? Is it an AR Bank sample?
Here is the command:
nextflow run cdcgov/phoenix -r v2.1.1-dev -latest -profile singularity -entry PHOENIX --input samplesheet.csv --kraken2db $kraken2db
@tang27abu, can you provide more detail on this sample? Is it an AR Bank sample? Here is the command:
nextflow run cdcgov/phoenix -r v2.1.1-dev -latest -profile singularity -entry PHOENIX --input samplesheet.csv --kraken2db $kraken2db
I was trying to run with this command
nextflow run cdcgov/phoenix -r v2.1.1-dev /scratch/zl7w2/tools/phoenix/main.nf -profile docker -entry PHOENIX --input /scratch/zl7w2/Matt/MUCRO4/reads/metadata.csv --kraken2db /scratch/zl7w2/tools/phoenix/k2db
And get the error below:[50/44fca7] process > PHOENIX:PHOENIX_EXTERNAL:GET_TAXA_FOR_AMRFINDER (AR-0074) [100%] 4 of 4 [66/48cce1] process > PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN (AR-0074) [100%] 4 of 4, failed: 1 [9d/a4abd0] process > PHOENIX:PHOENIX_EXTERNAL:CALCULATE_ASSEMBLY_RATIO (AR-0074) [100%] 4 of 4 [e6/2af222] process > PHOENIX:PHOENIX_EXTERNAL:GENERATE_PIPELINE_STATS_WF:GENERATE_PIPELINE_STATS (AR-0034) [100%] 3 of 3 [f2/01cce4] process > PHOENIX:PHOENIX_EXTERNAL:CREATE_SUMMARY_LINE (AR-0034) [100%] 3 of 3 [- ] process > PHOENIX:PHOENIX_EXTERNAL:FETCH_FAILED_SUMMARIES - [- ] process > PHOENIX:PHOENIX_EXTERNAL:GATHER_SUMMARY_LINES - [- ] process > PHOENIX:PHOENIX_EXTERNAL:GRIPHIN - [- ] process > PHOENIX:PHOENIX_EXTERNAL:CUSTOM_DUMPSOFTWAREVERSIONS - [- ] process > PHOENIX:PHOENIX_EXTERNAL:MULTIQC - -[cdcgov/phoenix] Pipeline completed with errors- WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info. Error executing process > 'PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN (AR-0074)' Caused by: Process `PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN (AR-0074)` terminated with an error exit status (1) Command executed: #adding python path for running srst2 on terra if [[ AR-0074.filtered.scaffolds.fa.gz = *.gz ]]; then NUC_FNAME=$(basename AR-0074.filtered.scaffolds.fa.gz .gz) gzip -c -d AR-0074.filtered.scaffolds.fa.gz > $NUC_FNAME else NUC_FNAME = AR-0074.filtered.scaffolds.fa.gz fi # decompress the amrfinder database tar xzvf amrfinderdb_v3.11_20231115.1.tar.gz amrfinder \ --nucleotide $NUC_FNAME \ --protein AR-0074.faa \ --gff AR-0074.gff \ --annotation_format prokka \ --mutation_all AR-0074_all_mutations.tsv \ --organism Klebsiella_oxytoca \ --plus \ --database amrfinderdb_v3.11_20231115.1 \ --threads 6 > AR-0074_all_genes.tsv sed -i '1s/ /_/g' AR-0074_all_genes.tsv cat <<-END_VERSIONS > versions.yml "PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN": amrfinderplus: $(amrfinder --version) amrfinderplus_db_version: $(head amrfinderdb_v3.11_20231115.1/version.txt) amrfinderplus_container: sha256:2311400ff8576f04e77a250e0665daa05f11b67f6a5901c8eac267378dccc932 END_VERSIONS #revert python path back to main envs for running on terra Command exit status: 1 Command output: amrfinderdb_v3.11_20231115.1/AMR_CDS.ndb amrfinderdb_v3.11_20231115.1/AMRProt.ptf amrfinderdb_v3.11_20231115.1/AMRProt.psq amrfinderdb_v3.11_20231115.1/AMR_DNA-Escherichia.nto amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.tab amrfinderdb_v3.11_20231115.1/AMR_DNA-Streptococcus_pneumoniae.nto amrfinderdb_v3.11_20231115.1/AMR_DNA-Salmonella.njs amrfinderdb_v3.11_20231115.1/AMR_DNA-Klebsiella_oxytoca.tab amrfinderdb_v3.11_20231115.1/AMR_DNA-Salmonella.nto amrfinderdb_v3.11_20231115.1/AMR_DNA-Campylobacter.not amrfinderdb_v3.11_20231115.1/AMRProt amrfinderdb_v3.11_20231115.1/AMR_DNA-Acinetobacter_baumannii.nhr amrfinderdb_v3.11_20231115.1/AMRProt.phr amrfinderdb_v3.11_20231115.1/AMR.LIB.h3p amrfinderdb_v3.11_20231115.1/AMR_DNA-Escherichia.njs amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecalis.nhr amrfinderdb_v3.11_20231115.1/AMR_DNA-Campylobacter.nto amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.nsq amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.nhr amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.not amrfinderdb_v3.11_20231115.1/AMR_DNA-Escherichia.ntf amrfinderdb_v3.11_20231115.1/AMR_DNA-Neisseria_gonorrhoeae.njs amrfinderdb_v3.11_20231115.1/AMR_CDS.nsq amrfinderdb_v3.11_20231115.1/AMRProt.pto amrfinderdb_v3.11_20231115.1/AMR_DNA-Streptococcus_pneumoniae.ndb amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.nin amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.nsq amrfinderdb_v3.11_20231115.1/ReferenceGeneCatalog.txt amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.ntf amrfinderdb_v3.11_20231115.1/AMR_DNA-Staphylococcus_aureus.tab amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.nto amrfinderdb_v3.11_20231115.1/AMR_DNA-Neisseria_gonorrhoeae.tab amrfinderdb_v3.11_20231115.1/AMRProt.pjs amrfinderdb_v3.11_20231115.1/AMR_DNA-Campylobacter.ndb amrfinderdb_v3.11_20231115.1/AMR_DNA-Campylobacter.tab amrfinderdb_v3.11_20231115.1/AMR_CDS.nto amrfinderdb_v3.11_20231115.1/AMR_DNA-Staphylococcus_aureus.not amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecalis.ndb amrfinderdb_v3.11_20231115.1/AMRProt.pin amrfinderdb_v3.11_20231115.1/AMR_DNA-Klebsiella_oxytoca.nhr amrfinderdb_v3.11_20231115.1/AMR_CDS.nhr amrfinderdb_v3.11_20231115.1/AMR_DNA-Streptococcus_pneumoniae.njs amrfinderdb_v3.11_20231115.1/AMR_DNA-Acinetobacter_baumannii.nin amrfinderdb_v3.11_20231115.1/AMR.LIB.h3m amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.tab amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.nhr amrfinderdb_v3.11_20231115.1/AMR_DNA-Streptococcus_pneumoniae.nin amrfinderdb_v3.11_20231115.1/AMR.LIB amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.ndb amrfinderdb_v3.11_20231115.1/AMR_DNA-Neisseria_gonorrhoeae.nsq Command error: Running: amrfinder --nucleotide AR-0074.filtered.scaffolds.fa --protein AR-0074.faa --gff AR-0074.gff --annotation_format prokka --mutation_all AR-0074_all_mutations.tsv --organism Klebsiella_oxytoca --plus --database amrfinderdb_v3.11_20231115.1 --threads 6 Software directory: '/amrfinder/' Software version: 3.11.26 Database directory: 'amrfinderdb_v3.11_20231115.1' Database version: 2023-11-15.1 AMRFinder combined translated and protein and mutation search Running blastp Running hmmsearch Running tblastn Running blastn *** ERROR *** '/ncbi-blast-2.14.0+/bin/blastn' -query 'AR-0074.filtered.scaffolds.fa' -db /tmp/amrfinder.tXGtz7/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 /tmp/amrfinder.tXGtz7/blastn > /tmp/amrfinder.tXGtz7/log 2> /tmp/amrfinder.tXGtz7/blastn-err status = 35584 Segmentation fault (core dumped) HOSTNAME: 1dcd48de1792 SHELL: ? PWD: /scratch/zl7w2/tools/phoenix/assets/databases/work/66/48cce13659da4d61b03151dcf8ebc0 PATH: /home/zl7w2/.nextflow/assets/cdcgov/phoenix/bin:/amrfinder:/ncbi-blast-2.14.0+/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin Progam name: amrfinder Command line: amrfinder --nucleotide AR-0074.filtered.scaffolds.fa --protein AR-0074.faa --gff AR-0074.gff --annotation_format prokka --mutation_all AR-0074_all_mutations.tsv --organism Klebsiella_oxytoca --plus --database amrfinderdb_v3.11_20231115.1 --threads 6 Work dir: /scratch/zl7w2/tools/phoenix/assets/databases/work/66/48cce13659da4d61b03151dcf8ebc0 Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
Is there anything else in the
.command.err
or.command.out
files that are in the work dir listed? Is this a public sample I could try and run on my end to see if I can reproduce the problem?
The .command.err and command.out are empty. I am starting another run to see if I can get any information. Here is the sample info
ID | Organism | Biosample |
---|---|---|
32 | Enterobacter cloacae | SAMN04014873 |
34 | Klebsiella pneumoniae | SAMN04014875 |
74 | Klebsiella aerogenes | SAMN04014915 |
76 | Klebsiella pneumoniae | SAMN04014917 |
93 | Enterobacter cloacae | SAMN04014917 |
100 | Pseudomonas aeruginosa | SAMN04014941 |
Hi,
The new run get this error, not sure why it cannot find the ResGANNCBI_20240131_srst2.fasta
[90/25d10f] process > PHOENIX:PHOENIX_EXTERNAL:GAMMA_AR (AR-0093) [100%] 1 of 1, failed: 1
[bf/b540c6] process > PHOENIX:PHOENIX_EXTERNAL:GAMMA_PF (AR-0093) [100%] 1 of 1 β
[b6/a23a64] process > PHOENIX:PHOENIX_EXTERNAL:QUAST (AR-0093) [100%] 1 of 1 β
[22/2d8e71] process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKEN2_WTASMBLD (AR-0093) [100%] 1 of 1
[- ] process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKENTOOLS_MAKEKREPORT -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KREPORT2KRONA_WTASMBLD -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKEN2_BH_WTASMBLD -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRONA_KTIMPORTTEXT_WTASMBLD -
[d9/95c122] process > PHOENIX:PHOENIX_EXTERNAL:MASH_DIST (AR-0093) [100%] 1 of 1 β
[- ] process > PHOENIX:PHOENIX_EXTERNAL:DETERMINE_TOP_MASH_HITS -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:FASTANI -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:FORMAT_ANI -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:DETERMINE_TAXA_ID -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:DO_MLST:MLST -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:DO_MLST:CHECK_MLST -
[4c/2411eb] process > PHOENIX:PHOENIX_EXTERNAL:PROKKA (AR-0093) [100%] 1 of 1 β
[- ] process > PHOENIX:PHOENIX_EXTERNAL:GET_TAXA_FOR_AMRFINDER -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:CALCULATE_ASSEMBLY_RATIO -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:GENERATE_PIPELINE_STATS_WF:GENERATE_PIPELINE_STATS -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:CREATE_SUMMARY_LINE -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:FETCH_FAILED_SUMMARIES -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:GATHER_SUMMARY_LINES -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:GRIPHIN -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:MULTIQC -
-[cdcgov/phoenix] Pipeline completed with errors-
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'PHOENIX:PHOENIX_EXTERNAL:GAMMA_AR (AR-0093)'
Caused by:
Process `PHOENIX:PHOENIX_EXTERNAL:GAMMA_AR (AR-0093)` terminated with an error exit status (1)
Command executed:
db_name=$(echo ResGANNCBI_20240131_srst2.fasta | sed 's:.*/::' | sed 's/.fasta//')
if [[ AR-0093.filtered.scaffolds.fa.gz == *.gz ]]
then
FNAME=$(basename AR-0093.filtered.scaffolds.fa.gz .gz)
gunzip -f AR-0093.filtered.scaffolds.fa.gz
GAMMA.py \
\
$FNAME \
ResGANNCBI_20240131_srst2.fasta \
AR-0093_$db_name
else
GAMMA.py \
\
AR-0093.filtered.scaffolds.fa.gz \
ResGANNCBI_20240131_srst2.fasta \
AR-0093_$db_name
fi
cat <<-END_VERSIONS > versions.yml
"PHOENIX:PHOENIX_EXTERNAL:GAMMA_AR":
gamma: 2.2
gamma_container: sha256:60d8ac58e016349a856fb7b443dd422ba69bae3f40e0dad83460d25ecf71101e
Database: ResGANNCBI_20240131_srst2.fasta
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
mustOpen: Can't open ResGANNCBI_20240131_srst2.fasta to read: No such file or directory
Traceback (most recent call last):
File "/GAMMA/GAMMA.py", line 1067, in <module>
sys.exit(main())
File "/GAMMA/GAMMA.py", line 1056, in main
GAMMA_Out(args.input_fasta, args.database, args.output, args.percent_identity, Verbose)
File "/GAMMA/GAMMA.py", line 1004, in GAMMA_Out
GAMA_Output(output +'.psl', fasta, gene_db, output + '.gamma', verbose)
File "/GAMMA/GAMMA.py", line 932, in GAMA_Output
List1 = GAMA_List(PSL, genome_fasta, genes_fasta, verbose)
File "/GAMMA/GAMMA.py", line 922, in GAMA_List
Lines = GAMA_Line_Maker(PSL, genome_fasta, genes_fasta, verbose)
File "/GAMMA/GAMMA.py", line 729, in GAMA_Line_Maker
Genes = SeqIO.to_dict(SeqIO.parse(genes_fasta, 'fasta'))
File "/usr/local/lib/python3.6/dist-packages/Bio/SeqIO/__init__.py", line 605, in parse
return iterator_generator(handle)
File "/usr/local/lib/python3.6/dist-packages/Bio/SeqIO/FastaIO.py", line 183, in __init__
super().__init__(source, mode="t", fmt="Fasta")
File "/usr/local/lib/python3.6/dist-packages/Bio/SeqIO/Interfaces.py", line 48, in __init__
self.stream = open(source, "r" + mode)
FileNotFoundError: [Errno 2] No such file or directory: 'ResGANNCBI_20240131_srst2.fasta'
Work dir:
/scratch/zl7w2/tools/phoenix/work/90/25d10f652e53eb05bdff86202b03ba
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
This the the file list under work dir
@tang27abu something is off here remove this from your command /scratch/zl7w2/tools/phoenix/main.nf so the it should just be nextflow run cdcgov/phoenix -r v2.1.1-dev -latest -profile docker -entry PHOENIX --input /scratch/zl7w2/Matt/MUCRO4/reads/metadata.csv --kraken2db /scratch/zl7w2/tools/phoenix/k2db
Can you tell me about the system you are running on? If its a laptop/desktop do you have other programs running on it at the same time?
@tang27abu something is off here remove this from your command /scratch/zl7w2/tools/phoenix/main.nf so the it should just be
nextflow run cdcgov/phoenix -r v2.1.1-dev -profile docker -entry PHOENIX --input /scratch/zl7w2/Matt/MUCRO4/reads/metadata.csv --kraken2db /scratch/zl7w2/tools/phoenix/k2db
Can you tell me about the system you are running on? If its a laptop/desktop do you have other programs running on it at the same time?
I am running on a Ubuntu system.
@jvhagey
I run the command nextflow run cdcgov/phoenix -r v2.1.1-dev -profile docker -entry PHOENIX --input /scratch/zl7w2/Matt/MUCRO4/reads/metadata.csv --kraken2db /scratch/zl7w2/tools/phoenix/k2db
below are the error, still cannot find that file.
[- ] process > PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:GENERATE_PIPELINE_STATS_FAILURE -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:CREATE_SUMMARY_LINE_FAILURE -
[37/1f83d0] process > PHOENIX:PHOENIX_EXTERNAL:RENAME_FASTA_HEADERS (AR-0093) [100%] 1 of 1
[73/249f8b] process > PHOENIX:PHOENIX_EXTERNAL:BBMAP_REFORMAT (AR-0093) [100%] 1 of 1
[4e/7146fc] process > PHOENIX:PHOENIX_EXTERNAL:SCAFFOLD_COUNT_CHECK (AR-0093) [100%] 1 of 1
[d8/b9527b] process > PHOENIX:PHOENIX_EXTERNAL:GAMMA_HV (AR-0093) [100%] 1 of 1
[17/2f4f24] process > PHOENIX:PHOENIX_EXTERNAL:GAMMA_AR (AR-0093) [100%] 1 of 1, failed: 1
[0d/68e78d] process > PHOENIX:PHOENIX_EXTERNAL:GAMMA_PF (AR-0093) [100%] 1 of 1 β
[4f/6c6205] process > PHOENIX:PHOENIX_EXTERNAL:QUAST (AR-0093) [100%] 1 of 1 β
[71/6c1238] process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKEN2_WTASMBLD (AR-0093) [100%] 1 of 1
[- ] process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKENTOOLS_MAKEKREPORT -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KREPORT2KRONA_WTASMBLD -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKEN2_BH_WTASMBLD -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRONA_KTIMPORTTEXT_WTASMBLD -
[51/af178c] process > PHOENIX:PHOENIX_EXTERNAL:MASH_DIST (AR-0093) [100%] 1 of 1 β
[- ] process > PHOENIX:PHOENIX_EXTERNAL:DETERMINE_TOP_MASH_HITS -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:FASTANI -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:FORMAT_ANI -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:DETERMINE_TAXA_ID -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:DO_MLST:MLST -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:DO_MLST:CHECK_MLST -
[64/feb7ca] process > PHOENIX:PHOENIX_EXTERNAL:PROKKA (AR-0093) [100%] 1 of 1 β
[- ] process > PHOENIX:PHOENIX_EXTERNAL:GET_TAXA_FOR_AMRFINDER -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:CALCULATE_ASSEMBLY_RATIO -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:GENERATE_PIPELINE_STATS_WF:GENERATE_PIPELINE_STATS -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:CREATE_SUMMARY_LINE -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:FETCH_FAILED_SUMMARIES -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:GATHER_SUMMARY_LINES -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:GRIPHIN -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:MULTIQC -
-[cdcgov/phoenix] Pipeline completed with errors-
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'PHOENIX:PHOENIX_EXTERNAL:GAMMA_AR (AR-0093)'
Caused by:
Process `PHOENIX:PHOENIX_EXTERNAL:GAMMA_AR (AR-0093)` terminated with an error exit status (1)
Command executed:
db_name=$(echo ResGANNCBI_20240131_srst2.fasta | sed 's:.*/::' | sed 's/.fasta//')
if [[ AR-0093.filtered.scaffolds.fa.gz == *.gz ]]
then
FNAME=$(basename AR-0093.filtered.scaffolds.fa.gz .gz)
gunzip -f AR-0093.filtered.scaffolds.fa.gz
GAMMA.py \
\
$FNAME \
ResGANNCBI_20240131_srst2.fasta \
AR-0093_$db_name
else
GAMMA.py \
\
AR-0093.filtered.scaffolds.fa.gz \
ResGANNCBI_20240131_srst2.fasta \
AR-0093_$db_name
fi
cat <<-END_VERSIONS > versions.yml
"PHOENIX:PHOENIX_EXTERNAL:GAMMA_AR":
gamma: 2.2
gamma_container: sha256:60d8ac58e016349a856fb7b443dd422ba69bae3f40e0dad83460d25ecf71101e
Database: ResGANNCBI_20240131_srst2.fasta
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
mustOpen: Can't open ResGANNCBI_20240131_srst2.fasta to read: No such file or directory
Traceback (most recent call last):
File "/GAMMA/GAMMA.py", line 1067, in <module>
sys.exit(main())
File "/GAMMA/GAMMA.py", line 1056, in main
GAMMA_Out(args.input_fasta, args.database, args.output, args.percent_identity, Verbose)
File "/GAMMA/GAMMA.py", line 1004, in GAMMA_Out
GAMA_Output(output +'.psl', fasta, gene_db, output + '.gamma', verbose)
File "/GAMMA/GAMMA.py", line 932, in GAMA_Output
List1 = GAMA_List(PSL, genome_fasta, genes_fasta, verbose)
File "/GAMMA/GAMMA.py", line 922, in GAMA_List
Lines = GAMA_Line_Maker(PSL, genome_fasta, genes_fasta, verbose)
File "/GAMMA/GAMMA.py", line 729, in GAMA_Line_Maker
Genes = SeqIO.to_dict(SeqIO.parse(genes_fasta, 'fasta'))
File "/usr/local/lib/python3.6/dist-packages/Bio/SeqIO/__init__.py", line 605, in parse
return iterator_generator(handle)
File "/usr/local/lib/python3.6/dist-packages/Bio/SeqIO/FastaIO.py", line 183, in __init__
super().__init__(source, mode="t", fmt="Fasta")
File "/usr/local/lib/python3.6/dist-packages/Bio/SeqIO/Interfaces.py", line 48, in __init__
self.stream = open(source, "r" + mode)
FileNotFoundError: [Errno 2] No such file or directory: 'ResGANNCBI_20240131_srst2.fasta'
Work dir:
/scratch/zl7w2/tools/phoenix/work/17/2f4f24d32e5c6008e492fded65d08d
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
should I git pull the repo first then run that command?
@tang27abu anytime you are testing a dev branch you need to add -latest
to your command. Dev branches are constantly in flux and I can't be sure we are comparing the same code unless you use -latest
, which will automatically pull the latest code from github if your copy isn't up-to-date. This only works if you are using nextflow run cdcgov/phoenix
and not running main.nf
after cloning/pulling the repo yourself.
In terms of your system, can you let me know the specs? What size is your RAM? The original problem might still be a memory one if you are using a laptop and have other programs running at the same time.
@tang27abu anytime you are testing a dev branch you need to add
-latest
to your command. Dev branches are constantly in flux and I can't be sure we are comparing the same code unless you use-latest
, which will automatically pull the latest code from github if your copy isn't up-to-date. This only works if you are usingnextflow run cdcgov/phoenix
and not runningmain.nf
after cloning/pulling the repo yourself.In terms of your system, can you let me know the specs? What size is your RAM? The original problem might still be a memory one if you are using a laptop and have other programs running at the same time.
I run this command nextflow run cdcgov/phoenix -r v2.1.1-dev -latest -profile docker -entry PHOENIX --input /scratch/zl7w2/Matt/MUCRO4/reads/metadata.csv --kraken2db /scratch/zl7w2/tools/phoenix/k2db
but still get the same error, FileNotFoundError: [Errno 2] No such file or directory: 'ResGANNCBI_20240131_srst2.fasta'
Here is the memory informations:
When I remove the sample 0074 - SAMN04014915, it works well with ver2.1.0.
Does the sample run on its own? Like if you didn't have it with other samples going at the same time?
Does the sample run on its own? Like if you didn't have it with other samples going at the same time?
Just try only run with 0074 sample and it gives same core dumped error
[ba/5836ea] process > PHOENIX:PHOENIX_EXTERNAL:GET_TAXA_FOR_AMRFINDER (AR-0074) [100%] 1 of 1 β
[7e/495ec8] process > PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN (AR-0074) [100%] 1 of 1, failed: 1 β
[02/cb9c30] process > PHOENIX:PHOENIX_EXTERNAL:CALCULATE_ASSEMBLY_RATIO (AR-0074) [100%] 1 of 1 β
[- ] process > PHOENIX:PHOENIX_EXTERNAL:GENERATE_PIPELINE_STATS_WF:GENERATE_PIPELINE_STATS -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:CREATE_SUMMARY_LINE -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:FETCH_FAILED_SUMMARIES (1) -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:GATHER_SUMMARY_LINES -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:GRIPHIN -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > PHOENIX:PHOENIX_EXTERNAL:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
-[cdcgov/phoenix] Pipeline completed with errors-
WARN: Killing running tasks (1)
WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info.
ERROR ~ Error executing process > 'PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN (AR-0074)'
Caused by:
Process `PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN (AR-0074)` terminated with an error exit status (1)
Command executed:
#adding python path for running srst2 on terra
if [[ AR-0074.filtered.scaffolds.fa.gz = *.gz ]]; then
NUC_FNAME=$(basename AR-0074.filtered.scaffolds.fa.gz .gz)
gzip -c -d AR-0074.filtered.scaffolds.fa.gz > $NUC_FNAME
else
NUC_FNAME = AR-0074.filtered.scaffolds.fa.gz
fi
# decompress the amrfinder database
tar xzvf amrfinderdb_v3.11_20231115.1.tar.gz
amrfinder \
--nucleotide $NUC_FNAME \
--protein AR-0074.faa \
--gff AR-0074.gff \
--annotation_format prokka \
--mutation_all AR-0074_all_mutations.tsv \
--organism Klebsiella_oxytoca \
--plus \
--database amrfinderdb_v3.11_20231115.1 \
--threads 6 > AR-0074_all_genes.tsv
sed -i '1s/ /_/g' AR-0074_all_genes.tsv
cat <<-END_VERSIONS > versions.yml
"PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN":
amrfinderplus: $(amrfinder --version)
amrfinderplus_db_version: $(head amrfinderdb_v3.11_20231115.1/version.txt)
amrfinderplus_container: sha256:2311400ff8576f04e77a250e0665daa05f11b67f6a5901c8eac267378dccc932
END_VERSIONS
#revert python path back to main envs for running on terra
Command exit status:
1
Command output:
amrfinderdb_v3.11_20231115.1/AMR_CDS.ndb
amrfinderdb_v3.11_20231115.1/AMRProt.ptf
amrfinderdb_v3.11_20231115.1/AMRProt.psq
amrfinderdb_v3.11_20231115.1/AMR_DNA-Escherichia.nto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.tab
amrfinderdb_v3.11_20231115.1/AMR_DNA-Streptococcus_pneumoniae.nto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Salmonella.njs
amrfinderdb_v3.11_20231115.1/AMR_DNA-Klebsiella_oxytoca.tab
amrfinderdb_v3.11_20231115.1/AMR_DNA-Salmonella.nto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Campylobacter.not
amrfinderdb_v3.11_20231115.1/AMRProt
amrfinderdb_v3.11_20231115.1/AMR_DNA-Acinetobacter_baumannii.nhr
amrfinderdb_v3.11_20231115.1/AMRProt.phr
amrfinderdb_v3.11_20231115.1/AMR.LIB.h3p
amrfinderdb_v3.11_20231115.1/AMR_DNA-Escherichia.njs
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecalis.nhr
amrfinderdb_v3.11_20231115.1/AMR_DNA-Campylobacter.nto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.nsq
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.nhr
amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.not
amrfinderdb_v3.11_20231115.1/AMR_DNA-Escherichia.ntf
amrfinderdb_v3.11_20231115.1/AMR_DNA-Neisseria_gonorrhoeae.njs
amrfinderdb_v3.11_20231115.1/AMR_CDS.nsq
amrfinderdb_v3.11_20231115.1/AMRProt.pto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Streptococcus_pneumoniae.ndb
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.nin
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.nsq
amrfinderdb_v3.11_20231115.1/ReferenceGeneCatalog.txt
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.ntf
amrfinderdb_v3.11_20231115.1/AMR_DNA-Staphylococcus_aureus.tab
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.nto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Neisseria_gonorrhoeae.tab
amrfinderdb_v3.11_20231115.1/AMRProt.pjs
amrfinderdb_v3.11_20231115.1/AMR_DNA-Campylobacter.ndb
amrfinderdb_v3.11_20231115.1/AMR_DNA-Campylobacter.tab
amrfinderdb_v3.11_20231115.1/AMR_CDS.nto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Staphylococcus_aureus.not
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecalis.ndb
amrfinderdb_v3.11_20231115.1/AMRProt.pin
amrfinderdb_v3.11_20231115.1/AMR_DNA-Klebsiella_oxytoca.nhr
amrfinderdb_v3.11_20231115.1/AMR_CDS.nhr
amrfinderdb_v3.11_20231115.1/AMR_DNA-Streptococcus_pneumoniae.njs
amrfinderdb_v3.11_20231115.1/AMR_DNA-Acinetobacter_baumannii.nin
amrfinderdb_v3.11_20231115.1/AMR.LIB.h3m
amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.tab
amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.nhr
amrfinderdb_v3.11_20231115.1/AMR_DNA-Streptococcus_pneumoniae.nin
amrfinderdb_v3.11_20231115.1/AMR.LIB
amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.ndb
amrfinderdb_v3.11_20231115.1/AMR_DNA-Neisseria_gonorrhoeae.nsq
Command error:
amrfinderdb_v3.11_20231115.1/AMR_CDS.nsq
amrfinderdb_v3.11_20231115.1/AMRProt.pto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Streptococcus_pneumoniae.ndb
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.nin
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.nsq
amrfinderdb_v3.11_20231115.1/ReferenceGeneCatalog.txt
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.ntf
amrfinderdb_v3.11_20231115.1/AMR_DNA-Staphylococcus_aureus.tab
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecium.nto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Neisseria_gonorrhoeae.tab
amrfinderdb_v3.11_20231115.1/AMRProt.pjs
amrfinderdb_v3.11_20231115.1/AMR_DNA-Campylobacter.ndb
amrfinderdb_v3.11_20231115.1/AMR_DNA-Campylobacter.tab
amrfinderdb_v3.11_20231115.1/AMR_CDS.nto
amrfinderdb_v3.11_20231115.1/AMR_DNA-Staphylococcus_aureus.not
amrfinderdb_v3.11_20231115.1/AMR_DNA-Enterococcus_faecalis.ndb
amrfinderdb_v3.11_20231115.1/AMRProt.pin
amrfinderdb_v3.11_20231115.1/AMR_DNA-Klebsiella_oxytoca.nhr
amrfinderdb_v3.11_20231115.1/AMR_CDS.nhr
amrfinderdb_v3.11_20231115.1/AMR_DNA-Streptococcus_pneumoniae.njs
amrfinderdb_v3.11_20231115.1/AMR_DNA-Acinetobacter_baumannii.nin
amrfinderdb_v3.11_20231115.1/AMR.LIB.h3m
amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.tab
amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.nhr
amrfinderdb_v3.11_20231115.1/AMR_DNA-Streptococcus_pneumoniae.nin
amrfinderdb_v3.11_20231115.1/AMR.LIB
amrfinderdb_v3.11_20231115.1/AMR_DNA-Clostridioides_difficile.ndb
amrfinderdb_v3.11_20231115.1/AMR_DNA-Neisseria_gonorrhoeae.nsq
Running: amrfinder --nucleotide AR-0074.filtered.scaffolds.fa --protein AR-0074.faa --gff AR-0074.gff --annotation_format prokka --mutation_all AR-0074_all_mutations.tsv --organism Klebsiella_oxytoca --plus --database amrfinderdb_v3.11_20231115.1 --threads 6
Software directory: '/amrfinder/'
Software version: 3.11.26
Database directory: 'amrfinderdb_v3.11_20231115.1'
Database version: 2023-11-15.1
AMRFinder combined translated and protein and mutation search
Running blastp
Running hmmsearch
Running tblastn
Running blastn
*** ERROR ***
'/ncbi-blast-2.14.0+/bin/blastn' -query 'AR-0074.filtered.scaffolds.fa' -db /tmp/amrfinder.qJQEm6/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 /tmp/amrfinder.qJQEm6/blastn > /tmp/amrfinder.qJQEm6/log 2> /tmp/amrfinder.qJQEm6/blastn-err
status = 35584
Segmentation fault (core dumped)
HOSTNAME: 19244c2d84a4
SHELL: ?
PWD: /scratch/zl7w2/tools/phoenix_v2.0.0/work/7e/495ec8c96d461971049e51c21118f4
PATH: /amrfinder:/ncbi-blast-2.14.0+/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/scratch/zl7w2/tools/phoenix/bin
Progam name: amrfinder
Command line: amrfinder --nucleotide AR-0074.filtered.scaffolds.fa --protein AR-0074.faa --gff AR-0074.gff --annotation_format prokka --mutation_all AR-0074_all_mutations.tsv --organism Klebsiella_oxytoca --plus --database amrfinderdb_v3.11_20231115.1 --threads 6
Work dir:
/scratch/zl7w2/tools/phoenix_v2.0.0/work/7e/495ec8c96d461971049e51c21118f4
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '.nextflow.log' file for details
Failure on AMRfinder run, error is printed below
I've repeated it twice (with different version of PhoeNIX) and gotten the same result both times.