Closed GomathiNayagam closed 1 year ago
Hi @GomathiNayagam ,
I don't see a silly error, and I'm having trouble reproducing your issue. With the test data distributed with AMRFinderPlus I get FASTA output:
$ NUC_FASTA=test_dna.fa
$ amrfinder --nucleotide $NUC_FASTA --ident_min 0.9 --coverage_min 0.89 --nucleotide_output out.fasta --threads 6 --output amrout.tsv
Running: amrfinder --nucleotide test_dna.fa --ident_min 0.9 --coverage_min 0.89 --nucleotide_output out.fasta --threads 6 --output amrout.tsv
Software directory: '/panfs/pan1.be-md.ncbi.nlm.nih.gov/bacterial_pathogens/backup/packages/AMRFinderPlus_v3.11.4/'
Software version: 3.11.4
Database directory: '/panfs/pan1.be-md.ncbi.nlm.nih.gov/bacterial_pathogens/backup/packages/AMRFinderPlusData/2023-02-23.1'
Database version: 2023-02-23.1
AMRFinder translated nucleotide search
- include -O ORGANISM, --organism ORGANISM option to add mutation searches and suppress common proteins
Running blastx ...
Making report ...
AMRFinder took 9 seconds to complete
The results look as I would expect:
$ wc -l amrout.tsv
6 amrout.tsv
$ fgrep -c '>' out.fasta
5
Could you paste in what AMRFinderPlus prints to the screen and attach your $NUC_FASTA file? That might help me reproduce your issue.
Thanks, Arjun
Hi, I too tried with the test data and it produces nuc_output. But it doesn't work for my file. So, I think it could be an error from my file. Please find my fasta file attached.
This is what the AMRfinder prints out.
Software directory: '/home/gomathinayagam/miniconda3/envs/amrfinder/bin/'
Software version: 3.11.4
Database directory: '/home/gomathinayagam/miniconda3/envs/amrfinder/share/amrfinderplus/data/2023-02-23.1'
Database version: 2023-02-23.1
AMRFinder translated nucleotide search
- include -O ORGANISM, --organism ORGANISM option to add mutation searches and suppress common proteins
Running tblastn ...
Making report ...
AMRFinder took 16 seconds to complete
Thank you for reporting this!
It is a bug in amrfinder
: leading underscore symbol is trimmed from the contig name in the report.
This will be fixed in version 3.11.5.
Yes, it is the 'unusual' FASTA header. It works after editing the headers. Thank you very much!
@GomathiNayagam I'm glad to hear it's working for you.
I'm going to reopen just for our tracking because we consider this a bug and plan to release a fix with the next AMRFinderPlus software release.
Thanks for reporting!
So the bug itself was fixed in release 3.11.8, but additionally we changed the behavior so if there is an error no empty -o
file will be created (release 3.11.14).
Hi, I am trying to find AMR genes in NUC_FASTA. Though AMRfinder identifies AMR in the input, it outputs an empty NUC_FASTA_OUT. I am probably making a silly error here. Could you help me out?
amrfinder --nucleotide $NUC_FASTA --ident_min 0.9 --coverage_min 0.89 --nucleotide_output out.fasta --threads 6 --output amrout.tsv