AMRProt does not exist

[nick-youngblut]

I'm using ncbi-amrfinderplus 3.10.1 h17dc2d4_1 bioconda, and I'm trying to use a local copy of the latest database (https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/).

I downloaded the latest database:

-rw-r--r-- 1 nyoungblut abt3 5.9K Mar 31 14:22 AMR_DNA-Campylobacter
-rw-r--r-- 1 nyoungblut abt3 7.3M Mar 31 14:22 AMR_CDS
drwxr-sr-x 2 nyoungblut abt3   89 Mar 31 14:22 allele_counts_by_year
-rw-r--r-- 1 nyoungblut abt3  406 Mar 31 14:22 AMR_DNA-Salmonella.tab
-rw-r--r-- 1 nyoungblut abt3 1.6K Mar 31 14:22 AMR_DNA-Salmonella
-rw-r--r-- 1 nyoungblut abt3 6.7K Mar 31 14:22 AMR_DNA-Escherichia.tab
-rw-r--r-- 1 nyoungblut abt3 6.4K Mar 31 14:22 AMR_DNA-Escherichia
-rw-r--r-- 1 nyoungblut abt3 1.4K Mar 31 14:22 AMR_DNA-Campylobacter.tab
-rw-r--r-- 1 nyoungblut abt3  825 Mar 31 14:22 AMR_DNA-Streptococcus_pneumoniae.tab
-rw-r--r-- 1 nyoungblut abt3 3.0K Mar 31 14:22 AMR_DNA-Streptococcus_pneumoniae
-rw-r--r-- 1 nyoungblut abt3 1.6K Mar 31 14:22 AMR_DNA-Staphylococcus_aureus.tab
-rw-r--r-- 1 nyoungblut abt3 3.0K Mar 31 14:22 AMR_DNA-Staphylococcus_aureus
-rw-r--r-- 1 nyoungblut abt3 3.7K Mar 31 14:22 AMRProt-susceptible.tab
-rw-r--r-- 1 nyoungblut abt3  581 Mar 31 14:22 AMRProt-suppress
-rw-r--r-- 1 nyoungblut abt3  73K Mar 31 14:22 AMRProt-mutation.tab
-rw-r--r-- 1 nyoungblut abt3 3.1M Mar 31 14:22 AMRProt
-rw-r--r-- 1 nyoungblut abt3  83M Mar 31 14:22 AMR.LIB
-rw-r--r-- 1 nyoungblut abt3 244K Mar 31 14:22 fam.tab
-rw-r--r-- 1 nyoungblut abt3    7 Mar 31 14:22 database_format_version.txt
-rw-r--r-- 1 nyoungblut abt3 525K Mar 31 14:22 changes.txt
-rw-r--r-- 1 nyoungblut abt3 525K Mar 31 14:22 changelog.txt
-rw-r--r-- 1 nyoungblut abt3 1.4M Mar 31 14:22 amr_targets.fa
-rw-r--r-- 1 nyoungblut abt3   13 Mar 31 14:22 version.txt
-rw-r--r-- 1 nyoungblut abt3  596 Mar 31 14:22 taxgroup.tab
-rw-r--r-- 1 nyoungblut abt3 1.3M Mar 31 14:22 ReferenceGeneCatalog.txt
-rw-r--r-- 1 nyoungblut abt3 3.6K Mar 31 14:22 index.html

and ran:

amrfinder --plus --threads 4 -d /ebio/abt3_projects/databases_no-backup/AMRFinder/2021-03-01.1 -p query.faa

I'm getting this error:

Running: amrfinder --plus --threads 4 -d /ebio/abt3_projects/databases_no-backup/AMRFinder/2021-03-01.1 -p query.faa
Software directory: '/ebio/abt3_projects/software/dev/miniconda3_dev/envs/genome/bin/'
Software version: 3.10.1
Database directory: '/ebio/abt3_projects/databases_no-backup/AMRFinder/2021-03-01.1'
Database version: 2021-03-01.1
AMRFinder protein-only search
  - include -n NUC_FASTA, --nucleotide NUC_FASTA and -g GFF_FILE, --gff GFF_FILE options to add translated searches
  - include -O ORGANISM, --organism ORGANISM option to add mutation searches and suppress common proteins

*** ERROR ***
BLAST database '/ebio/abt3_projects/databases_no-backup/AMRFinder/2021-03-01.1/AMRProt' does not exist

/ebio/abt3_projects/databases_no-backup/AMRFinder/2021-03-01.1/AMRProt does exist

[vbrover]

Does this symbolic link exist?

/ebio/abt3_projects/databases_no-backup/AMRFinder/latest

If it does then please run

amrfinder --plus --threads 4 -d /ebio/abt3_projects/databases_no-backup/AMRFinder -p query.faa

[nick-youngblut]

No, I just downloaded the files for version 2021-03-01.1.

It seems that amrfinder is not just checking for whether the file exists as what appears in the error:

BLAST database '/ebio/abt3_projects/databases_no-backup/AMRFinder/2021-03-01.1/AMRProt' does not exist

...given that the file does indeed exist, and is not a broken symlink or something like that.

[vbrover]

Please run this:

amrfinder_update  -d /ebio/abt3_projects/databases_no-backup/AMRFinder

and then

amrfinder --plus --threads 4 -d /ebio/abt3_projects/databases_no-backup/AMRFinder -p query.faa

[nick-youngblut]

Yeah, that worked. I had previously just copied the databases from the default location after it was installed via not provided -d for amrfinder. My issue is in the error message that is reported. The error message sounds like the database file is missing, even when it actually exists.

[vbrover]

The FASTA file AMRProt exists, but it is a not BLAST database file.
Protein BLAST database files have extensions .pdb, .phr, etc.

[nick-youngblut]

So the error should say:

BLAST database files
'/ebio/abt3_projects/databases_no-backup/AMRFinder/2021-03-01.1/AMRProt.pdb' 
'/ebio/abt3_projects/databases_no-backup/AMRFinder/2021-03-01.1/AMRProt.phr' 
[...]
do not exist

right? The fasta exists; it's the other database files that don't.

I know that this is a minor thing, but it could help prevent confusion, given that the fasta file exists, so the user could wonder: why am I getting this 'does not exists' error when the file that is listed does exist?

[vbrover]

Yes.
Thank you!

[evolarjun]

We just made a release with an improved error message so you know what's file is missing version 3.10.11. It may take a little while to percolate through bioconda.