tseemann / abricate Goto Github PK

according to KY352406, the length of mcr-1.6_1 should be 1626 bps, the same as the other mcr-1 variants. However, as you can see at the top, it shows 1826 bps.

I also double-checked it with the online version of resfinder, it gave a correct match with mcr-1 (1626), so I'm wondering where it went wrong.

Thanks so much

Hi!

I'd love to use this for other genes. Could you specify what the fasta description line should look like, for instance, which part(s) of it do you use where?

Currently, the blast search against the databases/query is only single-threaded. Blastn supports multi-threaded search natively. It would be great to expose -num_threads as an argument to abricate. Otherwise, search in metagenomic assemblies would take ages.

Need to check I ain't breaking any rules :-/

If you do abricate --help. the output contains exclamation marks after debug, quiet, version etc. These should not be included.

When I was explaining this to students, they thought it was confusing. Why add the exclamation mark when it should not be used?

Forgive me if this is a known or simple issue. I have all of the necessary perl modules and Abricate, itself, installed. I am trying to feed it a fasta file with ~6000 sequences in it. This fasta was converted from fastq format. I am receiving an error message saying "WARNING: can not find sequence data in 'file_name'

I have tried using EMBOSS' seqret program to reformat the file again. It's definitely a slightly different format, but the error persists.

It clearly has sequence data at roughly 150 bp per read and the standard Identifier line beginning with ">"

Any thoughts on this?

Thanks

Hi @tseemann ,

I would like to place a feature request for abricate --summary *.csv.

Thanks,

Mark

abricate --list
Database abricate has no sequences, please try: abricate-get_db --db abricate
argannot:  1749 sequences -  Aug 28, 2017
card:  2153 sequences -  Aug 28, 2017
ncbi:  4124 sequences -  Aug 28, 2017
ncbibetalactamase:  1557 sequences -  Aug 28, 2017
plasmidfinder:  263 sequences -  Aug 28, 2017
resfinder:  2228 sequences -  Aug 28, 2017
vfdb:  2597 sequences -  Aug 28, 2017

Thanks @schultzm

The first error line will still be STDOUT

I am trying to use the latest version of CRAD, which is 1.2 via

abricate-get_db --db card --force

Setting up 'card' in '/Users/pi/miniconda3/db/card'
Downloading: https://card.mcmaster.ca/download/0/broadstreet-v1.1.9.tar.gz
Result: 200
Destination: card.tar.bz2

However, the most recent version is 1.2.0.

I tried changing the card.tar.bz2 in the .../miniconda3/db/card/src/ and then reloaded the db with

abricate-get_db --db card

no effect, still uses 1.1.9

What am I doing wrong?

Issue #38 by @dutchscientist
https://cge.cbs.dtu.dk/services/SerotypeFinder/

@dutchscientist do you have the URL for the amplicon sequences?

Hi Torsten,
Feature requests:

• add --help to abricate-get_db
• allow user to specify db url or path to db if already downloaded (e.g., http://www.mgc.ac.cn/VFs/Down/VFDB_setB_nt.fas.gz instead of http://www.mgc.ac.cn/VFs/Down/VFDB_setA_nt.fas.gz )
• during the running of abricate-get_db, append unique identifier to locus tag so duplicate error does not occur (BLAST Database creation error: Error: Duplicate seq_ids are found:)

Cheers,

Mark

Biolinux8 is Ubuntu 14.04 LTS, and this one has BLAST+ v 2.2.28 as final one in its repositories. Hence Abricate won't run (it expects >= 2.2.30), and the check does not pick this up.

How easiest to correct?

When installing via brew, the installation aborts complaining about BioPerl not being installed. You might want to add this to the dependencies?

Currently Abricate will also report partial hits. An option to define the minimum coverage required (similar to --minid=95 or so) would be a good option. So say --mincov=90 or so?

Hi,
is it feasable to use abricate for mass screening of protein sequences instead of genes (i.e. use tblastn instead of blastn)?
Thanks,
Carlus

Hi Torsten, Jason, just checking.. is the ncbi database no longer used in abricate 0.5? Thanks, Rosie

needs || usage(1)

Hi Torsten

I couldn't install abricate via linuxbrew, any advice gratefully received, thanks

brew install abricate --HEAD
==> Installing abricate from tseemann/bioinformatics-linux
abricate: Unsatisfied dependency: File::Slurp
Homebrew does not provide special Perl dependencies; install with:
cpan -i File::Slurp
abricate: Unsatisfied dependency: Text::CSV
Homebrew does not provide special Perl dependencies; install with:
cpan -i Text::CSV
abricate: Unsatisfied dependency: JSON
Homebrew does not provide special Perl dependencies; install with:
cpan -i JSON
Error: Unsatisfied requirements failed this build.

I tried cpan -i File::Slurp with no effect on abricate installation

Loading internal null logger. Install Log::Log4perl for logging messages

CPAN.pm requires configuration, but most of it can be done automatically.
If you answer 'no' below, you will enter an interactive dialog for each
configuration option instead.

Would you like to configure as much as possible automatically? [yes] yes
Use of uninitialized value $what in concatenation (.) or string at /usr/share/perl/5.22/App/Cpan.pm line 633, line 1.

Warning: You do not have write permission for Perl library directories.

To install modules, you need to configure a local Perl library directory or
escalate your privileges. CPAN can help you by bootstrapping the local::lib
module or by configuring itself to use 'sudo' (if available). You may also
resolve this problem manually if you need to customize your setup.

What approach do you want? (Choose 'local::lib', 'sudo' or 'manual')
[local::lib] local::lib
Attempting to create directory /home/mike/perl5

Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for local::lib
Writing MYMETA.yml and MYMETA.json
cp lib/POD2/DE/local/lib.pod blib/lib/POD2/DE/local/lib.pod
cp lib/POD2/PT_BR/local/lib.pod blib/lib/POD2/PT_BR/local/lib.pod
cp lib/local/lib.pm blib/lib/local/lib.pm
cp lib/lib/core/only.pm blib/lib/lib/core/only.pm
Manifying 4 pod documents
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-I/home/mike/perl5/lib/perl5" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/.t
t/bad_variables.t ...... ok
t/carp-mismatch.t ...... ok
t/classmethod.t ........ ok
t/coderefs_in_inc.t .... ok
t/de-dup.t ............. ok
t/lib-core-only.t ...... ok
t/pipeline.t ........... ok
t/shell.t .............. ok
t/stackable.t .......... ok
t/subroutine-in-inc.t .. ok
t/taint-mode.t ......... ok
All tests successful.
Files=11, Tests=149, 2 wallclock secs ( 0.05 usr 0.01 sys + 0.94 cusr 0.06 csys = 1.06 CPU)
Result: PASS
Manifying 4 pod documents
Installing /home/mike/perl5/lib/perl5/POD2/PT_BR/local/lib.pod
Installing /home/mike/perl5/lib/perl5/POD2/DE/local/lib.pod
Installing /home/mike/perl5/lib/perl5/lib/core/only.pm
Installing /home/mike/perl5/lib/perl5/local/lib.pm
Installing /home/mike/perl5/man/man3/POD2::DE::local::lib.3pm
Installing /home/mike/perl5/man/man3/POD2::PT_BR::local::lib.3pm
Installing /home/mike/perl5/man/man3/lib::core::only.3pm
Installing /home/mike/perl5/man/man3/local::lib.3pm
Appending installation info to /home/mike/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/perllocal.pod

Would you like me to append that to /home/mike/.bashrc now? [yes] yes
Running install for module 'File::Slurp'
Fetching with LWP:
http://www.cpan.org/authors/id/U/UR/URI/File-Slurp-9999.19.tar.gz
Fetching with LWP:
http://www.cpan.org/authors/id/U/UR/URI/CHECKSUMS
Checksum for /home/mike/.cpan/sources/authors/id/U/UR/URI/File-Slurp-9999.19.tar.gz ok
Configuring U/UR/URI/File-Slurp-9999.19.tar.gz with Makefile.PL
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for File::Slurp
Writing MYMETA.yml and MYMETA.json
URI/File-Slurp-9999.19.tar.gz
/usr/bin/perl Makefile.PL INSTALLDIRS=site -- OK
Running make for U/UR/URI/File-Slurp-9999.19.tar.gz
cp lib/File/Slurp.pm blib/lib/File/Slurp.pm
Manifying 1 pod document
URI/File-Slurp-9999.19.tar.gz
/usr/bin/make -- OK
Running make test
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/.t
t/append_null.t ....... ok
t/binmode.t ........... ok
t/chomp.t ............. ok
t/data_list.t ......... ok
t/data_scalar.t ....... ok
t/edit_file.t ......... ok
t/error.t ............. ok
t/error_mode.t ........ ok
t/file_object.t ....... ok
t/handle.t ............ ok
t/inode.t ............. ok
t/large.t ............. ok
t/newline.t ........... ok
t/no_clobber.t ........ ok
t/original.t .......... ok
t/paragraph.t ......... ok
t/perms.t ............. ok
t/pod.t ............... skipped: Test::Pod 1.14 required for testing POD
t/pod_coverage.t ...... skipped: Test::Pod::Coverage 1.04 required for testing POD coverage
t/prepend_file.t ...... ok
t/pseudo.t ............ ok
t/read_dir.t .......... ok
t/signal.t ............ ok
t/slurp.t ............. ok
t/stdin.t ............. ok
t/stringify.t ......... ok
t/tainted.t ........... ok
t/write_file_win32.t .. ok
All tests successful.
Files=28, Tests=296, 3 wallclock secs ( 0.07 usr 0.02 sys + 0.72 cusr 0.05 csys = 0.86 CPU)
Result: PASS
URI/File-Slurp-9999.19.tar.gz
/usr/bin/make test -- OK
Running make install
Manifying 1 pod document
Installing /home/mike/perl5/lib/perl5/File/Slurp.pm
Installing /home/mike/perl5/man/man3/File::Slurp.3pm
Appending installation info to /home/mike/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/perllocal.pod
URI/File-Slurp-9999.19.tar.gz
/usr/bin/make install -- OK

brew install abricate --HEAD

==> Installing abricate from tseemann/bioinformatics-linux
abricate: Unsatisfied dependency: File::Slurp etc etc

brew doctor
Your system is ready to brew
brew update
Already up-to-date

brew config
HOMEBREW_VERSION: 1.1.10
ORIGIN: https://github.com/Linuxbrew/brew.git
HEAD: d8c8b867bf99c604c89bc848f58d1fae8afd599c
Last commit: 5 weeks ago
Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core
Core tap HEAD: 9f0d64e6326d616c0c2ceb996d1903b6ae456aec
Core tap last commit: 4 days ago
HOMEBREW_PREFIX: /home/mike/.linuxbrew
HOMEBREW_REPOSITORY: /home/mike/.linuxbrew
HOMEBREW_CELLAR: /home/mike/.linuxbrew/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com
CPU: quad-core 64-bit 0x65e
Homebrew Ruby: 2.3.1 => /usr/bin/ruby2.3
Clang: N/A
Git: 2.7.4 => /usr/bin/git
Perl: /usr/bin/perl
Python: /home/mike/.linuxbrew/bin/python => /home/mike/.linuxbrew/Cellar/python/2.7.13/bin/python2.7
Ruby: /usr/bin/ruby => /usr/bin/ruby2.3
Java: 1.8.0_112
Kernel: Linux 4.4.0-53-generic x86_64 GNU/Linux
OS: Ubuntu 16.04.1 LTS
Codename: xenial
OS glibc: 2.23
OS gcc: 5.4.0
Linuxbrew glibc: N/A
Linuxbrew gcc: 5.3.0
Linuxbrew xorg: N/A

Formats

• asm.{gbk,fna}[.gz]
• ensure same result

Cases

• missing file
• not valid format

There seems to be a small issue with the formatting of the last columns in the card_summary output file header, I believe they are supposed to read smeR, and then sul1, but for me, they appear concatenated, with no tab in between. Extremely minor issue, but I thought I'd let you know!

Thank you, I really appreciate the software!

https://card.mcmaster.ca/download/0/broadstreet-v1.1.9.tar.gz

On Ubuntu 14.04 LTS2 (Biolinux8) and Ubuntu 16.04 I have had to manually install JSON with CPANM to be able to use the "abricate-get_db --db resfinder --force".

Maybe add this to the readme?

"sudo cpanm install JSON".

@Slugger70 reports:

abricate --list
abricate: corrupt database? - /Users/Simon/miniconda3/bin/../db/abricate
argannot:  1749 sequences -  Jul 8, 2017
card:  2124 sequences -  Jul 8, 2017
ncbibetalactamase:  1557 sequences -  Mar 17, 2017
plasmidfinder:  263 sequences -  Mar 19, 2017
resfinder:  2228 sequences -  Jul 8, 2017
vfdb:  2597 sequences -  Mar 17, 2017

I am constructing binary matrix from abricate output and I can't decide what percentages to go with. The idea was to report only genes that has >95% coverage and from that >95% identity. But I am concerned that it could be too strict - what's your opinion on the subject?

@tseemann please lable this "Help wanted"!

Thanks in advance

Just upgraded to version 0.7, and found the summary option is broken.

Rather than making the summary of every genome assembly tested, it only lists the filename with percentages.

Restoring version 0.6 gives correct summary files, so it's not a problem with the source files.

Example:

#FILE	NUM_FOUND	Col(BS512)_1	Col(BS512)_1__NC_010656_dupe	Col(Ye4449)_1	Col156_1	Col8282_1	ColE10_1	ColRNAI_1	ColpVC_1	IncA/C2_1	IncFIB(AP001918)_1	IncFIB(K)_1_Kpn3	IncFIB(S)_1	IncFIB(pB171)_1_pB171	IncFIB(pHCM2)_1_pHCM2	IncFIC(FII)_1	IncFII(S)_1	IncFII(pCTU2)_1_pCTU2	IncFII(pKPX1)	IncFII_1	IncFII_1_pSFO	IncHI2A_1	IncHI2_1	IncI1_1_Alpha	IncI2_1_Delta	IncN2_1	IncN_1	IncP(6)_1	IncQ1_1	IncQ2_1	IncX1_1	IncX1_3	IncX3_1	IncY_1	TrfA_1	pENTAS02_1
filename_plasmidfinder.tsv	35	100.00;100.00	100.00;100.00	100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00	100.00;100.00;98.70;98.70;98.70;98.70;98.70;98.70;98.70;100.00;100.00	98.55	100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00	98.46;100.00;100.00;100.00;100.00;100.00;83.85;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;98.46;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;90.77;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;98.46;100.00;98.46;100.00;100.00;100.00;100.00;100.00;100.00;100.00;83.08;100.00;100.00;83.08;100.00;83.08;100.00;83.85;83.85;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;98.46;100.00;90.77;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;98.46;100.00;98.46;100.00;98.46;100.00;98.46;100.00;98.46;100.00;98.46;100.00;98.46;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;83.85;100.00;100.00;98.46;83.85;100.00;98.46;100.00;100.00;100.00;98.46;100.00;98.46;100.00;100.00;98.46;100.00;100.00;98.46;100.00;98.46;100.00;100.00	100.00;100.00	100.00;100.00;100.00;100.00;100.00	100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00	100.00;100.00;100.00;100.00;100.00;100.00;100.00	100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00	100.00;99.84;99.84;100.00	100.00	99.60;99.60;99.60;99.60;99.60;99.60;99.60;99.60;99.60;99.60;99.60;99.60;99.60;99.60;99.60;99.60	100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00	100.00	100.00	100.00	99.61;99.61;99.61;99.61;99.61;99.61;99.61;99.61;99.61;99.61;99.61;99.61;99.61;99.61;99.61;99.61;99.61;100.00	100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00	100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00	100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00	100.00;100.00	100.00	100.00;100.00;100.00;100.00;100.00;100.00;100.00	100.00	100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;100.00;95.33;100.00	98.67;98.67;98.67;98.67;98.67;98.67;98.67;98.67;98.67;98.67;98.67;98.67	100.00;100.00	100.00;100.00;100.00;100.00;100.00	90.37	100.00;100.00;100.00;100.00;100.00;100.00	99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66;99.66	98.47;98.57;98.57

Just send sequences and add --setupdb option?

Updated their IMP-4 to use the AF244145.1 sequence rather than the previous DQ307573 sequence (with 2 SNPs in it).

Hi @tseemann ,

Feature request: add a new column to the abricate output that contains 'DESCRIPTION' information. For example, the ncbi database has

>ncbi~~~mcr-1~~~A7J11_03461 phosphoethanolamine--lipid A transferase MCR-1
>ncbi~~~mcr-1.2~~~A7J11_03754 phosphoethanolamine--lipid A transferase MCR-1.2
>ncbi~~~mcr-1.3~~~A7J11_04944 phosphoethanolamine--lipid A transferase MCR-1.3

in the headers. I would like to be able to extract from the abricate stdout that mcr-1.3 is a phosphoethanolamine--lipid A transferase

Thanks

While using abricate to get resistance genes out of a set of sequences, I have noticed that card entries do not have aro accessions in the report file, instead have ncbi accessions (which is fine of course). However, aro accessions are also very useful when using card because they allow you to make direct links to CARD website. I have started digging your fasta files and found the one for card. However, each entry is like this one:

>card~~~AAC(1)~~~HM036080:132-597 Acetylation of paromomycin, and apramycin, on the amino group at position 1 in E. coli, Actinomycete, Campylobacter spp.

So, there is no aro accession at all. Therefore for my specific problem I just made a dictionary that matched ncbi accession numbers with the respective aro accession using cards file (available here). I used the aro_index.csv, but original card fastas already have a header like this:

>gb|GQ343019|+|132-1023|ARO:3002999|CblA-1 [mixed culture bacterium AX_gF3SD01_15]

Perhaps you can find a way to maintain these "links" on your card fasta database.

It would make it easier to screen Genbank Assemblies.

A.

Is there anyway to do this?
The script seems to allow for a database update, but it seems to only be for Res-Finder.
Thank you.

Hi Torsten,

I was trying to update the CARD database to the most updated version using the abricate-get_db command but the command failed with the following error:

Downloading: https://card.mcmaster.ca/download/0/broadstreet-v1.1.9.tar.gz
Result: 501
Destination: card.tar.bz2
Filesize:  bytes
tar: card.tar.bz2: Cannot open: No such file or directory

Looks like the CARD database finally made the switch to tar.gz. Can you update the get_db script to change the .bz2 to .gz?

Thanks!

In the output, only the top blast hit is shown.
For some genes eg. blaTEM, if both TEM-1 and TEM-45 were present in a genome, only TEM-1 would be reported. However, the activity and clinical significance of the two beta-lactamases is different.

This is because I have a folder and a README

Issue #38 by @dutchscientist

https://github.com/katholt/srst2/tree/master/data

I propose TSV format for programs that need to parse for available DBs.

I have converted the SerotypeFinder and EcOH (SRST2) databases for E. coli serotyping to Abricate format. Are you interested in such databases to be made generally available? I am happy to share.

Having trouble with the installation?
Used brew initially, had to do cpan -i Slurp/CSV/JSON as well. Then:

brew install abricate --HEAD
==> Installing abricate from tseemann/bioinformatics-linux
==> Installing dependencies for tseemann/bioinformatics-linux/abricate: blast
==> Installing tseemann/bioinformatics-linux/abricate dependency: blast�[39
Error: homebrew/science/blast cannot be built with any available compilers.
Install Clang or brew install gcc

Tried brew install gcc, no joy.

Also tried installing BLAST into home directory.

No luck with git clone:
git clone https://github.com/tseemann/abricate.git./abricate/bin/abricate
Cloning into 'abricate'...
remote: Not Found
fatal: repository 'https://github.com/tseemann/abricate.git./abricate/bin/abricate/' not found

Or with conda:
~/miniconda2/bin$ ls
2to3 cmfetch c_rehash openssl smtpd.py
activate cmpress deactivate pip sqlite3
cmalign cmscan easy_install pydoc tclsh8.5
cmbuild cmsearch easy_install-2.7 python wheel
cmcalibrate cmstat f2py python2 wish8.5
cmconvert conda idle python2.7
cmemit conda-env integron_finder python-config

~/miniconda2/bin$ conda install abricate
Fetching package metadata .............

PackageNotFoundError: Package missing in current linux-64 channels:

• abricate

Close matches found; did you mean one of these?

abricate: fabric

Can you please help? I'm a newbie, working on Ubuntu

Thanks

Hello Torsten,
brew seems not to have hdf5 available. I installed via ubuntu but still not recognized by abricate. Perhaps, the dependecies need to be changed and the place where to find hdf5?

brew install abricate
Updating Homebrew...
==> Installing abricate from tseemann/bioinformatics-linux
Error: No available formula with the name "hdf5" (dependency of tseemann/bioinformatics-linux/abricate)
It was migrated from homebrew/science to homebrew/core.

But COVERAGE only has 2 ?

Example abricate output:

2012-17035.fna	gnl|Prokka|2012-17035_4	51134	51309	aadA1	1-184/972	===...../......	8	18.11	94.565
2012-17035.fna	gnl|Prokka|2012-17035_2	27659	27769	aadA1	679-789/789	............===	0	14.07	99.099
2012-17035.fna	gnl|Prokka|2012-17035_4	52211	53002	aadA2	1-792/792	===============	0	100.00	99.874
2012-17035.fna	gnl|Prokka|2012-17035_4	61539	62354	aph(3')-Ia	1-816/816	===============	0	100.00	100.000
2012-17035.fna	gnl|Prokka|2012-17035_2	37261	38142	blaKPC-2	1-882/882	===============	0	100.00	100.000
2012-17035.fna	gnl|Prokka|2012-17035_2	26775	27614	blaOXA-9	1-840/840	===============	0	100.00	99.881
2012-17035.fna	gnl|Prokka|2012-17035_1	2712753	2713613	blaSHV-11	1-861/861	===============	0	100.00	100.000
2012-17035.fna	gnl|Prokka|2012-17035_3	6395	7237	blaSHV-12	1-861/861	========/======	18	97.91	97.909
2012-17035.fna	gnl|Prokka|2012-17035_2	25215	26075	blaTEM-1A	1-861/861	===============	0	100.00	99.884
2012-17035.fna	gnl|Prokka|2012-17035_4	44636	45295	catA1	1-660/660	===============	0	100.00	99.848
2012-17035.fna	gnl|Prokka|2012-17035_4	51306	51803	dfrA12	1-498/498	===============	0	100.00	100.000
2012-17035.fna	gnl|Prokka|2012-17035_1	4674590	4675009	fosA	1-420/420	===============	0	100.00	98.571
2012-17035.fna	gnl|Prokka|2012-17035_4	59641	60562	mph(A)	1-921/921	========/======	1	100.00	99.675
2012-17035.fna	gnl|Prokka|2012-17035_4	59657	60562	mph(A)	1-906/906	===============	0	100.00	100.000
2012-17035.fna	gnl|Prokka|2012-17035_1	1200950	1202125	oqxA	1-1176/1176	===============	0	100.00	100.000
2012-17035.fna	gnl|Prokka|2012-17035_1	1197774	1200926	oqxB	1-3153/3153	===============	0	100.00	100.000
2012-17035.fna	gnl|Prokka|2012-17035_4	53420	54346	sul1	1-927/927	===============	0	100.00	100.000

However, blaOXA-9 has a TAG stop codon in the middle, probably rendering the gene non-functional. It would be useful feature to see this in the mini-map.

(Ariba currently detects this and outputs it in the table.)

Is it possible to run with multiple databases? I tried to run with all the database using comma to separate the databases , but did not work.

abricate --list gives

abricate: corrupt database? - /usr/local/Cellar/abricate/0.5/bin/../db/abricate

how to resolve it?

Thanks

Hi there,

I tried to update the database with command "abricate-get_db --force --db ncbi", however it failed throwing out 501 https error.
I then installed LWP::Protocol::https via "cpanm LWP::Protocol::https" and turned out the same error message persisted. After that I also tried "sudo cpanm LWP::Protocol::https" which installed it with the other perl location I suppose, but still not working.
Both ways successfully installed LWP::Protocol::https, but still did not resolve the problem.
I'm a bit new to all of these, can someone show me how to resolve it, thanks much!

Yu

0.15s$ bin/abricate --setupdb
Database argannot has not been indexed; formatting now.
sh: 1: makeblastdb: not found
Database card has not been indexed; formatting now.
sh: 1: makeblastdb: not found
Database ncbi has not been indexed; formatting now.
sh: 1: makeblastdb: not found
Database ncbibetalactamase has not been indexed; formatting now.
sh: 1: makeblastdb: not found
Database plasmidfinder has not been indexed; formatting now.
sh: 1: makeblastdb: not found
Database resfinder has not been indexed; formatting now.
sh: 1: makeblastdb: not found
Database vfdb has not been indexed; formatting now.
sh: 1: makeblastdb: not found