RGI (Resistance Gene Identifier) is a robust antimicrobial resistance (AMR) gene predicting tool. It is based on newly curated Comprehensive Antibiotic Research Database (CARD) and allows detection detect AMR genes from thirteen genomes of Pseudomonas strains.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive [user@cn3107 ~]$ module load RGI [+] Loading singularity 3.10.5 on cn4203 [+] Loading RGI 6.0.2RGI is used to predict resistome(s) from protein or nucleotide data based on homology and SNP models.
[user@cn3107 ~]$ rgi -h my_command= exec usage: rgiEnd the interactive session:[ ] commands are: --------------------------------------------------------------------------------------- Database --------------------------------------------------------------------------------------- auto_load Automatically loads CARD database, annotations and k-mer database load Loads CARD database, annotations and k-mer database clean Removes BLAST databases and temporary files database Information on installed card database galaxy Galaxy project wrapper --------------------------------------------------------------------------------------- Genomic --------------------------------------------------------------------------------------- main Runs rgi application tab Creates a Tab-delimited from rgi results parser Creates categorical JSON files RGI wheel visualization heatmap Heatmap for multiple analysis --------------------------------------------------------------------------------------- Metagenomic --------------------------------------------------------------------------------------- bwt Align reads to CARD and in silico predicted allelic variants (beta) --------------------------------------------------------------------------------------- Baits validation --------------------------------------------------------------------------------------- tm Baits Melting Temperature --------------------------------------------------------------------------------------- Annotations --------------------------------------------------------------------------------------- card_annotation Create fasta files with annotations from card.json wildcard_annotation Create fasta files with annotations from variants baits_annotation Create fasta files with annotations from baits (experimental) remove_duplicates Removes duplicate sequences (experimental) --------------------------------------------------------------------------------------- Pathogen of origin --------------------------------------------------------------------------------------- kmer_build Build AMR specific k-mers database used for pathogen of origin (beta) kmer_query Query sequences against AMR k-mers database to predict pathogen of origin (beta) Resistance Gene Identifier - 6.0.2 positional arguments: {main,tab,parser,load,auto_load,clean,galaxy,database,bwt,tm,card_annotation,wildcard_annotation,baits_annotation,remove_duplicates,heatmap,kmer_build,kmer_query} Subcommand to run optional arguments: -h, --help show this help message and exit Use the Resistance Gene Identifier to predict resistome(s) from protein or nucleotide data based on homology and SNP models. Check https://card.mcmaster.ca/download for software and data updates. Receive email notification of monthly CARD updates via the CARD Mailing List (https://mailman.mcmaster.ca/mailman/listinfo/card-l) [user@cn3107 ~]$ wget https://github.com/arpcard/rgi/archive/refs/tags/6.0.2.tar.gz [user@cn3107 ~]$ tar -zxf 6.0.2.tar.gz && rm -f 6.0.2.tar.gz && cd rgi-6.0.2 [user@cn3107 ~]$ ./test.sh =================================== CHECK DEPENDENCIES VERSIONS =================================== my_command= exec blastp: 2.9.0+ Package: blast 2.9.0, build Jun 19 2020 17:01:47 my_command= exec /opt/conda/envs/rgi/bin/bowtie2-align-s version 2.4.2 64-bit Built on default-bf91a638-95fa-4b77-97c5-abccd9855c3e Mon Nov 2 17:44:37 UTC 2020 Compiler: gcc version 7.5.0 (crosstool-NG 1.24.0.131_87df0e6_dirty) Options: -O3 -msse2 -funroll-loops -g3 -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/rgi/include -fdebug-prefix-map=/opt/conda/conda-bld/bowtie2_1604337828546/work=/usr/local/src/conda/bowtie2-2.4.2 -fdebug-prefix-map=/opt/conda/envs/rgi=/usr/local/src/conda-prefix -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 ... Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8} my_command= exec diamond version 2.1.7 my_command= exec samtools 1.9 Using htslib 1.9 Copyright (C) 2018 Genome Research Ltd. my_command= exec bamtools 2.5.1 Part of BamTools API and toolkit Primary authors: Derek Barnett, Erik Garrison, Michael Stromberg (c) 2009-2012 Marth Lab, Biology Dept., Boston College my_command= exec bedtools v2.30.0 my_command= exec jellyfish 1.1.10 my_command= exec KMA-1.3.23 =================================== RGI EXECUTABLE LOCATION =================================== /usr/local/apps/RGI/6.0.2/bin/rgi ... =================================== DOWNLOAD CARD CANONICAL DATA ===================================--2023-06-06 20:38:45-- https://card.mcmaster.ca/latest/data Resolving dtn10-e0 (dtn10-e0)... 10.1.200.192 Connecting to dtn10-e0 (dtn10-e0)|10.1.200.192|:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3896906 (3.7M) [application/x-bzip2] Saving to: ‘card_data.tar.bz2’ 0K .......... .......... .......... .......... .......... 1% 706K 5s 50K .......... .......... .......... .......... .......... 2% 1.39M 4s 100K .......... .......... .......... .......... .......... 3% 62.4M 3s ... 3550K .......... .......... .......... .......... .......... 94% 242M 0s 3600K .......... .......... .......... .......... .......... 95% 215M 0s 3650K .......... .......... .......... .......... .......... 97% 240M 0s 3700K .......... .......... .......... .......... .......... 98% 249M 0s 3750K .......... .......... .......... .......... .......... 99% 249M 0s 3800K ..... 100% 154M=0.3s 2023-06-06 20:38:46 (12.9 MB/s) - ‘card_data.tar.bz2’ saved [3896906/3896906] =================================== DOWNLOAD CARD VARIANTS DATA =================================== --2023-06-06 20:38:47-- https://card.mcmaster.ca/download/6/prevalence-v4.0.0.tar.bz2 Resolving dtn10-e0 (dtn10-e0)... 10.1.200.192 Connecting to dtn10-e0 (dtn10-e0)|10.1.200.192|:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1537517791 (1.4G) [application/x-bzip2] Saving to: ‘prevalence-v4.0.0.tar.bz2’ 0K .......... .......... .......... .......... .......... 0% 701K 35m41s 50K .......... .......... .......... .......... .......... 0% 1.39M 26m40s 100K .......... .......... .......... .......... .......... 0% 42.6M 17m58s ... 1501000K .......... .......... .......... .......... .......... 99% 227M 0s 1501050K .......... .......... .......... .......... .......... 99% 268M 0s 1501100K .......... .......... .......... .......... .......... 99% 260M 0s 1501150K .......... .......... .......... .......... .......... 99% 274M 0s 1501200K .......... .......... .......... .......... .......... 99% 237M 0s 1501250K .......... .......... .......... .......... .......... 99% 264M 0s 1501300K .......... .......... .......... .......... .......... 99% 258M 0s 1501350K .......... .......... .......... .......... .......... 99% 260M 0s 1501400K .......... .......... .......... .......... .......... 99% 233M 0s 1501450K .......... .......... .......... .. 100% 269M=16s 2023-06-06 20:39:04 (89.5 MB/s) - ‘prevalence-v4.0.0.tar.bz2’ saved [1537517791/1537517791] =================================== CARD CANONICAL ANNOTATIONS =================================== COMMAND rgi card_annotation --input card_data/card.json my_command= exec =================================== VERSIONS =================================== COMMAND data_version: 3.2.7 COMMAND variants_version: 4.0.0 =================================== CARD VARIANTS ANNOTATIONS =================================== COMMAND rgi wildcard_annotation --input_directory card_variants --version '4.0.0' --card_json card_data/card.json my_command= exec =================================== CLEAN OLD DATABASES =================================== COMMAND rgi clean --debug my_command= exec INFO 2023-06-07 14:29:59,649 : Remove: /vf/users/user/RGI/rgi-6.0.2/app/_db/16s_rRNA.txt INFO 2023-06-07 14:29:59,652 : Remove: /vf/users/user/RGI/rgi-6.0.2/app/_db/23s_rRNA.txt ... INFO 2023-06-07 14:30:00,144 : Remove: /vf/users/user/RGI/rgi-6.0.2/app/_data/variants INFO 2023-06-07 14:30:00,365 : Cleaned directory: /vf/users/user/RGI/rgi-6.0.2/app/_data/ INFO 2023-06-07 14:30:00,367 : Cleaned directory: /vf/users/user/RGI/rgi-6.0.2/app/_db/ =================================== LOAD DATABASES =================================== COMMAND rgi load --card_json card_data/card.json --card_annotation card_database_v3.2.7.fasta --wildcard_index card_variants/index-for-model-sequences.txt --wildcard_version '4.0.0' --wildcard_annotation wildcard_database_v4.0.0.fasta --debug ...
[user@cn3107 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$