yoda-usc

Requirements:

1. Install Docker

Usage:

1. docker run --name yoda-usc -dit bberenberg/yoda-usc bash
2. docker exec -it yoda-usc /bin/bash
3. Download data from https://www.ncbi.nlm.nih.gov/sites/batchentrez and get the URL for the file you need
   • Example for Firefox (2 is a right click):
4. Run this command but replace with the URL from the previous step wget 'https://www.ncbi.nlm.nih.gov/projects/r_gencoll/ftp_service/nph-gc-ftp-service.cgi/?HistoryId=MCID_600d998359bf921f582c9124&QueryKey=6&ReleaseType=GenBank&FileType=GENOME_FASTA&Flat=true' -O ~/genome-data/genome.tar
5. tar -x -f ~/genome-data/genome.tar -C ~/genome-data/
6. gunzip ~/genome-data/ncbi-genomes-2021-01-24/*.gz
7. nohup ~/.local/bin/kaptive.py -v -t 8 -k ~/kaptive/Acinetobacter_baumannii_k_locus_primary_reference.gbk -a ~/genome-data/ncbi-genomes-2021-01-24/*.fna -o ~/output/ &> ~/output/console.log &
   • Review the Kaptive options. In particular, the above command uses -t 8 which means 8 threads in parallel. This number should not exceed the number of available cores on your system / available to docker.
8. Monitor what is happening with the following options
   • See what is being logged less +F ~/output/console.log (this takes a few minutes to show anything)
   • See a live number of the items that have been processed watch 'grep "Assembly:" ~/output/console.log | wc -l'
     • You are waiting for it to get to whatever number you get when you run this command ls -l ~/genome-data/ncbi-genomes-2021-01-24/*.fna | wc -l
9. Once this is done, you can compress everything using a command like tar -czvf ~/output.tar.gz ~/output/ then push it to a temporary host curl bashupload.com -T ~/output.tar.gz which will give you a link like http://bashupload.com/kjSHb/output.tar.gz which you can then download.

Reset:

1. rm -rf ~/*.fasta ~/kaptive_temp_* ~/output_table.txt ~/output/* ~/genome-data/genome.tar
2. Go to step 6 above

Uses:

• Kaptive - Make sure to read the portion on citation
• Biopython
• Blast+