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sanger-pathogens / ariba

Antimicrobial Resistance Identification By Assembly
http://sanger-pathogens.github.io/ariba/
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Use ariba run for several isolates in batch #262

Closed BaMagalhaes closed 5 years ago

BaMagalhaes commented 5 years ago

I would like to check resistance in my isolate collection (74 isolates) by performing ariba run on all isolates at the same time. However, I would like to have a report.tsv for each isolate individually, in order to create a presence/absence table.

I have tried two ways: 1- Concatenation of the forward and reverse reads in two files. However, I only get one report of the pooled resistance of all isolates; 2- The following command: $ docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/ariba ariba run --verbose /data/out.card.prepareref /data/_R1.fastq.gz /data/_R2.fastq.gz /data/out_individual_st1076.run But it doesn't detect the reads, which are on /home/ubuntu/data:/data.

Do you have any suggestion?

kpepper commented 5 years ago

Hi @BaMagalhaes,

  1. Use a bash "for" loop to call ariba run via the docker command, for each of your isolate files, specifying a different output directory for each run (e.g. use a counter to append to the output directory name) - so that you end up with one output directory & report per isolate. You could also do this easily if you have access to a compute farm, via bsub.
  2. How do you mean it doesn't detect the reads - do you get an error reported? Your files are in the /home/ubuntu/data folder?
kpepper commented 5 years ago

Closing this issue, as it's now several months old.