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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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fastq read limit for rgi bwt? #202

Closed annettemcgrath closed 10 months ago

annettemcgrath commented 1 year ago

Hi, I have been trying to run rgi bwt on trimmed metagenomic reads. The input paired end illumina read files are big: I have been using files containing from 65M reads to 122M reads each. I also have files with >300M reads to process.

Analysis proceeds through the sam, bam file creation quickly but hangs once bwa.model_species_data_type.temp.txt bwa.reference_mapping_stats.txt bwa.coverage_all_positions.summary.temp.txt bwa.coverage_all_positions.temp.txt files are created until the script times out. This happens for both kma and bwa. I have not tried bowtie.

I have used subsets of the data - 50M, 20M and 10M paired reads - and get the same behaviour, again with both kma and bwa.

So far the only read set that has successfully completed is a 1M paired read subset.

I am using RGI 6.0.1 with a local database, including wildcards.

Thanks for your help

raphenya commented 1 year ago

@annettemcgrath Is it possible to send me the 10M paired reads so that I can test them? Please also send me the commands you are using. Cheers.

github-actions[bot] commented 10 months ago

Issue is stale and will be closed in 7 days unless there is new activity