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Shamir-Lab / Recycler

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir
BSD 3-Clause "New" or "Revised" License
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Samtools sort changed #46

Closed termithorbor closed 2 years ago

termithorbor commented 2 years ago

Hi,

when I use the following command samtools sort reads_pe_primary.bam reads_pe_primary.sort.bam I get this error:

[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set) -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam --no-PG do not add a PG line --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] -@, --threads INT Number of additional threads to use [0] --verbosity INT Set level of verbosity

When I add -o like this samtools sort reads_pe_primary.bam -o reads_pe_primary.sort.bam it is working. My samtools version is 1.15.

dpellow commented 2 years ago

OK. The instructions were tested for the given samtools version noted. You should use the command compatible with your version of samtools. Note that our tool SCAPP aims to replace Recycler for assembling plasmids in metagenomic samples if that is what you are trying to do.