Hi Albert, You are using a very old version of samtools, can you try samtools v0.1.19 (last release before the htslib changes) or try the current release samtools v1.2 (but be careful as some of the options were changed).
Peter On Mon, Jul 6, 2015 at 9:29 AM, Albert Vilella <[email protected]> wrote: > Hi, > > I am just reporting on something I saw over the weekend. A samtools > sort command executed on Friday was still running this morning on a > file that should have taken a relatively short time to sort. > > The input file is about 241M, and this morning, samtools-0.1.18 sort > was producing a file that was 1000x bigger, 236G and growing when I > killed it. > > samtools > > Program: samtools (Tools for alignments in the SAM format) > Version: 0.1.18 (r982:295) > > Usage: samtools <command> [options] > > Command: view SAM<->BAM conversion > sort sort alignment file > mpileup multi-way pileup > depth compute the depth > faidx index/extract FASTA > tview text alignment viewer > index index alignment > idxstats BAM index stats (r595 or later) > fixmate fix mate information > flagstat simple stats > calmd recalculate MD/NM tags and '=' bases > merge merge sorted alignments > rmdup remove PCR duplicates > reheader replace BAM header > cat concatenate BAMs > targetcut cut fosmid regions (for fosmid pool only) > phase phase heterozygotes > > > Not sure if this weird behaviour has been seen before, I am just > reporting it here to log what happened. I will try the same file with > a newer version of samtools as well as sambamba to see if it's > something inherent to the file. > > Thanks, > > Albert Vilella, PhD. > > ------------------------------------------------------------------------------ > Don't Limit Your Business. Reach for the Cloud. > GigeNET's Cloud Solutions provide you with the tools and support that > you need to offload your IT needs and focus on growing your business. > Configured For All Businesses. Start Your Cloud Today. > https://www.gigenetcloud.com/ > _______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
