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.
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