Hi Martin
Thanks for the suggestion - I'll give it a try!
Best
Sergej
Dr. Sergej Nowoshilow
Post-doc in Tanaka Lab
Elly Tanaka group
Animal models of regeneration
Campus-Vienna-Biocenter 1
1030 Vienna
email: sergej.nowoshi...@imp.ac.at
phone: +43 (0) 1 79730 3203
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Am 10.03.18, 12:51 schrieb "Martin MOKREJŠ" <mmokr...@gmail.com>:
Hi Sergei,
maybe you want to try biobambam2 (based on libmaus2). The bamsort is IMO
superior to samtools. The tricks are to increase write chunk sizes. You can
eventually for mu Closed issue on github under biobambam2 project where I
experienced performance issues, resulting in the below tweaks.
Nowoshilow,Sergej napsal(a):
>
> The reads map beyond 1,073,741,824.
>
>
>
> I guess I’ll just write a small sorting utility.
take_memory=57344 # * 1024 = 56GB through bamsort
sort_bam_file(){
# samtools sort of a 149GB BAM file takes 1.2TB RAM and uses only a
single thread despite '-@ 15' argument
# samtools sort -@ $xthreads -m "$gb_mem_per_thread"G -O bam -T "$1" -o
"$2".sorted.bam "$2".bam || exit 255
LIBMAUS2_POSIXFDINPUT_BLOCKSIZE_OVERRIDE==1m
export LIBMAUS2_POSIXFDINPUT_BLOCKSIZE_OVERRIDE
bamsort SO=coordinate blockmb="$take_memory"
sortthreads="$sort_threads" inputthreads="$input_threads"
outputthreads="$output_threads" level=9 index=1 I="$2".bam O="$2".sorted.bam ||
exit 255
}
sort_bam_file_by_name(){
# samtools sort of a 149GB BAM file takes 1.2TB RAM and uses only a
single thread despite '-@ 15' argument
# samtools sort -@ "${xthreads}" -n -m "${gb_mem_per_thread}"G -O bam
-T "$1" -o "$2".namesorted.bam "$2".bam || exit 255
LIBMAUS2_POSIXFDINPUT_BLOCKSIZE_OVERRIDE==1m
export LIBMAUS2_POSIXFDINPUT_BLOCKSIZE_OVERRIDE
bamsort SO=queryname blockmb="$take_memory" sortthreads="$sort_threads"
inputthreads="$input_threads" outputthreads="$output_threads" level=9 index=1
I="$2".bam O="$2".namesorted.bam || exit 255
}
Hope this helps,
Martin
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