Question: Bowtie memory warning
0
gravatar for umn_bist
3.0 years ago by
umn_bist320
umn_bist320 wrote:

I am aligning my files with bowtie 1.0.0 via our HPC.

bowtie /UCSC/hg19/Sequence/BowtieIndex/genome -p 16 --chunkmbs 16 -t -m 1 -S --max ${file1:0:9}_multimap.fastq -1 ${file1} -2 ${file2} ${file3}

With or without --chunkmbs, I still get the warning. I have tried reducing the amount of threads (-p 4) but still no luck.

Warning: Exhausted best-first chunk memory for read SRRXXXXXX.93100 HWI-ST706:161:C11YEACXX:5:1101:3338:27152 length=101/1 (patid 89557); skipping read
Warning: Exhausted best-first chunk memory for read SRRXXXXXX.93659 HWI-ST706:161:C11YEACXX:5:1101:15215:27237 length=101/1 (patid 89708); skipping read
Warning: Exhausted best-first chunk memory for read SRRXXXXXX.93679 HWI-ST706:161:C11YEACXX:5:1101:15767:27194 length=101/1 (patid 89728); skipping read
Warning: Exhausted best-first chunk memory for read SRRXXXXXX.93748 HWI-ST706:161:C11YEACXX:5:1101:17333:27035 length=101/1 (patid 89794); skipping read
bowtie • 2.0k views
ADD COMMENTlink modified 3.0 years ago by Istvan Albert ♦♦ 80k • written 3.0 years ago by umn_bist320
1

Can you try a higher number --chunkmbs 200 ? There are indications that this fixes the problem.

ADD REPLYlink written 3.0 years ago by genomax65k

Test sample. This is a deleted post.Test sample. This is a deleted post.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by umn_bist320

Hi, I have got the same problems. I try --chunkmbs 1000, -p 5, it is still warning.

ADD REPLYlink written 20 months ago by Francis10
1
gravatar for Govardhan Anande
3.0 years ago by
Australia
Govardhan Anande130 wrote:

you can try bowtie2, this problem is fixed in it.

Few modification in following command will do

bowtie2 -p 16 -N 1 -x $Bowtie2Index -S AlignesReads.sam -1 $R1File -2 $R2File
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Govardhan Anande130
0
gravatar for jotan
3.0 years ago by
jotan1.2k
Australia
jotan1.2k wrote:

I see those warnings all the time for unmappable reads. I still get good mapped data. Are you getting any mapped reads? What percentage?

ADD COMMENTlink written 3.0 years ago by jotan1.2k
0
gravatar for Biogeek
3.0 years ago by
Biogeek350
Biogeek350 wrote:

Sometimes in the job queue I've found if my chunkmbs is fine, lower your threads around ten less than the server allocation. Generally helps me.

ADD COMMENTlink written 3.0 years ago by Biogeek350

@umn_bist has said in OP that lowering the # of threads to 4 did not help.

ADD REPLYlink written 3.0 years ago by genomax65k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 931 users visited in the last hour