Bowtie memory warning

Question

[umn_bist]

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

[GenoMax]

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

[umn_bist]

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

[Francis]

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

Answer 1

[Govardhan Anande]

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

Answer 2

[jotan]

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

Answer 3

[Biogeek]

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.

[GenoMax]

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