error bowtie2-align exited with value 134

Question

[Lila M]

Hi there, I'm using bowtie2 to align some fastq files downloaded from ENA

I've first run a quality check to see if there is something annoying, but in general terms it is fine. Then, I've run bowtie-2 as follow:

bowtie2 -x human_index_bowtie/human_index_bwt -U SRR11557616.fastq.gz -S 5h.sam

But I got this error message:

Error: Read SRR11557616.1 ugc_599_6_F3_0002_0/1 has more quality values than read characters.
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134

the head of the file is a bit weird:

head -n 8

@SRR11557614.1 ugc_599_3_F3_0001_0 length=74
T3.0321.1000.133...11...011..20...11...21...10...11...31....0....2....1....
+SRR11557614.1 ugc_599_3_F3_0001_0 length=74
!aB_aaaBa^aQBWaYBBBaYBBBOa_BBWSBBBKaBBBNWBBBWOBBBS^BBBN`BBBBSBBBBPBBBBaBBBB
@SRR11557614.2 ugc_599_3_F3_0001_1 length=74
T2.3313.1031.030...30...231..10...22...00...02...22...13....0....2....2....
+SRR11557614.2 ugc_599_3_F3_0001_1 length=74
!aBaaaaBaa_]BPa^BBBbaBBBaaaBBaaBBB\`BBBa\BBBaaBBBaaBBBWPBBBBaBBBBaBBBBaBBBB

Any ideas how to solve the problem? or I should select a different file?

Thanks!

Answer 1

[ATpoint]

The problem is that this is a colorspace file (like ABI SOLiD system, not Illumina), and bowtie2 does not support colorspace alignment. bowtie (aka bowtie1) used to support it, but support got dropped in recent versions afaik.

See: http://bowtie-bio.sourceforge.net/news.shtml

Colorspace support was dropped in versions 1.3.0 and later so you would need to download a version prior to that, then build an index bowtie-build with the -C option to enable colorspace, and then align your data. See manual for details, I never used colorspace myself.

[Lila M]

Thank you for the tip!! And do you know it it would be possible to remove the ugc_599_3_F3_0001_0 with a zgrep command or something similar?

[ATpoint]

As I said, the error comes from the sample being a colorspace file, it is not a problem with the file itself, therefore just change aligner and it should work without manipulating the file.