Question: Bowtie2 Error: *.* has more quality values than read characters
gravatar for rbronste
3 months ago by
rbronste300 wrote:

Running into an error with Bowtie 2 paired end alignment as follows:

bowtie2 -p 12 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail --phred33 --minins 10 --maxins 700 -x /genomes/bowtie2_mm10_index -1  IgG_EB_2_S10_R1_001_adapqual.fastq -2  IgG_EB_2_S10_R2_001_adapqual.fastq -S IgG_male_2.sam

Error: Read NB551387:262:H3FMVBGXC:2:13312:12350:6675 1:N:0:TAGCTT has more quality values than read characters.

terminate called after throwing an instance of 'int' (ERR):    bowtie2-align died with signal 6 (ABRT) (core dumped)

When I do the following to look at the read in the paired fastqs I get this:

grep -A 3 "NB551387:262:H3FMVBGXC:2:13312:12350:6675" IgG_EB_2_S10_R1_001_adapqual.fastq

@NB551387:262:H3FMVBGXC:2:13312:12350:6675 1:N:0:TAGCTT




grep -A 3 "NB551387:262:H3FMVBGXC:2:13312:12350:6675" IgG_EB_2_S10_R2_001_adapqual.fastq

@NB551387:262:H3FMVBGXC:2:13312:12350:6675 2:N:0:TAGCTT




Wondering what may be happening? Thanks.

fastq bowtie2 software error • 196 views
ADD COMMENTlink modified 7 weeks ago by Biostar ♦♦ 20 • written 3 months ago by rbronste300

There appears to be a :2: in the read sequence of the first read. Is that really there or is it a cut and paste error?

ADD REPLYlink written 3 months ago by i.sudbery6.3k

If the sequence on the first read contains XC:2:1 smells like your file is corrupted, hopefully, you have a back-up file with their checksums to validate integrity.

ADD REPLYlink written 3 months ago by JC9.1k

These parsing errors are in my experience a signal of low memory. How much RAM do you have available?

ADD REPLYlink written 3 months ago by ATpoint26k
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