Bowtie 2 error?

Question

[star]

I have run Bowtie2 for aligning ChIP-seq data and in one data I faced the below error Error: Read SN7001318:103:H86L8ADXX:2:2102:16521:69527 1:N:0:8 has more read characters than quality values.

terminate called after throwing an instance of 'int'

Aborted (core dumped)

(ERR): bowtie2-align exited with value 134

I like to know, can I continue with the output of bowtie (I still have .bam file) or I should remove related read?

[ATpoint]

In my experience that happens when you are out of memory. Should check memory consumption first. Next, grep out that read: zgrep 'SN7001318:103:H86L8ADXX:2:2102:16521:69527' your.fastq.gz and check if it is malformatted.

[star]

Yes, I have enough, at least for a .bam file.

[GenoMax]

But perhaps not enough for the file to be written completely and then have the process exit normally? As of now the aligner is crashing without a normal program ending.

Note: Assuming the read checks out as correct/normal using @ATPoint's command. Add -A 3 to that command to get the full fastq record for that ID.

[star]

Thanks for reply.

I did it and I think it does not have enough quality score.

$ grep '@SN7001318:103:H86L8ADXX:2:2102:16521:69527' -A 3 data.fastq

@SN7001318:103:H86L8ADXX:2:2102:16521:69527 1:N:0:8

AAAAGAAAGCCCATGGAAGTGAGGCATTTTGTGCTGCAGTCACACAAGATGGAATTCAAGACCTCAACAGTGCACAAGTTTACCTCCACCAATAATCAGA

+

BBBFFFFFFFFFFIIIIIIBFFIIIIIIIIIFFIII

Shall i ignore it?

[ATpoint]

Try running repair.sh from bbmap and then check how many reads have been eliminated. If it is a minor number, just ignore it.

[star]

It is only one read (last read). Would you please let me know , How Can I remove it?

[GenoMax]

That may be an indication that even the trimming may have not been complete and resulted in an incomplete fastq record?

[ATpoint]

head -n -4 data.fastq

I still would re-do the trimming and pipe it directly to bowtie2 like (given your trimmer supports writing to stdout, cutadapt does)

trimmingtools (options...) your_original.data | bowtie2 (options) -U - | samtools view -o out.bam