stampy error: Mixed single- and paired-end input

[gwo]

Dear forum members,

I am mapping a couple of samples using stampy with bwa mapping. Most of the samples map fine, but in two cases I get the error message:

stampy: Error: Mixed single- and paired-end in input; BWA can't handle this.

The data actually are paired end data, the two matching fastq files have the same number of lines, so I am not sure, what could be the reason for this. Any idea? And what would be the easiest way to extract paired-end or single end reads from the fastq files?

Any hint is highly appreciated.

Best,

Georg

[dpryan]

Can you post the exact workflow you used that produced the error message?

[gwo]

I used fastq files from an Illumina Miseq, I had to trim the sequencing primers using cutadapt, then I ran stampy

here is my command line:

stampy.py --keepreforder --solexa -g Homo_sapiens.GRCh37.71 -h Homo_sapiens.GRCh37.71 -M /fastq_1_sequence.txt.gz,/fastq_2_sequence.txt.gz --bwaoptions="-q10 Homo_sapiens.GRCh37.71.fa" 2>output.stampy.err | samtools view -bh -o output.bam -S - &

stampy version 1.0.11, bwa version 0.5.8c

Cheers,

Georg