bowtie2 inpipe1 inpipe2

Question

[yliueagle]

I used the following bowtie script to do the alignment:

bowtie2 -x ./hg19 -p 22 -1 my_R1_001.fastq.gz -2 my_R2_001.fastq.gz -S out.sam

however, in the out.sam header it looks like this:

@PG     ID:bowtie2      PN:bowtie2      VN:2.2.9        CL:"xx/3.Software_packages/bowtie2-2.2.9/bowtie2-align-s --wrapper basic-0 -x ./hg19 -p 22 -S ./out.sam -1 /tmp/16093.inpipe1 -2 /tmp/16093.inpipe2"

why the original fastq file names were replaced with inpipe1 and inpipe2? How should I avoid this?

@PG     ID:bowtie2      PN:bowtie2      VN:2.2.9        CL:"xx/3.Software_packages/bowtie2-2.2.9/bowtie2-align-s --wrapper basic-0 -x ./hg19 -p 22 -S out.sam -1 my_R1_001.fastq.gz -2 my_R2_001.fastq.gz"

Thanks!

[Ram]

One reason I can think of is that bowtie2 replaces the file with <(gzip -dc file.gz) because the FASTQ file is compressed. If that's the case, there's not much you can do to avoid it except maybe uncompress the FASTQ or check if named pipes bypass that problem for you. In any case, let's see what others say.