Problem with lists of multiple fastq.gz files as input

[Barry Bismuth]

Hi all,

I recently upgraded from version 2.3.0e to the latest 2.3.1z4 version due to improvements in chimeric read placement. However, it appears that under certain conditions, this version no longer deals with multiple fastq.gz input files correctly. For a set of paired end reads, using two lists of comma-separated fastq.gz files as parameters for --readFilesIn, and using the --readFilesCommand zcat option, I get the following errors:
---
test_231__tmp//readsCommand_read2: line 5: test_231__tmp/tmp.fifo.read2: No such file or directory
test_231__tmp//readsCommand_read2: line 6: test_231__tmp/tmp.fifo.read2: No such file or directory
test_231__tmp//readsCommand_read2: line 7: test_231__tmp/tmp.fifo.read2: No such file or directory
test_231__tmp//readsCommand_read1: line 5: test_231__tmp/tmp.fifo.read1: No such file or directory
test_231__tmp//readsCommand_read1: line 6: test_231__tmp/tmp.fifo.read1: No such file or directory
test_231__tmp//readsCommand_read1: line 7: test_231__tmp/tmp.fifo.read1: No such file or directory
---
and only the first file is processed.

This does not seem to happen with lists of ungzipped files, or with very small test files. I can get around this by concatenating all my gzipped files into a single one, but this command line used to work just fine with the 2.3.0e version, so I thought this may be a bug. Has anyone else seen this? I am using the STARstatic executable.

Thanks,
Barry

[Alexander Dobin]

Hi Barry,

this was indeed a bug, thanks for reporting it. Please try this patch, and let me know if it solves the problem.

Cheers

Alex

[Barry Bismuth]

Works perfectly. Thanks, Alex!
Barry

[Clement Kent]

I have been experiencing the same problem Barry Bismuth reported, using the most recent 2.5.4b Linux_x86_64_static/STAR. Has there been a reversion?

Clement Kent

[Clement Kent]

Found problem. My command line looked like this:

STAR --genomeDir "$gdir" --readFilesIn "$2 $3" ...

I changed it to this and it worked:

 

STAR --genomeDir "$gdir" --readFilesIn "$2" "$3" ...

So, no problem.