Tophat2 Error "Segment-based junction...... error opening SAM file"

Question

[CraigM]

Hi all,

I've been doing an RNA-Seq alignment with Tophat with 24 samples and one of them is not running for some reason. I'm using the same command line for each sample (with the exception of the file I/Os) and the same genome and transcriptome index.

Command:

tophat2 --transcriptome-index=path/to/transcriptome -p 32 -o tophat_out/sample9/ path/to/genome sample9_1_p.fq.gz sample9_2_p.fq.gz

Error:

[2015-04-16 02:21:08] Searching for junctions via segment mapping
        [FAILED]
Error: segment-based junction search failed with err =1
Error opening SAM file tophat_out/sample9/tmp/right_kept_reads.m2g_um_seg8.bam

I've reran this a couple of times, and on another occasion it failed to open right_kept_reads.m2g_um_seg5.bam

From googling the error people have suggested a problem with the genome or transcriptome index, but the same one has been used to 23 other samples so how could this be?

I've also done a samtools view tophat_out/sample9/tmp/right_kept_reads.m2g_um_seg8.bam to ensure the files actually exist and they do.

Thanks in advance

[CraigM]

To add to this, there is no issue with the FASTQ files either. Both were able to be aligned when using the -T flag in a previous alignment.

Also have read permissions to access the temp bam files.