So I've been doing RNA-seq analysis using tophat on a Ubuntu virtual machine, using shared folders to hold the fastq files and the indexes.
I noticed that it was taking an unordinate amount of time at any step that would involve index building using bowtie-build if the said index was on the shared folder, but not the local virtual machine one. This involve transcriptome index building, which can be circumvented, but also splice junction index building, if the saving folder for the analysis happen to be on a shared drive.
Specifically, the process seem to hang at a bowtie --sam /indexOnTheVmFolder/indexName /dev/null, after the index was successfully built. Linux process reports 'rtR0SemEventMultiLnxWait.isra.2' as a waiting channel. If I replicate the same command piping to the screen, I get the output, but then it hangs at the end of the SAM header.
Obviously all of this can be circumvented by using the drive in the virtual machine, but you might want to find the cause of this in case it happens in other scenarios.
Latest versions of everything (samtools 0.1.19, bowtie 1.0.0, tophat 2.0.9). Tried recompiling without spinlock, same effect. This problem happened only upon upgrading versions of everything, so thus far I can't pinpoint what upgrade caused it, but it was definitely working with previous versions of bowtie/tophat. I'll investigate that.