Tophat2 ignoring -o and always writing to ./tophat_out

[afkoeppel]

I'm running tophat2, version 2.0.7 on a 64-bit linux server.

Everything seems to be working fine with my alignments, except that the output is always written to "./tophat_out", even when I'm using the -o flag to try to send the output somewhere else.

I'm calling tophat2 as part of a shell script as follows (though I have also tried it outside the script with the actual file paths instead of the variable names and get the same result):

tophat2 $GENOMEDIR/mm9 $workingdir/${fastaheader}read1.cFiltered.Scythed.Sickled.fastq $workingdir/${fastaheader}read2.cFiltered.Scythed.Sickled.fastq -G $GENOMEDIR/mm9.genes.gtf -M -T --no-novel-
juncs --transcriptome-index="$workingdir/transcriptome_data/known" -o "$workingdir/tophat_out"

Also, --transcriptome-index isn't writing anything either. This would have led me to believe that I lack permissions on $workingdir or something like that, except that other parts of the script write to that same directory without a problem. Also, as a workaround, I've just been moving ./tophat_out to $workingdir in the next line of the script and that works fine for the output, but doesn't help for --transcriptome-index since that doesn't seem to be getting written anywhere at all (not even empty directories).

I've also tried variations on the syntax (e.g. with and without quotes, using --output-dir= instead of -o), but nothing seems to coerce it into writing where I want it to.

Any help or advice would be much appreciated.
Thanks

[kevin9y9]

I'm fairly new to this myself, but I'm nearly sure that all the optional commands need to be moved to immediately after "tophat2", and the last three items should always be the genome, the left reads and the right reads.

[afkoeppel]

This did the trick. Thanks so much for your help.