EXITING because of FATAL ERROR: could not create output file ./_STARtmp//Unmapped.out.mate1.thread14

[Luciano Cosme]

Hi,
  First, thanks so much for this amazing software. I am trying to run STAR and write the results in a hard drive mounted in /media called /media/CLC. I have a script that calls STAR and make directories for each sample, rename the output and move the unmapped reads to a new directory. It worked before, however now it is giving me this error

EXITING because of FATAL ERROR: could not create output file ./_STARtmp//Unmapped.out.mate1.thread14

I thought the problem was the permissions in Linux. So I went ahead and change everything to rwx (STAR executable, script, and the directory where it should right the data). I also change the ownership of everything (using chown root:root). So I suppose to be able to write everything in that hard drive, but I keep getting this error. I tried to run it from other directories but I keep getting the same error.


What exactly does it mean?

./_STARtmp//Unmapped.out.mate1.thread14

Thank you.

[Luciano Cosme]

Hi,
  I found out what the problem was. I was using --runThreadN 23 and creating output as sorted bam. So I changed it to --runThreadN 12 and it works. If I run  --runThreadN 24 it gives me the same error. I am not sure what is the number of threads we can use. I will stick with 12 for now.
Best,

Luciano

[googl...@schwarzelan.de]

Luciano,

yes, this is directly dependend on #of threads,

also see my posts (and Alex' replies) here:

https://groups.google.com/forum/#!topic/rna-star/dr7Kb99E7OA

You could either up ulimit -n (number of open files) to 30k+

or use the latest git-version which allows one to set the number of sorting threads 

separately from mapping-threads...

Best

-Jonathan