Open GoogleCodeExporter opened 9 years ago
Hi @saddy01
Did the crash happen at the genome generation step?
Could you please share with me the .fasta file that caused the crash, so that I
can replicate the problem.
Thanks
Alex
Original comment by adobin@gmail.com
on 12 Feb 2013 at 2:24
Hi,
I have the same problem. My reference genome is about 300.000 fasta sequences
and about 300MB in size.
I get this message:
Feb 18 11:25:11 ..... Started STAR run
Feb 18 11:25:11 ... Starting to generate Genome files
/var/spool/slurmd/job1306271/slurm_script: line 9: 12129 Killed
Jon
Original comment by jon.br...@gmail.com
on 18 Feb 2013 at 10:28
It crashes at genome generation. I'm sorry I can't share my file. But I think
it should be fine if you generate a large enough fasta (many short sequences)
with random bases.
Original comment by sadd...@gmail.com
on 19 Feb 2013 at 12:44
@saddy01
This is likely to be insufficient RAM problem. STAR bins genome sequence in a
way that each chromosome (contig) starts at a new bin, which creates an
overhead of Nchromosomes*BinSize, where BinSize=2^genomeChrBinNbits. By
default, --genomeChrBinNbits = 18.
I suggest that you try a much smaller value of --genomeChrBinNbits 12. This
would require just a few GB of RAM and should allow you to generate the genome
files. I have not tried STAR with more than 50,000 contigs, and I suspect there
might be significant slowdown in the mapping speed when the number of contigs
is too big.
Please check this discussion thread
http://seqanswers.com/forums/showpost.php?p=96821&postcount=16
If this still does not work, please generate "the random" genome matching the
sizes of your real genome contigs, check that it still fails to run, and send
me the genome. I need to replicate the problem to fix it.
Original comment by adobin@gmail.com
on 20 Feb 2013 at 2:39
Original issue reported on code.google.com by
sadd...@gmail.com
on 12 Feb 2013 at 10:18