Hey Alex,
I am having problems indexing h19 on ec2 (m3.2xlarge) with STAR_2.3.0e_r291.
Any thoughts on what is going on? There is 31GB of RAM, so it should all fit:
cat /proc/meminfo | grep Mem
MemTotal: 30828584 kB
MemFree: 29358328 kB
Log.out:
Aug 05 00:41:01 ..... Started STAR run
Aug 05 00:41:01 ... Starting to generate Genome files
Aug 05 00:42:23 ... starting to sort Suffix Array. This may take a long time...
Aug 05 00:42:44 ... sorting Suffix Array chunks and saving them to disk...
Aug 05 01:07:44 ... loading chunks from disk, packing SA...
Aug 05 01:12:00 ... writing Suffix Array to disk ...
Aug 05 01:13:46 ... Finished generating suffix array
Aug 05 01:13:46 ... starting to generate Suffix Array index...
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
run.sh: line 5: 11810 Aborted STAR --runMode genomeGenerate
--genomeDir .../human_g1k_v37/star/ --genomeFastaFiles
....human_g1k_v37/human_g1k_v37.fasta --sjdbGTFfile .../human_g1k_v37/...gtf
--runThreadN 8
Original issue reported on code.google.com by nilsho...@gmail.com on 5 Aug 2014 at 1:24
Original issue reported on code.google.com by
nilsho...@gmail.comon 5 Aug 2014 at 1:24