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Weeks-UNC / shapemapper2

Public repository for ShapeMapper 2 releases
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memory error #11

Open xfliu1995 opened 5 years ago

xfliu1995 commented 5 years ago

Too much memory is occupied by software operation, when mapping by STAR. This often causes software to fail.How do you limit the maximum amount of memory that your software can use while it is running?

shapemapper commented 5 years ago

What are your alignment target sequences?

If you're attempting to align against a large number of transcripts, see FAQ. On the other hand, if you're trying to align against a small number of large sequences (for example the human genome), the aligner index will just require a lot of memory (~30Gb in the case of the human genome), and that's not easily worked around without changing the aligner.

shapemapper commented 5 years ago

I should also add that you can adjust the speed/memory tradeoff with the --genomeSAindexNbase parameter, which is passed through to STAR during the genome index building phase.

xfliu1995 commented 5 years ago

When I add --genomeSAindexNbase parameter for shapemapper2，shapemapper2 running error. Traceback (most recent call last): File "/BioII/lulab_b/shibinbin/projects/shapemap/python/cli.py", line 108, in run(sys.argv) File "/BioII/lulab_b/shibinbin/projects/shapemap/python/cli.py", line 46, in run pipeline = ap.construct(rest_args) File "/BioII/lulab_b/shibinbin/projects/shapemap/python/pyshapemap/pipeline_arg_parser.py", line 595, in construct params, fastqs = parse_args(args) File "/BioII/lulab_b/shibinbin/projects/shapemap/python/pyshapemap/pipeline_arg_parser.py", line 440, in parse_args raise RuntimeError("Error: unrecognized argument(s): {}".format(rest)) RuntimeError: Error: unrecognized argument(s): ['--genomeSAindexNbases']

shapemapper commented 5 years ago

Are you running the most recent version of shapemapper?