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STAR test script is not working #4

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friend1ws opened this issue Jan 22, 2018 · 6 comments
Closed

STAR test script is not working #4

friend1ws opened this issue Jan 22, 2018 · 6 comments
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@otiai10
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@friend1ws
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awsub STAR test does not seem to work well currently.
When I perform the test script modyifing the paths of the output directory of task file,
following message appears:

?download failed: s3://hgc-otiai10-test/examples/genomon_rna/db/GRCh37.STAR-2.5.2a/SA to tmp/GRCh37.STAR-2.5.2a/SA [Errno 28] No space left on device

and empty bam file is copied to the S3.
@otiai10 otiai10 self-assigned this Jan 22, 2018
@otiai10 otiai10 added the bug label Jan 22, 2018
@otiai10
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otiai10 commented Jan 22, 2018

seems a bug of quick guide text

@friend1ws
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I thought this is related to the default storage size specified to EC2 by docker-machine. The document of docker-machine says the default size is 16GB for Amazon EC2. This is not sufficient for downloading STAR index files..

@otiai10
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otiai10 commented Jan 22, 2018

ah, I'd add more options. thanks

@friend1ws
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But in that case, why awsub worked well at first? The storage size option is hard coded before and got deleted at some point?

@otiai10
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otiai10 commented Jan 22, 2018

I suspect this commit b32db0c

@otiai10 otiai10 mentioned this issue Jan 22, 2018
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otiai10 added a commit that referenced this issue Jan 22, 2018
@otiai10
Enable specifying disk size as optional flag
e5a726c 
Related #4
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otiai10 commented Jan 22, 2018

seems fixed. plz check https://github.com/otiai10/awsub/tree/master/test/star
@friend1ws

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