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Hey there - I just hit a snag that is partially my fault, but I'm wondering if the raw FASTQS from CASAVA 1.8.4 can be used with bcbio? I hit this error that my read pair-names don't match. Which is k…
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Hi -
I am testing bcbio at the Texas Advanced Computing Center at UT Austin. We are looking into offering this package to our user community. I did an isolated install without any problems, and now…
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The following 2 tests are failing.
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## FAIL: Make sure data set compression behaves correctly.
Traceback (most recent call last):
File "/home/glebk/Projects/churchlab/genome-designer-v2/genome_de…
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While running some tests, I've come across several files that make quip crash. The errors seem to be dependent on the name of the files, although I haven't been able to determine a pattern for what co…
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Most importantly, should use the proper file_transaction function from bcbio.distributed.transaction. Otherwise, this doesn't work with distributed mode. Currently broken.
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I am evaluating quip for possible installation on a High Performance Computing cluster available to investigators at the National institutes of Health.
Using quip to compress a SAM file obtained from…
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During our test on quip compression of 16 fastq files, one file failed. The quip application hangs there. Do we have to take note of anything during the usage of -a during compression.
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- [x] title for Paul ASAP
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Hello, I understand SamToFastq.jar is part of Picard, but I just tried running the example exactly as you suggest and got the following error:
[Wed Feb 15 11:09:17 PST 2012] net.sf.picard.sam.SamToFa…