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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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lumpyexpress - samblaster:input file is empty. #337

Open kaelanelson opened 4 years ago

kaelanelson commented 4 years ago

Hi, I'm following the preprocessing steps with a pre-realigned,recalibrated bam file (so i skip the first pre-processing step) as follows:

Screen Shot 2020-06-10 at 10 31 26 AM

and i run lumpy express as:

Screen Shot 2020-06-10 at 10 36 14 AM

and get the following error:

Screen Shot 2020-06-10 at 10 36 43 AM

however, the files are not empty, so i'm wondering what the issue might be?

sztup commented 2 years ago

Hi, I get the same error message, have you figured out this problem? samblaster shouldn't even run, since we provided disconcordants and splitters bams.