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Understand your transcriptome assembly
http://hibberdlab.com/transrate
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SNAP error in Transrate with large dataset #235

Open upendra2020 opened 4 years ago

upendra2020 commented 4 years ago

Hi,

I am having this SNP error (I found this in the sanp.log file) when I ran Transrate on a large dataset.

Loading index from directory... 0s.  193003239 bases, seed size 23
Aligning.
Welcome to SNAP version 1.0dev.96.

Failed to decompress BAM file at offset 4487905280
SNAP exited with exit code 1 from line 1930 of file SNAPLib/DataReader.cpp

The Transrate finishes well on a smaller subset of the dataset but not with the larger dataset. I googled but I couldn't find a solution to this problem. Is it something to do with memory?

Please help.

Thanks

lmuenter commented 3 years ago

Hi, try downloading the Oyster River Protocol and use the packaged Transrate.