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saima-tithi / FastViromeExplorer

FastViromeExplorer project. Forked from https://code.vt.edu/saima5/FastViromeExplorer
BSD 2-Clause "Simplified" License
13 stars 2 forks source link

Empty sam file #4

Closed michoug closed 5 years ago

michoug commented 5 years ago

Hi, When running the test example, the pseudoalignments.bam is 1.6 Mb and the FastViromeExplorer-reads-mapped-sorted.sam file is empty. I think that it is due to the samtools software whose options changed between version 1.5 and 1.8/1.9 Best Greg

saima-tithi commented 5 years ago

Hi, Could you please check the kallisto version you are using? pseudoalignments.bam file is produced by kallisto version 0.44 and later. Here for developing FastViromeExplorer we used kallisto version 0.43.1. As in later versions of kallisto, the output format of pseudoalignments is different, our tool is not compatible with later versions of kallisto, please use Kallisto version 0.43.0 or 0.43.1.

michoug commented 5 years ago

Thanks, indeed it worked !

sarahgraff commented 4 years ago

I am having this issue even though I am using Kallisto 0.43.1 - was this updated for a newer version of Kallisto?