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7.7 years ago
ranzhou1005
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0
Hi~ I recently use hisat2 for RNA-seq analysis. First, I execute 'hisat2-build' for generating index with the reference about exonsites and splice sites(hisat2-build --s splicesite.txt --exon exonsites.txt), but it alway can't accomplish. The hisat2 would warn up with "is not reverse-deterministic, so reverse-determinize...", and occupied a lot of memory, the maximum is 400G. the program generated eight .ht2 files ,I don't know if the files are complete.I need help...
i have the same question,i wonder if you have solved the problem ?
Please move your comment to comment section (add comment) as it does not answer the question.
Can you type your entire build command? Memory usage is expected. You can check the manual.
Did you try running your command line on a smaller reference (for eg chromosome Y or on mitochondrial sequence)? if it works, then you may have memory issues (assuming that files and executables are in place). If it fails, then you have issues with code.