Question: hisat2-build failed with 'is not reverse-deterministic, so reverse-determinize'2
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gravatar for ranzhou1005
3.2 years ago by
ranzhou10050 wrote:

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...

rna-seq • 1.9k views
ADD COMMENTlink modified 2.1 years ago by yinhongwei19890 • written 3.2 years ago by ranzhou10050

i have the same question,i wonder if you have solved the problem ?

ADD REPLYlink written 2.1 years ago by yinhongwei19890

Please move your comment to comment section (add comment) as it does not answer the question.

ADD REPLYlink written 2.1 years ago by Satyajeet Khare1.5k

Can you type your entire build command? Memory usage is expected. You can check the manual.

ADD REPLYlink written 2.1 years ago by Satyajeet Khare1.5k

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.

ADD REPLYlink written 2.1 years ago by cpad011212k
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