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DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)
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Hisat2-build not working when using the ss and exon option #216

Open sk1350 opened 4 years ago

sk1350 commented 4 years ago

Hello Hisat2-build does not work when I use the ss and exon files produced by extract code. Here is the error I get: Joining reference sequences Time to join reference sequences: 00:00:05 Time to read SNPs and splice sites: 00:00:02 Warning: no variants or splice sites in this graph

Error: Encountered exception: 'Nongraph exception' Command: hisat2-build --wrapper basic-0 -p 5 --ss hisat.ss.txt --exon hisat.exon.txt XT9_1.fa XT9_1_3010_index

The ss and exon tables look fine.

parkchanhee commented 4 years ago

This error message occurs when hisat2 tries to build a graph index and there is no splice site or snps.

There are many cases where hisat2 filters splice site information. If a splice site is in a repetitive sequence region or is in an ambiguous sequence (like 'NNNNN'), hisat2 filters it out. Also, hisat2 filters it if the chromosome name cannot be found in the reference.

It looks like all splice sites information in the hisat.ss.txt has been filtered.