As mentioned in the paper I first extracted splice-sites and then exons. Next I used hisat2-build
hisat2-build --ss gencode.v27.primary_assembly.annotation.ss --exon gencode.v27.primary_assembly.annotation.exon annot_AND_refFASTA/Homo_sapiens.GRCh38.dna.primary_assembly.fa Hisat2index
After few minutes this is what I saw:
Strings: unpacked Local offset rate: 3 (one in 8) Local fTable chars: 6 Local sequence length: 57344 Local sequence overlap between two consecutive indexes: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: annot_AND_refFASTA/Homo_sapiens.GRCh38.dna.primary_assembly.fa Reading reference sizes Time reading reference sizes: 00:00:34 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:01:10 Time to read SNPs and splice sites: 00:00:01 Killed
Does Killed mean there is some error?
But I see files like Hisat2index.0.rf, Hisat2index.1.ht2, Hisat2index.2.ht2, Hisat2index.3.ht2, Hisat2index.4.ht2, Hisat2index.5.ht2, Hisat2index.6.ht2, Hisat2index.7.ht2, Hisat2index.8.ht2
Did everything went well or do I need to fix something?