I'm getting the most random error on my genome build the output is killer 9, i've seen very conflicting reports on stackexchange and the goggles, does anyone have advice on what this means and how i can fix or look into this??
It outputs .ht2 files but is missing some of them. It only outputs the 1,2,3,4,7,8 .ht2 files (missing 5
D-128-95-53-182:mm9 rehlab$ /Applications/hisat2//hisat2-build -p 4 genome.fa --ss genome.ss --exon genome.exon test/genome_tran Settings: Output files: "test/genome_tran.*.ht2" Line rate: 7 (line is 128 bytes) Lines per side: 1 (side is 128 bytes) Offset rate: 4 (one in 16) FTable chars: 10 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: genome.fa Reading reference sizes Time reading reference sizes: 00:00:33 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:18 Time to read SNPs and splice sites: 00:00:02 Killed: 9