hisat2-build 建立索引的時候出現(xiàn) Error: Encountered internal HISAT2 exception (#1)

在使用hisat2建立轉(zhuǎn)錄本的索引文件的時候報錯

extract_exons.py hg19.gff > hg19.exons
extract_splice_sites.py hg19.gff > hg19.ss
hisat2-build --exon hg19.exons -ss hg19.ss -p 6 hg19.fa hg19

錯誤信息為：

Settings:
  Output files: "hg19.fa.*.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: enabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  rn6.ss
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Reference file does not seem to be a FASTA file
  Time to join reference sequences: 00:00:00
Total time for call to driver() for forward index: 00:00:00
Error: Encountered internal HISAT2 exception (#1)
Command: hisat2-build --wrapper basic-0 --exon hg19.exons -ss -p 6 -f hg19.ss hg19.fa hg19
Deleting "hg19.fa.1.ht2" file written during aborted indexing attempt.
Deleting "hg19.fa.2.ht2" file written during aborted indexing attempt.
Deleting "hg19.fa.3.ht2" file written during aborted indexing attempt.
Deleting "hg19.fa.4.ht2" file written during aborted indexing attempt.
Deleting "hg19.fa.5.ht2" file written during aborted indexing attempt.
Deleting "hg19.fa.6.ht2" file written during aborted indexing attempt.
Deleting "hg19.fa.7.ht2" file written during aborted indexing attempt.
Deleting "hg19.fa.8.ht2" file written during aborted indexing attempt.

可是按照hisat2的說明是這樣的

Usage: hisat2-build [options]* <reference_in> <ht2_index_base>

但是更據(jù)報錯信息中的命令卻是這樣，感覺亂套了

hisat2-build --wrapper basic-0 --exon hg19.exons -ss -p 6 -f hg19.ss hg19.fa hg19

解決辦法

hisat2-build hg19.fa --exon hg19.exons -ss hg19.ss -p 6 hg19