hisat2-build 建立索引的时候出现 Error: Encountered internal HISAT2 exception (#1)

在使用hisat2建立转录本的索引文件的时候报错

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

错误信息为：

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的说明是这样的

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

但是更据报错信息中的命令却是这样，感觉乱套了

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

解决办法

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