I am newbie to linux and NGS. Whle trying to build an index with hisat2 for my project, im getting following error:

    "Error: could not open 2.fa
    Total time for call to driver() for forward index: 00:00:00
    Error: Encountered internal HISAT2 exception (#1)
    Command: hisat2-build --wrapper basic-0"

the command and output of the terminal is as follows:

    ./hisat2-build /data/memona/reference/1.fa,2.fa,3.fa,4.fa,5.fa,6.fa,7.fa,8.fa,9.fa,10.fa,11.fa,12.fa,13.fa hisat_index

    Settings:
      Output files: "hisat_index.*.ht2"
      Line rate: 6 (line is 64 bytes)
      Lines per side: 1 (side is 64 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:
      /data/memona/reference/1.fa
      2.fa
      3.fa
      4.fa
      5.fa
      6.fa
      7.fa
      8.fa
      9.fa
      10.fa
      11.fa
      12.fa
      13.fa
    Error: could not open 2.fa
    Total time for call to driver() for forward index: 00:00:00
    Error: Encountered internal HISAT2 exception (#1)
    Command: hisat2-build --wrapper basic-0 /data/memona/reference/1.fa,2.fa,3.fa,4.fa,5.fa,6.fa,7.fa,8.fa,9.fa,10.fa,11.fa,12.fa,13.fa hisat_index


the hisat2-build file have all the permissions

    -rwxrwxrwx 1 memona memona     2807 Mar 12  2016 hisat2-build

need kind help to resolve the issue


Hi,

You're missing one thing with your parameter expansion in bash. Try the following commnd line:

    ./hisat2-build /data/memona/reference/{1.fa,2.fa,3.fa,4.fa,5.fa,6.fa,7.fa,8.fa,9.fa,10.fa,11.fa,12.fa,13.fa} hisat_index

It should be better, as I think all your fasta files are in the reference directory.
Have a look at this conversation in [Stack][1]


  [1]: https://stackoverflow.com/questions/5349718/how-can-i-repeat-a-character-in-bash#5349842