Access to HISAT2 folder under miniconda

Question

[wq]

Hi,

I am learning how to use HISAT2 installed under bioconda.

I am running the following command from an example on the HISAT2 webpage,

$HISAT2_HOME/hisat2-build $HISAT2_HOME/example/reference/22_20-21M.fa --snp $HISAT2_HOME/example/reference/22_20-21M.snp 22_20-21M_snp

In my work environment, I used the following command. I got an error message saying the pkgs sub-folder inside /miniconda3 is not accessible. Any advice on how to solve the problem is appreciated.

hisat2-build $pkgs/hisat2-2.0.5-py27_1/bin/example/reference/22_20-21M.fa --snp $pkgs/hisat2-2.0.5-py27_1/bin/example/reference/22_20-21M.snp 22_20-21M_snp

Settings:
  Output files: "22_20-21M_snp.*.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:
  /hisat2-2.0.5-py27_1/bin/example/reference/22_20-21M.fa
Error: could not open /hisat2-2.0.5-py27_1/bin/example/reference/22_20-21M.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 --snp /hisat2-2.0.5-py27_1/bin/example/reference/22_20-21M.snp /hisat2-2.0.5-py27_1/bin/example/reference/22_20-21M.fa 22_20-21M_snp

Best, Wendy

[WouterDeCoster]

Can you check the variable $pkgs? I suspect it's not set. Just use

echo $pkgs

[Devon Ryan]

Please execute which hisat2-build. From the bioconda recipe, the fasta file will then be /whatever/that/says/example/reference/22_20-21M.fa.