Program options for hisat2: 

/var/spool/slurm/d/job4466820/slurm_script: line 153: -h: command not found


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Program options for hisat2_splice_sites: 

usage: hisat2_extract_splice_sites.py [-h] [-v] [gtf_file]

Extract splice junctions from a GTF file

positional arguments:
  gtf_file       input GTF file (use "-" for stdin)

optional arguments:
  -h, --help     show this help message and exit
  -v, --verbose  also print some statistics to stderr


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Program options for hisat2_build: 

HISAT2 version 2.2.0 by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo)
Usage: hisat2-build [options]* <reference_in> <ht2_index_base>
    reference_in            comma-separated list of files with ref sequences
    hisat2_index_base       write ht2 data to files with this dir/basename
Options:
    -c                      reference sequences given on cmd line (as
                            <reference_in>)
    --large-index           force generated index to be 'large', even if ref
                            has fewer than 4 billion nucleotides
    -a/--noauto             disable automatic -p/--bmax/--dcv memory-fitting
    -p <int>                number of threads
    --bmax <int>            max bucket sz for blockwise suffix-array builder
    --bmaxdivn <int>        max bucket sz as divisor of ref len (default: 4)
    --dcv <int>             diff-cover period for blockwise (default: 1024)
    --nodc                  disable diff-cover (algorithm becomes quadratic)
    -r/--noref              don't build .3/.4.ht2 (packed reference) portion
    -3/--justref            just build .3/.4.ht2 (packed reference) portion
    -o/--offrate <int>      SA is sampled every 2^offRate BWT chars (default: 5)
    -t/--ftabchars <int>    # of chars consumed in initial lookup (default: 10)
    --localoffrate <int>    SA (local) is sampled every 2^offRate BWT chars (default: 3)
    --localftabchars <int>  # of chars consumed in initial lookup in a local index (default: 6)
    --snp <path>            SNP file name
    --haplotype <path>      haplotype file name
    --ss <path>             Splice site file name
    --exon <path>           Exon file name
    --repeat-ref <path>     Repeat reference file name
    --repeat-info <path>    Repeat information file name
    --repeat-snp <path>     Repeat snp file name
    --repeat-haplotype <path>   Repeat haplotype file name
    --seed <int>            seed for random number generator
    -q/--quiet              disable verbose output (for debugging)
    -h/--help               print detailed description of tool and its options
    --usage                 print this usage message
    --version               print version information and quit


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Program options for hisat2_exons: 

usage: hisat2_extract_exons.py [-h] [-v] [gtf_file]

Extract exons from a GTF file

positional arguments:
  gtf_file       input GTF file (use "-" for stdin)

optional arguments:
  -h, --help     show this help message and exit
  -v, --verbose  also print some statistics to stderr


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