building standard hisat-3n indices with --base-change but not --repeat-index about hisat2 HOT 4 CLOSED

Hello Conner,

I just test the hisat-3n-build --base-change C,T /PATH/reference.fa genome on my side and it works well.

Could you try it again? Make sure you use hisat-3n-build rather than hisat2-build.

Best,
Leo

from hisat2.

Thanks for the quick response Leo! I am running this on a remote computing cluster where I did not install hisat-3n, but it does appear to be version 2.2.1-3n. I ran again and had the same error. I have posted the whole error message below.

Here is the exact code I ran:
hisat-3n-build --base-change C,T /PATH/Homo_sapiens.GRCh38.dna.primary_assembly.fa human.GRCh38.106

Here is the error message:

hisat2-build: unrecognized option '--base-change'
HISAT2 version 2.2.1-3n by Daehwan Kim ([email protected], 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 number of threads
--bmax max bucket sz for blockwise suffix-array builder
--bmaxdivn max bucket sz as divisor of ref len (default: 4)
--dcv 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 SA is sampled every 2^offRate BWT chars (default: 5)
-t/--ftabchars # of chars consumed in initial lookup (default: 10)
--localoffrate SA (local) is sampled every 2^offRate BWT chars (default: 3)
--localftabchars # of chars consumed in initial lookup in a local index (default: 6)
--snp SNP file name
--haplotype haplotype file name
--ss Splice site file name
--exon Exon file name
--repeat-ref Repeat reference file name
--repeat-info Repeat information file name
--repeat-snp Repeat snp file name
--repeat-haplotype Repeat haplotype file name
--seed seed for random number generator
--3N build 3N index rather than standard hisat2 index
--repeat-index-[,-] automatically build repeat database and repeat index, enter the minimum-maximum repeat length pairs (default: 100-300)
-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
Error: Encountered internal HISAT2 exception (#1)
Command: hisat2-build --wrapper basic-0 --base-change T,C /PATH/reference.fa genome --3N

from hisat2.

I guess this is a bug in old hisat-3n version. Could you pull the newest hisat-3n code and try again?

from hisat2.

After pulling the newest version I had no issues. Thanks for the help Leo!

from hisat2.