Comments (4)
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.
Related Issues (20)
- Output files(.snp, .haplotype) of hisat2_extract_snps_haplotypes_*.py are empty
- Please add the pbat option of hisat-3n
- A question about methylation information extraction
- Any plans to support Apple Silicon architecture? HOT 1
- Installation Issue Error 1 - make HOT 1
- -np argument seemingly not working
- ERR): "fastq file.fastq" does not exist. Exiting now ...
- [Bug Report] hisat2-align exited with value 137, space complexity of hisat2
- hisat2 location does not exist
- Hisat-3N mapping quality
- hisat2-build index for circRNA-seq
- hisat2-build failed for Segmentation fault
- [Future request] hisat-3n table option to report conversions summarized to genomic feature or reads counts
- Issue with hisatgenotype HOT 1
- Mapping using different parameters --very-sensitive and default
- (ERR): "ref.genome" does not exist Exiting now ...
- --directional-mapping-reverse vs. --rna-strandness on HISAT3N
- Question about calculation of base counts in hisat3Ntable
- mkfifo failed error and change $temp_dir HOT 1
- Question about Hisat-3N align
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from hisat2.