Comments (2)
infphilo
commented on July 22, 2024
Thanks for the detailed info!
First I need to reproduce the problem so that I can know where to put warning or error messages. How did you get those extra MHC (or HLA) sequences?
from hisat2.
sklages
commented on July 22, 2024
We are using Ensembl's GRCh37, ftp://ftp.ensembl.org/pub/grch37/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.toplevel.fa.gz.
Here I extracted all main chromosomes plus HSCHR6_MHC* sequences (7x).
I ran hisat2-build with --ss and --exon. As it successfully created the index when I ran hisat2-build on a "himem machine", I assume my colleague ran out of memory on a less potent server. Nevertheless he wasn't aware of any error occuring in the build process... so it was probably not very obvious ;-)
from hisat2.
Related Issues (20)
- hisat-3n conda installation HOT 3
- How to determine correct RNA strandness for single end reads?
- BUG: exons and splice sites don't raise an error when supplied as the index
- long processing time solved by --no-temp-splicesite
- hisat-3n for RNA align HOT 5
- Ensembl uses a one-based coordinate system, whereas UCSC uses a zero-based coordinate system.
- error 134
- hisat-3n directional-mapping and repeat mode on single-cell methylome data HOT 2
- (ERR): ValueError: invalid literal for int() with base 10: '.' HOT 1
- Hisat2 does not align almost exact reads with snptran index
- forks not cleaned up when `-x` passed file that does not exist
- libc++abi: terminating in hisat-3n-table HOT 5
- Bam output?
- hisat2 command error
- Genome Indexing - Encountered internal HISAT2 exception (#1) HOT 2
- `hisat-3n-table` can not parse base quality correctly HOT 1
- directional-mapping mode is not consistent is flag and YZ tag.
- Issue with aligning with hisat2
- Any plans for supporting mac arm architecture?
- (ERR): hisat2-align died with signal 6 (ABRT) (core dumped) HOT 3
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.