Comments (4)
Hi @ewallace,
Sorry for the late response. Would you like to send me the files so that I can reproduce and fix the issue?
from hisat2.
I released a new version of HISAT2 (2.0.4) three days ago, which may include some fixes for your issue. I'll close this thread and reopen if this issue still occurs.
from hisat2.
In 2.0.4, I also get into the same trouble when I build index for Nicotiana benthamiana.
It's my command:
hisat2-build -p 12 --ss ${ss_file} --exon ${exon_file} ${genome_file} ${index_file}
but I get this information:
is not reverse-deterministic, so reverse-determinize...
b.sh: line 1: 29864 Killed hisat2-build -p 12 --ss ${ss_file} --exon ${exon_file} ${genome_file} ${index_file}
my cluster have 500G memory, the hsat2-build would occupy up to 400G after warning up with "is not reverse-deterministic, so reverse-determinize"
after scanning HISAT2's tutorial, I execute the command for two part:
hisat2-build -3 -p 12 --ss ${ss_file} --exon ${exon_file} ${genome_file} ${index_file}
hisat2-build -r -p 12 --ss ${ss_file} --exon ${exon_file} ${genome_file} ${index_file}
the first command which only build *.3.ht2 and *.4.ht2 is fine, but the second command also can't work, this is the error :
Error: Encountered internal HISAT2 exception (#1)
Command: hisat2-build --wrapper basic-0 -r -p 12 --ss ${ss_file} --exon ${exon_file} ${genome_file} ${index_file}
Deleting "Nb_genome.1.ht2" file written during aborted indexing attempt.
Deleting "Nb_genome.2.ht2" file written during aborted indexing attempt.
Deleting "Nb_genome.5.ht2" file written during aborted indexing attempt.
Deleting "Nb_genome.6.ht2" file written during aborted indexing attempt.
Deleting "Nb_genome.7.ht2" file written during aborted indexing attempt.
Deleting "Nb_genome.8.ht2" file written during aborted indexing attempt.
from hisat2.
I still get the same error with HISAT2 2.2.1 . Is there any reason or a workaround for this?
from hisat2.
Related Issues (20)
- (ERR): hisat2-align died with signal 6 (ABRT) (core dumped) HOT 3
- Could not locate a HISAT2 index HOT 2
- Forcing alignment only to the forward reference for HISAT-3N HOT 1
- *** Error in `hisat2-build': double free or corruption (!prev): 0x00002b5724374370 *** HOT 1
- mapped read length
- Question regarding the runtime for hisat-3n-table
- hisat2-build DOES NOT work for me! HOT 1
- building standard hisat-3n indices with --base-change but not --repeat-index HOT 4
- "Local Graph Exploded" warning for hisat2 build using --snp,--haplotype,--exon and --ss.
- Hisat2 [Errno 2] No such file or directory
- Align ATAC-seq with Hisat2?
- error minimum intron length with hisat2 v. 2.2.1
- Repeat mapping with different result
- Feature request: Add support for xz and zstd
- hisat2 hangs aligning axolotl reads HOT 1
- 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?
- Installation Issue Error 1 - make HOT 1
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.