Comments (5)
You may have reads with same names or same part splited by space. Check it like this:
zcat input.fa.gz | perl -ne 'print "$1\n" if />(\S+)/' | sort | uniq -d
from miniasm.
Thank you, I used rename.sh in=input.fasta out=output.fasta prefix=test
and it fixed the names problem
from miniasm.
For others who might encounter this issue too, I thought I'd just add here that rename.sh
is a script in the BBtools package: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
from miniasm.
So what is the likely issue when one encounters this error but you don't have duplicated IDs?
[M::main] ===> Step 5: generating unitigs <===
miniasm: asm.c:267: ma_ug_seq: Assertion `sub[id].e - sub[id].s <= ks->seq.l' failed.
/bin/bash: line 1: 13225 Aborted (core dumped) miniasm -f filtered/DC_concat.fq.gz overlaps/DC_concat.paf.gz > miniasm/DC_concat.gfa
from miniasm.
@mw55309 I don't know. I have only seen this assertion failure when there are duplicated read names.
from miniasm.
Related Issues (20)
- how to calculated identity? HOT 1
- No output in GFA file after miniasm run. HOT 4
- Explanation of GFA file format HOT 1
- PAF end coordinates HOT 2
- Segmentation fault (core dumped) while running miniasm HOT 1
- Can miniasm be used for contigs HOT 1
- Hello there, HOT 3
- Number of rounds for short overlap removal
- miniasm prints no gfa if PAF file contains self-mapped read HOT 3
- Conceptual Question About Miniasm
- Empty gfa file after miniasm run HOT 4
- Decreasing minimum required read coverage for assembly
- Miniasm killed process
- PAF Format detail HOT 1
- Not results generating? HOT 5
- Empty paf file. No error message.
- The main disadvantages of Miniasm compared to more modern assemblers
- combine replicates
- Assemble of DNA and RNA amplicons from PacBio run HOT 1
- Next Step after generating assembly.gfa file.
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 miniasm.