Comments (10)
you rock! thanks, @rchikhi!
from bcalm.
Oddly enough my shorter automated workflow https://github.com/ctb/2018-bcalm-debug doesn't detect any problems. Must not trigger the right problem.
Note that when I compile bcalm from scratch on my HPC the spacegraphcats-twofoo-example above runs just fine and passes the reciprocal edges test.
from bcalm.
Thanks for the detailed report! I confirm that I can reproduce the behavior of #37 (comment) on my own Linux, when using bioconda's bcalm. The problem doesn't occur when using the current master branch of bcalm. So something must be going on with bioconda's version, I'm on it.
from bcalm.
from bcalm.
I think I see what's going on. Two bugs: 1) I thought BCALM outputted consecutive unitig IDs, but apparently with some compilers it had some rare inversions (e.g. 9,10,12,11,13,14,..). Likely a multi-threading bug. 2) The procedure used to link unitigs silently and wrongly assumed that unitigs needed to have consecutive IDs. I've commited a fix for both bugs and will release BCALM 2.2.1. @natir could you please update Conda when you have time, or show me how?
from bcalm.
ping! I'd suggest withdrawing bcalm from bioconda until someone has time to fix it.
from bcalm.
pinging @natir: bcalm 2.2.1 is released and needs to be updated in bioconda please :)
from bcalm.
@epruesse update bioconda bcalm to 2.2.1 in this pull request bioconda/bioconda-recipes#12811
from bcalm.
merci!
from bcalm.
from bcalm.
Related Issues (20)
- new release soon? HOT 2
- Running bcalm raises error: `cannot create a union-find data structure, too many elements.` HOT 6
- error: 'predecessors' following the 'template' keyword does not refer to a template HOT 8
- Error: libc++abi.dylib: terminating with uncaught exception of type std::out_of_range: basic_string HOT 5
- Compiling bcalm causes trouble when no .git repository is found HOT 1
- Output of bcalm2 similar to minia 3.2.1 unitigs? HOT 2
- Memory error with many reference genomes as input HOT 16
- High frequency of nodes with degree of two with length = 2k-1 HOT 2
- .fa files contain lowercase `km` instead of the documented uppercase `KM` HOT 3
- bcalm 2.2.1 on conda for Mac OS X produces incorrect cDBG (the zombie bug returns!!) HOT 12
- Add better input parsing HOT 1
- Improve error message for bad fasta input HOT 1
- Apparently bcalm crashes with very large k's (4096) HOT 1
- bcalm -version return code 1 to shell
- Glue is too strong, because glue files are not deleted.
- insert unitig disregarding the reverse complement HOT 1
- Option `-out-dir` is not used ? HOT 1
- bug report on a metagenomics dataset HOT 3
- Add header description with `-all-abundance-counts` HOT 2
- Is the output file reproducible? HOT 2
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 bcalm.