Comments (8)
Hi bofster,
Thanks for your feedback. Your suggestion make sense to me. It is not a tough job, but I am tied up with other tasks at this stage. I will probably add the this feature to MEGAHIT in one to two weeks.
Dinghua
from megahit.
Thanks ... that would be really great.
On Sun, Jan 18, 2015 at 12:46 AM, Dinghua Li [email protected]
wrote:
Hi bofster,
Thanks for your feedback. Your suggestion make sense to me. It is not a
tough job, but I am tied up with other tasks at this stage. I will probably
add the this feature to MEGAHIT in one to two weeks.
Dinghua—
Reply to this email directly or view it on GitHub
#12 (comment).
from megahit.
bofster,
Please check out the commit 0d6e306 on the branch dev-continue-mode
. To continue a interrupted run, please run MEGAHIT with option --continue -o OUTPUT_DIR
. I've done several tests on a small dataset with the continue mode. See whether it works for you. I look forward to your feedback.
Cheers,
Dinghua
from megahit.
It looks like it is working for me on small datasets too. I will test it on larger sets. This is a great feature!
Would it be possible to be able to specify --continue on the first run also? Maybe disregard the --continue flag if it is a first run? If it were allowed on first run, the user would not have to change the command line at all for resubmission after failure.
from megahit.
Please try this commit e248ce0
Using --continue
on the first run will raise a warning message but switch to the normal mode after then.
from megahit.
It looks good to me. -continue mode works on initial run and restarting failures. Thanks!
I did notice it prints 8 messages.(I was using 8 threads)
Cannot find ./megahit_out/opts.txt
Please check whether the output directory is correctly set by "-o"
Now switching to normal mode.
Cannot find ./megahit_out/opts.txt
Please check whether the output directory is correctly set by "-o"
Now switching to normal mode.
Cannot find ./megahit_out/opts.txt
Please check whether the output directory is correctly set by "-o"
Now switching to normal mode.
Cannot find ./megahit_out/opts.txt
....
from megahit.
Fixed. b97ae36
And fix a bug when using both --continue
and --input-cmd
. 3f4c93b
The branch of continue mode has been merged to master branch.
from megahit.
I downloaded and tried MEGAHIT v0.2.0 master branch. Great release!
from megahit.
Related Issues (20)
- Understanding kmer contigs for FASTG Output HOT 2
- assembly error
- Paired-end reads and --min-count HOT 1
- Does memory avaliable need to be >= size of input data?
- Assembly killed exit code 9 despite sufficient memory? HOT 1
- Interpretation of Fasta Headers
- Exit code 6 when assembling kmers HOT 1
- Can we use megahit to assemble rna-seq data? HOT 2
- [All datasets] Suspicious report of identical # unitigs disconnected in graph pruning
- Which minimum kmer is supposed to be used on the 701G merged single-end .fa reads? HOT 1
- Exit code 9. HOT 1
- Question: how megahit deals with different size read sets?
- Exit code -15
- number of cpus//threads HOT 2
- ID in header
- I set 560 threads,but i got this log.
- When I run the command, Megahit can only recognize one fq file, what happens
- Problem with big assembly HOT 1
- Error with latest OS X Bioconda recipe HOT 1
- Assembly contiguity & sequencing depth
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 megahit.