Comments (1)
Hi @Fuyt27 thank you for using nf-LO
!
I'm afraid I need some more details about the failure. Can you please share the .nextflow.log
file in the working directory and possibly the work/db/556bfd*/.command.err
and work/db/556bfd*/.command.out
? (alternatively any .command.err/out
in one of the failed folders).
The name of the folder where to find the logs can be seen in the beginning of the line. For example: [db/556bfd] NOTE: Process ALIGNER:lastz (lastz_near.11.tgt8) failed -- Execution is retried (1)
, the working directory starts with work/db/556bfd*
.
Finally, if the test run worked fine, I suggest to have a look at how you configured your analysis. Sometimes fragmenting the genome too much (or too little) might cause some lastz processes to fail. Try to change the settings of --srcSize
, --tgtSize
, --tgtOvlp
and --srcOvlp
to regulate the size of the chunks for source/target and the overlap between chunks.
from nf-lo.
Related Issues (20)
- Process requirement exceed available CPUs -- req: 2; avail: 1 HOT 9
- ALIGNER:chainMerge (chainmerge) FAILED HOT 7
- error exit status (255) HOT 4
- liftover failed with cross map HOT 7
- having trouble installing nf-lo manually HOT 1
- minimap2: Stdin is empty HOT 16
- cannot build singularity/docker images with the current continuumio/miniconda3 image
- grouptgt error HOT 1
- Too large of a bash script for slurm in chainMerge HOT 3
- Issue about Annotation HOT 2
- A problem while using nf-LO HOT 1
- Issue regarding 'nextflow run evotools/nf-LO' HOT 2
- Process `ALIGNER:chainMerge (chainmerge)` terminated with an error exit status (1) -- Execution is retried (1) HOT 19
- The current r-environment.yml never resolves HOT 7
- Minimap2 and gsalign using too few cpus HOT 2
- pipeline commands HOT 1
- environment.yml error even while running via docker HOT 6
- Having trouble in test nf-LO using conda HOT 3
- How to merge chain file from different chromosome 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 nf-lo.