Comments (5)
My experience is that such errors are the result of specifying paths for input or output files. minia doesn't deal well with that. If I start in my project root and call, for instance
./gatb-pipeline/gatb -1 data/reads1.fq -2 data/reads2.fq ...
then minia fill produce files with "file lists" that contain the data/ path prefix, but it will look for them not relative to the project root (.) but to something else (perhaps the directory where gatb is, I don't know) and then it may not find the .fq files; a similar issue seems to arise if it wants to read or write h5 files, perhaps a directory that is assumed to exist does not exist.
My workaround was not to include any paths in filenames. This is not beautiful, especially if you want to combine this with workflow management such as Snakemake, but it works.
from gatb-minia-pipeline.
hi Sven, yes in fact, gatb-pipeline is even less robust than minia (as it accumulates the bugs of both :) ). Sorry about that, it's indeed a more sure thing to specify full paths rather than relative paths. And regarding output, it's a byproduct of the fact that I always run analyses in current folders (e.g. cd /my/data && /path/to/gatb_pipeline/gatb -l file.fastq
), not the most versatile handling of paths, I know.
from gatb-minia-pipeline.
Hi Thomas,
I'm not sure about this one. Can you make sure that the input files do exist and that the metafiles
folder exists?
Does the pipeline not run on any input on this system, even the simple test provided with it?
Rayan
from gatb-minia-pipeline.
I'm going to close this one, feel free to reopen in case the problem occurs again.
from gatb-minia-pipeline.
I understand that I am incredibly late to the party but I ran into this problem again and remembered that this ticket exists. Thank you @rchikhi and @svenrahmann for commenting on this and providing valuable hints! For the gatb-minia-pipeline in particular specifying the absolute path for the output folder (parameter -o) solved the issue.
Bonus: specifying the absolute path for the input files only does not help. It looks like it does at first but, due to the required solution above, the run breaks after the first iteration.
from gatb-minia-pipeline.
Related Issues (20)
- make test failed and number of cores not limitable? HOT 5
- gatb-pipeline requires a Linux 64 bits system HOT 2
- Problem with BESST in the pipeline HOT 12
- Execution of 'perl tools/sga-deinterleave.pl' HOT 4
- Problems with assembling the data beyond kmer 127 and other queries. HOT 4
- Combining multiple libraries HOT 5
- Add version info on prerequisites HOT 1
- Error with `make test` HOT 3
- 920: syntax error in expression (error token is "920") HOT 1
- GFA output HOT 1
- BESST: error: unrecognized arguments: fr HOT 3
- Flag to remove intermediate files HOT 4
- Release package?
- Question about input file type HOT 2
- ZeroDivisionError while running BESST HOT 1
- BESST: error: argument -orientation is required HOT 3
- OSError: [Errno 17] File exists HOT 1
- test if bwa version is high enough
- Error with samtools in `make test` 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 gatb-minia-pipeline.