Comments (4)
Yes, that is exactly the image I am trying to use.
It turned out that my original problem was because I did not supply the Singularity image with a bind-path to my home-folder on the cluster. However, the behaviour that CRISPRCasFinder will change to the home-directory to run, and only later copies file to the specified output folder, still causes some trouble (since there are size constraints on my home directory, which is not the case for the scratch directory where I would like to put the output). Is there any way to stop CRISPRCasFinder from creating files under my home directory?
from crisprcasfinder.
Dear @JSHuisman , sorry for the delayed response, we are looking at this issue. We hope that the problem will be fixed for the next release.
I will let you know.
from crisprcasfinder.
Dear @JSHuisman
Thank you for your message.
Sorry, I have not yet seen this error before.
Have you tried this Singularity hub : https://singularity-hub.org/collections/1625 ?
Maybe @bneron could provide better explanations about this Singularity error.
from crisprcasfinder.
Yes, that is exactly the image I am trying to use.
It turned out that my original problem was because I did not supply the Singularity image with a bind-path to my home-folder on the cluster. However, the behaviour that CRISPRCasFinder will change to the home-directory to run, and only later copies file to the specified output folder, still causes some trouble (since there are size constraints on my home directory, which is not the case for the scratch directory where I would like to put the output). Is there any way to stop CRISPRCasFinder from creating files under my home directory?
This is a fairly old issue, but I am leaving a response just in case. It seems CRISPRCasFinder uses the current directory as a temporary directory and I have found that in some cases singularity does not mount the current directory (symbolic links might cause problems). In that case, the user's home directory becomes the current directory inside singularity and CRISPRCasFinder create temporary files there. If you can mount a directory with more space and cd
there, you can avoid having files created in your home directory.
from crisprcasfinder.
Related Issues (20)
- CRISPRCasFinder.pl: command not found HOT 5
- Using new version of MacSyFinder on CRISPRCasFinder.pl HOT 7
- Too many intermediate files HOT 2
- CRISPERCasFinder does not handle vmatch results with multi line sequence correctly HOT 2
- Recent Singularity container is not recognized by Singularity versions <2.6.1 HOT 1
- Installation of Date::Calc failed HOT 3
- Dependency issues using Singularity image HOT 1
- Flank sequence near contig edge has negative coordinate HOT 1
- MSG: No file or directory called HOT 1
- Error in `muscle': double free or corruption (out): 0x00007ffceb581bf0 HOT 12
- How to use CRISPRCasFinder through singularity container HOT 4
- error in using crisprcasfinder with subprocess, snakemake and Rscript HOT 10
- The result of CRISPR-Cas_summary.tsv don't have Cas Types/Subtypes HOT 1
- No CRISPR/CAS detection on fasta files with more than 100 contigs HOT 1
- CRISPRCasFinder.pl did not report any errors but produced three unknown core files HOT 2
- [FEATURE REQUEST] macsyfinder models custom dir
- Could not open output GFF in result/result2/ because No such file or directory
- json output sometimes "forgets" closing ] in "Cas": [] line
- a particular set of parameters for CCF fails to produce results for all genomes we tried HOT 3
- Error when result folder is not in source folder
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 crisprcasfinder.