fuxialexander / marvel Goto Github PK
View Code? Open in Web Editor NEWMultigranular Analysis of Regulatory Variants on the Epigenomic Landscape
License: MIT License
Multigranular Analysis of Regulatory Variants on the Epigenomic Landscape
License: MIT License
Hi, I tried to run marvel for motif prediction but the jobs always killed by the exceeded limit of cpus, seems the parameter --max_cpus
didn't work.
I try to set --max_cpus 1
or --max_cpus 2
etc., they all have similar results, like
number "4" in the log file is the cpu I set when the job summitted, not the same with what I set in marvel's script --max_cpus
Could you please help me have a check?
Thank you.
Hi,
I am trying to test marvel with the test_input file but could not get the ".ngz " result and summary result, and didn't have anything error messages, but with a lot of log messages related with R install.packages('glmpath'), however, I make sure that my R has installed "glmpath" already.
This is my codes for testing:
conda activate fuxialexander-marvel-1.1dev
/software/Nextflow/20.07.1/bin/nextflow run /home/software/marvel -profile conda --fasta /psychipc01/disk2/references/GATK/bundle/2.8/hg19/ucsc.hg19.fasta --enhancer /home/software/marvel/test_input/regions/enhancer.bed --promoter /home/software/marvel/test_input/regions/promoter.bed --vcf /home/software/marvel/test_input/variants/test.vcf.gz --vcf_index /home/software/marvel/test_input/variants/test.vcf.gz.tbi --phenocov /home/software/marvel/test_input/samples/pheno_covar.txt --chunk_size 100 --permutation_multiplier 10 --motif_scan_threshold 0.0001 --outdir /home/software/marvel/test2 -w /home/software/marvel/test2/work --max_memory '20.GB' --max_cpus 1
I also tried "nextflow main.nf -profile test,conda", and it generated the same result and log message. Attached with the result info and log file.
Thank you!
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.