fuxialexander / marvel Goto Github PK

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, thanks for developing the MARVEL .
I have tried to run it, but encounter an error:

I have no ideas what's wrong
And the input is

Could you 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!

test.result.tree.txt
test.sh.log