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vanheeringen-lab / gimmemotifs

Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples.
https://gimmemotifs.readthedocs.io/en/master
MIT License
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Gimme motifs not using -f (fraction) provided #166

Closed adeben1 closed 3 years ago

adeben1 commented 3 years ago

Describe the bug Gimme motifs is not apparently using the -f value provided.

To Reproduce I've run gimme motifs commnad providing input, background and genome in fasta format with the -s flag set to 0 as well as -f set to 0.5. Here is one example. gimme motifs diff_peaks_down_MB.bed.fa down_MB_nocenteredx2_b_f0,5 -g ../../genome/Nfu_20150522.softmasked_genome.fa -b ../nucfree/allPeaks_MB.bed.fa -s 0 -f 0.5

Expected behavior In the file params.txt, the fraction should indicate 0.5, however it appears the default 0.2.

Error logs I copy the content of the file params.txt.

fraction 0.2 use_strand False abs_max 1000 analysis xl enrichment 1.5 size 0 lsize 500 background ['custom'] cluster_threshold 0.95 scan_cutoff 0.9 available_tools MDmodule,MEME,MEMEW,DREME,Weeder,GADEM,MotifSampler,Trawler,Improbizer,BioProspector,Posmo,ChIPMunk,AMD,HMS,Homer,XXmotif,ProSampler,DiNAMO tools MEME,Homer,BioProspector pvalue 0.001 max_time -1.0 ncpus 12 motif_db gimme.vertebrate.v5.0.pfm use_cache False custom_background ../nucfree/allPeaks_MB.bed.fa genome ../../genome/Nfu_20150522.softmasked_genome.fa

In addition, the .log file says it is using 0.2 as a fraction. From gimmemotifs.log: 2021-01-13 09:32:15,478 - gimme.config - DEBUG - fraction: 0.2

Installation information (please complete the following information):

simonvh commented 3 years ago

I'll have a look, thanks for reporting!

kirbyziegler commented 3 years ago

Easy fix here:

https://github.com/vanheeringen-lab/gimmemotifs/issues/177