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Gimme motifs not using -f (fraction) provided #166

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adeben1 opened this issue Jan 13, 2021 · 2 comments
Closed

Gimme motifs not using -f (fraction) provided #166

adeben1 opened this issue Jan 13, 2021 · 2 comments

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@adeben1
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adeben1 commented Jan 13, 2021

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):

  • OS: Linux
  • Installation conda
  • Version v0.14.4
@simonvh
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simonvh commented Jan 14, 2021

I'll have a look, thanks for reporting!

@kirbyziegler
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Easy fix here:

#177

@adeben1 adeben1 closed this as completed Mar 24, 2021
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3 participants