MMARGE.pl denovo_motifs error

[aciernia]

Hi!

I am trying to examine de novo motifs in a set of ATACseq peak bed files compared to a background file using MMARGE.pl denovo_motifs. I have run into the following error when the shifting vectors are being loaded: Intervals must have positive width at /afs/.genomecenter.ucdavis.edu/software/mmarge/1.0/lssc0-linux//bin/analysis_tree.pm line 1079.
(see below).
My bed file runs fine with HOMER findMotifsGenome.pl, so I don't think it is a problem with the input peaks. Please let me know what I should do to fix this!

Thanks,

Annie

MMARGE.pl denovo_motifs BTBRmedia_greater_C57media.bed mm10 mmarge_denovomotifs_BTBRmedia_greater_C57media -bg Allconsensuspeaks.bed -fg_strain BTBR_T+_ITPR3TF_J -bg_strain C57BL6J -size given -p 30 -data_dir /share/lasallelab/Annie/BMDM/ATACanalysis_4_2018/BTBR_genome -genome_dir /share/lasallelab/Annie/BMDM/ATACanalysis_4_2018/BTBR_genome

Position file = BTBRmedia_greater_C57media.bed
Genome = mm10
Output Directory = mmarge_denovomotifs_BTBRmedia_greater_C57media
background position file: Allconsensuspeaks.bed
Using actual sizes of regions (-size given)
Fragment size set to given
Using 30 CPUs

/share/lasallelab/Annie/BMDM/ATACanalysis_4_2018/BTBR_genome/C57BL6J/preparsed/
Found mset for "mouse", will check against vertebrates motifs
Peak/BED file conversion summary:
BED/Header formatted lines: 37049
peakfile formatted lines: 0

Peak File Statistics:
	Total Peaks: 37049
	Redundant Peak IDs: 0
	Peaks lacking information: 0 (need at least 5 columns per peak)
	Peaks with misformatted coordinates: 0 (should be integer)
	Peaks with misformatted strand: 0 (should be either +/- or 0/1)

Peak file looks good!

Peak/BED file conversion summary:
	BED/Header formatted lines: 129420
	peakfile formatted lines: 0

remove overlapping target and background positions
Max distance to merge: direct overlap required (-d given)
Calculating co-bound peaks relative to reference: mmarge_denovomotifs_BTBRmedia_greater_C57media/bg.clean.pos

Comparing peaks: (peakfile, overlapping peaks, logRatio(obs/expected), logP)
	mmarge_denovomotifs_BTBRmedia_greater_C57media/target.clean..pos	37051	3.13	0.00

Co-bound by 0 peaks: 92369
Co-bound by 1 peaks: 37051 (max: 37051 effective total)

mv mmarge_denovomotifs_BTBRmedia_greater_C57media/0.410142421097593.2.tmp.coBoundBy0.txt mmarge_denovomotifs_BTBRmedia_greater_C57media/bg.clean.pos
Saving peaks
This it is: mmarge_denovomotifs_BTBRmedia_greater_C57media/targetgiven.pos
Loading shift vectors
Intervals must have positive width at /afs/.genomecenter.ucdavis.edu/software/mmarge/1.0/lssc0-linux//bin/analysis_tree.pm line 1079.
readline() on closed filehandle IN at /software/homer/4.9/lssc0-linux/bin/cleanUpSequences.pl line 31.
rm: cannot remove 'mmarge_denovomotifs_BTBRmedia_greater_C57media/0.410142421097593.tmp': No such file or directory
Not removing redundant sequences

Sequences processed:
	0 total

Here we do calculate targetCGBins
Frequency Bins: 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.6 0.7 0.8
Freq Bin Count
Illegal division by zero at /software/homer/4.9/lssc0-linux/bin/assignGeneWeights.pl line 63.
Normalizing lower order oligos using homer2

[vlink]

Hi! It seems to be a problem with the way MMARGE generates the genome. Could you share your VCF genome file for the BTBR_T+_ITPR3TF_J genome so I can try to trace back the error? Thanks! On 1/7/19, 2:15 PM, "Annie Vogel Ciernia" <notifications@github.com<mailto:notifications@github.com>> wrote: Hi! I am trying to examine de novo motifs in a set of ATACseq peak bed files compared to a background file using MMARGE.pl denovo_motifs. I have run into the following error when the shifting vectors are being loaded: Intervals must have positive width at /afs/.genomecenter.ucdavis.edu/software/mmarge/1.0/lssc0-linux//bin/analysis_tree.pm line 1079. (see below). My bed file runs fine with HOMER findMotifsGenome.pl, so I don't think it is a problem with the input peaks. Please let me know what I should do to fix this! Thanks, Annie MMARGE.pl denovo_motifs BTBRmedia_greater_C57media.bed mm10 mmarge_denovomotifs_BTBRmedia_greater_C57media -bg Allconsensuspeaks.bed -fg_strain BTBR_T+_ITPR3TF_J -bg_strain C57BL6J -size given -p 30 -data_dir /share/lasallelab/Annie/BMDM/ATACanalysis_4_2018/BTBR_genome -genome_dir /share/lasallelab/Annie/BMDM/ATACanalysis_4_2018/BTBR_genome Position file = BTBRmedia_greater_C57media.bed Genome = mm10 Output Directory = mmarge_denovomotifs_BTBRmedia_greater_C57media background position file: Allconsensuspeaks.bed Using actual sizes of regions (-size given) Fragment size set to given Using 30 CPUs /share/lasallelab/Annie/BMDM/ATACanalysis_4_2018/BTBR_genome/C57BL6J/preparsed/ Found mset for "mouse", will check against vertebrates motifs Peak/BED file conversion summary: BED/Header formatted lines: 37049 peakfile formatted lines: 0 Peak File Statistics: Total Peaks: 37049 Redundant Peak IDs: 0 Peaks lacking information: 0 (need at least 5 columns per peak) Peaks with misformatted coordinates: 0 (should be integer) Peaks with misformatted strand: 0 (should be either +/- or 0/1) Peak file looks good! Peak/BED file conversion summary: BED/Header formatted lines: 129420 peakfile formatted lines: 0 remove overlapping target and background positions Max distance to merge: direct overlap required (-d given) Calculating co-bound peaks relative to reference: mmarge_denovomotifs_BTBRmedia_greater_C57media/bg.clean.pos Comparing peaks: (peakfile, overlapping peaks, logRatio(obs/expected), logP) mmarge_denovomotifs_BTBRmedia_greater_C57media/target.clean..pos 37051 3.13 0.00 Co-bound by 0 peaks: 92369 Co-bound by 1 peaks: 37051 (max: 37051 effective total) mv mmarge_denovomotifs_BTBRmedia_greater_C57media/0.410142421097593.2.tmp.coBoundBy0.txt mmarge_denovomotifs_BTBRmedia_greater_C57media/bg.clean.pos Saving peaks This it is: mmarge_denovomotifs_BTBRmedia_greater_C57media/targetgiven.pos Loading shift vectors Intervals must have positive width at /afs/.genomecenter.ucdavis.edu/software/mmarge/1.0/lssc0-linux//bin/analysis_tree.pm line 1079. readline() on closed filehandle IN at /software/homer/4.9/lssc0-linux/bin/cleanUpSequences.pl line 31. rm: cannot remove 'mmarge_denovomotifs_BTBRmedia_greater_C57media/0.410142421097593.tmp': No such file or directory Not removing redundant sequences Sequences processed: 0 total Here we do calculate targetCGBins Frequency Bins: 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.6 0.7 0.8 Freq Bin Count Illegal division by zero at /software/homer/4.9/lssc0-linux/bin/assignGeneWeights.pl line 63. Normalizing lower order oligos using homer2 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#5>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AD8p6DahJrLbUL-xRnLBmaHoV-F9DWikks5vA5ntgaJpZM4Z0Df->.

[aciernia]

I am more than happy to share the files. What is the best way to transfer them to you? They are 1.2 GB for the snps and ~350MB for the indels. Thanks so much!

[vlink]

Can you upload them somewhere so I can download them? You can send the link directly to my email (verena.m.link@gmail.com<mailto:verena.m.link@gmail.com>) if you don’t want to share your data publicly. Best, Verena On 1/8/19, 12:16 PM, "Annie Vogel Ciernia" <notifications@github.com<mailto:notifications@github.com>> wrote: I am more than happy to share the files. What is the best way to transfer them to you? They are 1.2 GB for the snps and ~350MB for the indels. Thanks so much! — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#5 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AD8p6Gb0-9Z6CktX-VV4VT3m2Y5ckmM3ks5vBNJmgaJpZM4Z0Df->.

[aciernia]

Terrific. I just sent links to your email. Please let me know if you didn't receive them. I really appreciate all the help!!!

[PhrenoVermouth]

Facing the same issue in PWK strain. Since two years have passed, any possible suggestions? Thanks a lot!

[krovi137]

Hello! Was there any resolution to this? I'm facing the same issue. Any help would be really appreciated! Thanks!