vlink
commented
5 years ago 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: 0remove 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 0.00Co-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 totalHere 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
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aciernia
PhrenoVermouth
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
/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
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
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
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