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[其他] chip-seq findMotifsGenome.pl出问题了

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发表于 2017-8-28 21:54:43 | 显示全部楼层 |阅读模式
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xuenjundeMacBook-Pro:CHIP-seq xuenjun$ ./Homer/bin/findMotifsGenome.pl myc1_vs_input1.txt tair10 motif_based_on_myc1_vs_input1_cleaned_peaks/ -size given

	Position file = myc1_vs_input1.txt
	Genome = tair10
	Output Directory = motif_based_on_myc1_vs_input1_cleaned_peaks/
	Using actual sizes of regions (-size given)
	Fragment size set to given
	Found mset for "arabidopsis", will check against plants motifs
	Peak/BED file conversion summary:
		BED/Header formatted lines: 0
		peakfile formatted lines: 4467

	Peak File Statistics:
		Total Peaks: 4467
		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!

	Background fragment size set to 138 (avg size of targets)
	Background files for 138 bp fragments found.

	Extracting sequences from file: /Users/xuenjun/Documents/CHIP-seq/Homer/.//data/genomes/tair10///genome.fa
	Looking for peak sequences in a single file (/Users/xuenjun/Documents/CHIP-seq/Homer/.//data/genomes/tair10///genome.fa)

	Not removing redundant sequences


	Sequences processed:
		0 total

	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

	Total sequences set to 50000

	Choosing background that matches in CpG/GC content...
Illegal division by zero at /Users/xuenjun/Documents/CHIP-seq/homer/bin/assignGeneWeights.pl line 63.
	Assembling sequence file...
	Normalizing lower order oligos using homer2

	Reading input files...
	0 total sequences read
	Autonormalization: 1-mers (4 total)
		A	inf%	inf%	nan
		C	inf%	inf%	nan
		G	inf%	inf%	nan
		T	inf%	inf%	nan
	Autonormalization: 2-mers (16 total)
		AA	inf%	inf%	nan
		CA	inf%	inf%	nan
		GA	inf%	inf%	nan
		TA	inf%	inf%	nan
		AC	inf%	inf%	nan
		CC	inf%	inf%	nan
		GC	inf%	inf%	nan
		TC	inf%	inf%	nan
		AG	inf%	inf%	nan
		CG	inf%	inf%	nan
		GG	inf%	inf%	nan
		TG	inf%	inf%	nan
		AT	inf%	inf%	nan
		CT	inf%	inf%	nan
		GT	inf%	inf%	nan
		TT	inf%	inf%	nan
	Autonormalization: 3-mers (64 total)
	Normalization weights can be found in file: motif_based_on_myc1_vs_input1_cleaned_peaks//seq.autonorm.tsv
	Converging on autonormalization solution:
	...............................................................................
	Final normalization:	Autonormalization: 1-mers (4 total)
		A	inf%	inf%	nan
		C	inf%	inf%	nan
		G	inf%	inf%	nan
		T	inf%	inf%	nan
	Autonormalization: 2-mers (16 total)
		AA	inf%	inf%	nan
		CA	inf%	inf%	nan
		GA	inf%	inf%	nan
		TA	inf%	inf%	nan
		AC	inf%	inf%	nan
		CC	inf%	inf%	nan
		GC	inf%	inf%	nan
		TC	inf%	inf%	nan
		AG	inf%	inf%	nan
		CG	inf%	inf%	nan
		GG	inf%	inf%	nan
		TG	inf%	inf%	nan
		AT	inf%	inf%	nan
		CT	inf%	inf%	nan
		GT	inf%	inf%	nan
		TT	inf%	inf%	nan
	Autonormalization: 3-mers (64 total)
	Finished preparing sequence/group files

	----------------------------------------------------------
	Known motif enrichment

	Reading input files...
	0 total sequences read
	502 motifs loaded
	Cache length = 11180
	Using binomial scoring
	Checking enrichment of 502 motif(s)
	|0%                                    50%                                  100%|
	=================================================================================
Illegal division by zero at /Users/xuenjun/Documents/CHIP-seq/homer/bin/findKnownMotifs.pl line 152.
	----------------------------------------------------------
	De novo motif finding (HOMER)

	Scanning input files...
!!! Something is wrong... are you sure you chose the right length for motif finding?
!!! i.e. also check your sequence file!!!

	Scanning input files...
!!! Something is wrong... are you sure you chose the right length for motif finding?
!!! i.e. also check your sequence file!!!

	-blen automatically set to 2
	Scanning input files...
!!! Something is wrong... are you sure you chose the right length for motif finding?
!!! i.e. also check your sequence file!!!
Use of uninitialized value in numeric gt (>) at /Users/xuenjun/Documents/CHIP-seq/homer/bin/compareMotifs.pl line 1381.
	!!! Filtered out all motifs!!!
	Job finished - if results look good, please send beer to ..

	Cleaning up tmp files...



试过各种长度的motif finding可是都不好使,到底是哪里有问题呢,非常感谢
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 楼主| 发表于 2017-8-30 13:46:13 | 显示全部楼层
没有人遇到过这个问题吗?
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