CEAS perform gene-cantered annotation ZeroDivisionError
I encountered an error when executing CEAS (Cis-regulatory Element Annotation System) at "#3 perform gene-cantered annotation" step. Here are the error output:
INFO @ Thu, 09 Jun 2016 09:04:45:
# ARGUMENTS:
# name = H3K4me3_ceas
# gene annotation table = /silicon-2/projects/changhao/02H3K4/results/hg38.refGene
# BED file = H3K4me3_merged_peaks.bed
# WIG file = H3K4me3_merged.wig
# extra BED file = None
# ChIP annotation = On
# gene-centered annotation = On
# average profiling = On
# dump profiles = Off
# re-annotation for genome background (ChIP region annotation) = False
# promoter sizes (ChIP region annotation) = 1000,2000,3000 bp
# downstream sizes (ChIP region annotation) = 1000,2000,3000 bp
# bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp
# span size (gene-centered annotation) = 10000 bp
# profiling resolution (average profiling) = 50 bp
# relative distance wrt TSS and TTS (average profiling) = 10000 bp
INFO @ Thu, 09 Jun 2016 09:04:45: #1 read the gene table...
INFO @ Thu, 09 Jun 2016 09:04:57: #2 read the bed file of ChIP regions...
INFO @ Thu, 09 Jun 2016 09:04:57: #3 perform gene-centered annotation...
Traceback (most recent call last):
File "/silicon-2/projects/changhao/local/bin/ceas", line 1343, in <module>
main()
File "/silicon-2/projects/changhao/local/bin/ceas", line 121, in main
GAnnotator.annotate(GeneT, ChIP, u=options.span, d=options.span)
File "/silicon-2/projects/changhao/local/lib/python2.7/site-packages/CEAS/annotator.py", line 1280, in annotate
annotation = self.annotate_single_gene(txStart, txEnd, strand, u, d, exonStarts, exonEnds, ChIP_start[pointerBeg:j], ChIP_end[pointerBeg:j], precision=2)
File "/silicon-2/projects/changhao/local/lib/python2.7/site-packages/CEAS/annotator.py", line 1461, in annotate_single_gene
annot_nearTSS = [1.0*a/l for a, l in itertools.izip(annot_nearTSS, len_in_bp_nearTSS)]
ZeroDivisionError: float division by zero
I have several samples, and others can have the normal output. This error puzzles me a lot!
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GenoMax
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Changhao Li •
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Changhao Li •
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What is your exact CEAS command, and please check input file format and path, especially check genome background annotation file
Thank you Mike, I finally figured it out. This is because several bed items have chromosomes which are not annotated in the annotation file.
I also met that problem. Could you give me some suggestions on how to figure out the bed file ??