CEAS perform gene-cantered annotation ZeroDivisionError

Question

[Changhao Li]

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!

[Mike]

What is your exact CEAS command, and please check input file format and path, especially check genome background annotation file

[Changhao Li]

Thank you Mike, I finally figured it out. This is because several bed items have chromosomes which are not annotated in the annotation file.

[jimmy0958073736]

I also met that problem. Could you give me some suggestions on how to figure out the bed file ??