Question: MACs Peak Calling Zero Division Error
0
gravatar for coltrepar
2.5 years ago by
coltrepar0
United States
coltrepar0 wrote:

I am trying to use IGB for ChIP-Seq analyses and comparisons.  I am starting with fastq files.  I am grooming the data with the FASTQ Groomer and then aligning the data using Map w/ Bowtie for Illumina.  I then filter the data using Filter Sam and convert to a BAM file.  When I try to use MACs peak calling I repeatedly get a float division by zero error.

INFO  @ Thu, 13 Aug 2015 14:07:40:
# ARGUMENTS LIST:
# name = MACS_in_Galaxy
# format = BAM
# ChIP-seq file = /galaxy-repl/main/files/012/160/dataset_12160005.dat
# control file = None
# effective genome size = 2.70e+09
# tag size = 36
# band width = 200
# model fold = 10
# pvalue cutoff = 1.00e-05
# Ranges for calculating regional lambda are : peak_region,1000,5000,10000
INFO  @ Thu, 13 Aug 2015 14:07:40: #1 read tag files...
INFO  @ Thu, 13 Aug 2015 14:07:40: #1 read treatment tags...
Traceback (most recent call last):
  File "/galaxy/main/deps/macs/1.3.7.1/devteam/package_macs_1_3_7_1/a7ea583a35d2/bin/macs", line 273, in <module>
    main()
  File "/galaxy/main/deps/macs/1.3.7.1/devteam/package_macs_1_3_7_1/a7ea583a35d2/bin/macs", line 71, in main
    options.bg_redundant = bg_r (treat,options.max_dup_tags) # average
  File "/galaxy/main/deps/macs/1.3.7.1/devteam/package_macs_1_3_7_1/a7ea583a35d2/bin/macs", line 225, in bg_r
    return float(total_duplicates)/(total_tags)
ZeroDivisionError: float division by zero

What do I need to do to resolve this error?

Colin 

peak calling • 1.2k views
ADD COMMENTlink modified 2.5 years ago by Jennifer Hillman Jackson24k • written 2.5 years ago by coltrepar0
0
gravatar for Jennifer Hillman Jackson
2.5 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

This error could be for a few different reasons. Confirming inputs is the first step (I suspect the BAM files does not have alignment data). Confirm that the correct target reference database was used. Then confirm that the input sequence data is in "fastqsanger" format. And finally, check the BAM file itself to confirm that alignment was successful - tools in the groups Samtools and Picard can help generate alignment statistics.

Best, Jen, Galaxy team

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Jennifer Hillman Jackson24k
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