Question: Error with MACS2 peak calling
0
gravatar for 340072256
7 months ago by
3400722560
3400722560 wrote:

Hi dear all, i am new to ChIP-seq analysis and i have been recently using MACS2 callpeaks on galaxy. The but it always fails and i don't know why..... plz help me and thank you all in advance :)

Here's the parameters set

ChIP-Seq Treatment File              42: Chipseq_NSC_H3K4me3_trimmed_unique_BT2.bam 
ChIP-Seq Control File                43: Chipseq_NSC_input_trimmed_unique_BT2.bam   

Are your inputs Paired-end BAM files?   True    
Effective genome size                   2451960000  
Band width for picking regions to compute fragment size 300 

mfold   
Set lower mfold bound   5   
Set upper mfold bound   50  

Peak detection based on qvalue  
Minimum FDR (q-value) cutoff for peak detection              0.05   

Build Model                                                 create_model    

Outputs Peaks as tabular file Peak summits Scores in bedGraph files (--bdg) Summary page (html) Plot in PDF 

Advanced options    off

Here's the error report

Fatal error: Exit code 2 ()

INFO  @ Sat, 29 Apr 2017 13:29:38: 
# Command line: callpeak --name MACS2 -t /galaxy-repl/main/files/019/759/dataset_19759955.dat -c /galaxy-repl/main/files/019/759/dataset_19759956.dat --format BAMPE --gsize 2451960000 --bw 200 --mfold 40 80 --bdg --qvalue 0.05
# ARGUMENTS LIST:
# name = MACS2
# format = BAMPE
# ChIP-seq file = ['/galaxy-repl/main/files/019/759/dataset_19759955.dat']
# control file = ['/galaxy-repl/main/files/019/759/dataset_19759956.dat']
# effective genome size = 2.45e+09
# band width = 300
# model fold = [5, 50]
# qvalue cutoff = 5.00e-02
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# Paired-End mode is on

INFO  @ Sat, 29 Apr 2017 13:29:38: #1 read fragment files... 
INFO  @ Sat, 29 Apr 2017 13:29:38: #1 read treatment fragments... 
INFO  @ Sat, 29 Apr 2017 13:29:53:  1000000 
INFO  @ Sat, 29 Apr 2017 13:30:08:  2000000 
INFO  @ Sat, 29 Apr 2017 13:30:23:  3000000 
INFO  @ Sat, 29 Apr 2017 13:30:38:  4000000 
INFO  @ Sat, 29 Apr 2017 13:30:53:  5000000 
INFO  @ Sat, 29 Apr 2017 13:31:08:  6000000 
INFO  @ Sat, 29 Apr 2017 13:31:23:  7000000 
INFO  @ Sat, 29 Apr 2017 13:31:38:  8000000 
INFO  @ Sat, 29 Apr 2017 13:31:53:  9000000 
INFO  @ Sat, 29 Apr 2017 13:32:07:  10000000 
INFO  @ Sat, 29 Apr 2017 13:32:22:  11000000 
INFO  @ Sat, 29 Apr 2017 13:32:37:  12000000 
INFO  @ Sat, 29 Apr 2017 13:32:52:  13000000 
INFO  @ Sat, 29 Apr 2017 13:33:07:  14000000 
INFO  @ Sat, 29 Apr 2017 13:33:20: #1.2 read input fragments... 
INFO  @ Sat, 29 Apr 2017 13:33:36:  1000000 
INFO  @ Sat, 29 Apr 2017 13:33:51:  2000000 
INFO  @ Sat, 29 Apr 2017 13:34:07:  3000000 
INFO  @ Sat, 29 Apr 2017 13:34:22:  4000000 
INFO  @ Sat, 29 Apr 2017 13:34:38:  5000000 
INFO  @ Sat, 29 Apr 2017 13:34:54:  6000000 
INFO  @ Sat, 29 Apr 2017 13:35:10:  7000000 
INFO  @ Sat, 29 Apr 2017 13:35:24: #1 mean fragment size is determined as 221 bp from treatment 
INFO  @ Sat, 29 Apr 2017 13:35:24: #1 note: mean fragment size in control is 216 bp -- value ignored 
INFO  @ Sat, 29 Apr 2017 13:35:24: #1 fragment size = 221 
INFO  @ Sat, 29 Apr 2017 13:35:24: #1  total fragments in treatment: 14330631 
INFO  @ Sat, 29 Apr 2017 13:35:24: #1 user defined the maximum fragments... 
INFO  @ Sat, 29 Apr 2017 13:35:24: #1 filter out redundant fragments by allowing at most 1 identical fragment(s) 
INFO  @ Sat, 29 Apr 2017 13:36:09: #1  fragments after filtering in treatment: 9983930 
INFO  @ Sat, 29 Apr 2017 13:36:09: #1  Redundant rate of treatment: 0.30 
INFO  @ Sat, 29 Apr 2017 13:36:09: #1  total fragments in control: 7630985 
INFO  @ Sat, 29 Apr 2017 13:36:09: #1 user defined the maximum fragments... 
INFO  @ Sat, 29 Apr 2017 13:36:09: #1 filter out redundant fragments by allowing at most 1 identical fragment(s) 
INFO  @ Sat, 29 Apr 2017 13:36:30: #1  fragments after filtering in control: 4959605 
INFO  @ Sat, 29 Apr 2017 13:36:30: #1  Redundant rate of control: 0.35 
INFO  @ Sat, 29 Apr 2017 13:36:30: #1 finished! 
INFO  @ Sat, 29 Apr 2017 13:36:30: #2 Build Peak Model... 
INFO  @ Sat, 29 Apr 2017 13:36:30: #2 Skipped... 
INFO  @ Sat, 29 Apr 2017 13:36:30: #2 Use 221 as fragment length 
INFO  @ Sat, 29 Apr 2017 13:36:30: #3 Call peaks... 
INFO  @ Sat, 29 Apr 2017 13:36:30: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sat, 29 Apr 2017 13:37:45: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sat, 29 Apr 2017 13:37:45: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... MACS2_treat_pileup.bdg 
INFO  @ Sat, 29 Apr 2017 13:37:45: #3   Write bedGraph files for control lambda (after scaling if necessary)... MACS2_control_lambda.bdg 
INFO  @ Sat, 29 Apr 2017 13:37:45: #3   Pileup will be based on sequencing depth in control. 
INFO  @ Sat, 29 Apr 2017 13:37:45: #3 Call peaks for each chromosome... 
INFO  @ Sat, 29 Apr 2017 13:40:39: #4 Write output xls file... MACS2_peaks.xls 
INFO  @ Sat, 29 Apr 2017 13:40:39: #4 Write peak in narrowPeak format file... MACS2_peaks.narrowPeak 
INFO  @ Sat, 29 Apr 2017 13:40:40: #4 Write summits bed file... MACS2_summits.bed 
INFO  @ Sat, 29 Apr 2017 13:40:40: Done!
chip-seq • 308 views
ADD COMMENTlink modified 7 months ago by Devon Ryan1.8k • written 7 months ago by 3400722560
1
gravatar for Devon Ryan
7 months ago by
Devon Ryan1.8k
Germany
Devon Ryan1.8k wrote:

The problem is the PDF output. The "Build Peak Model" step was skipped, so there was nothing to make a PDF out of. This is actually a common problem.

ADD COMMENTlink written 7 months ago by Devon Ryan1.8k

Thank you very much ! I have tried to disable the PDF output and it was not failed this time :) But I still don't understand why the " Build peak model" was skipped? isn't MACS2 supposed to call peaks based on the peak model it builds?

ADD REPLYlink written 7 months ago by 3400722560

I'm not sure why, that particular wording should only happen if you instruct MACS2 not to build a model, which is not something you did.

ADD REPLYlink written 7 months ago by Devon Ryan1.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 118 users visited in the last hour