Question: Error with MACS2 peak calling
0
340072256 • 0 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!
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modified 19 months ago
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Devon Ryan • 1.9k
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340072256 • 0
