Additional Files:
Messages from MACS2:
INFO @ Sun, 15 May 2016 00:56:14:
# Command line: callpeak --name MACS2 -t /galaxy-repl/main/files/015/807/dataset_15807821.dat -c /galaxy-repl/main/files/015/807/dataset_15807838.dat --format=BAM --gsize 2451960000 --bw=300 --ratio 1.0 --slocal 500 --llocal 10000 --keep-dup 1 --bdg --qvalue 0.001
# ARGUMENTS LIST:
# name = MACS2
# format = BAM
# ChIP-seq file = ['/galaxy-repl/main/files/015/807/dataset_15807821.dat']
# control file = ['/galaxy-repl/main/files/015/807/dataset_15807838.dat']
# effective genome size = 2.45e+09
# band width = 300
# model fold = [5, 50]
# qvalue cutoff = 1.00e-03
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 500 bps and 10000 bps
# Broad region calling is off
INFO @ Sun, 15 May 2016 00:56:14: #1 read tag files...
INFO @ Sun, 15 May 2016 00:56:14: #1 read treatment tags...
INFO @ Sun, 15 May 2016 00:56:19: 1000000
INFO @ Sun, 15 May 2016 00:56:24: 2000000
INFO @ Sun, 15 May 2016 00:56:27: 3000000
INFO @ Sun, 15 May 2016 00:56:29: #1.2 read input tags...
INFO @ Sun, 15 May 2016 00:56:34: 1000000
INFO @ Sun, 15 May 2016 00:56:39: 2000000
INFO @ Sun, 15 May 2016 00:56:44: 3000000
INFO @ Sun, 15 May 2016 00:56:48: 4000000
INFO @ Sun, 15 May 2016 00:56:51: 5000000
INFO @ Sun, 15 May 2016 00:56:51: #1 tag size is determined as 36 bps
INFO @ Sun, 15 May 2016 00:56:51: #1 tag size = 36
INFO @ Sun, 15 May 2016 00:56:51: #1 total tags in treatment: 2134676
INFO @ Sun, 15 May 2016 00:56:51: #1 user defined the maximum tags...
INFO @ Sun, 15 May 2016 00:56:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO @ Sun, 15 May 2016 00:56:51: #1 tags after filtering in treatment: 1742227
INFO @ Sun, 15 May 2016 00:56:51: #1 Redundant rate of treatment: 0.18
INFO @ Sun, 15 May 2016 00:56:51: #1 total tags in control: 3621061
INFO @ Sun, 15 May 2016 00:56:51: #1 user defined the maximum tags...
INFO @ Sun, 15 May 2016 00:56:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO @ Sun, 15 May 2016 00:56:52: #1 tags after filtering in control: 3010528
INFO @ Sun, 15 May 2016 00:56:52: #1 Redundant rate of control: 0.17
INFO @ Sun, 15 May 2016 00:56:52: #1 finished!
INFO @ Sun, 15 May 2016 00:56:52: #2 Build Peak Model...
INFO @ Sun, 15 May 2016 00:56:52: #2 looking for paired plus/minus strand peaks...
INFO @ Sun, 15 May 2016 00:56:58: #2 number of paired peaks: 90322
INFO @ Sun, 15 May 2016 00:56:58: start model_add_line...
INFO @ Sun, 15 May 2016 00:56:58: start X-correlation...
INFO @ Sun, 15 May 2016 00:56:58: end of X-cor
INFO @ Sun, 15 May 2016 00:56:58: #2 finished!
INFO @ Sun, 15 May 2016 00:56:58: #2 predicted fragment length is 69 bps
INFO @ Sun, 15 May 2016 00:56:58: #2 alternative fragment length(s) may be 69,274 bps
INFO @ Sun, 15 May 2016 00:56:58: #2.2 Generate R script for model : MACS2_model.r
WARNING @ Sun, 15 May 2016 00:56:58: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem!
WARNING @ Sun, 15 May 2016 00:56:58: #2 You may need to consider one of the other alternative d(s): 69,274
WARNING @ Sun, 15 May 2016 00:56:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing.
INFO @ Sun, 15 May 2016 00:56:58: #3 Call peaks...
INFO @ Sun, 15 May 2016 00:56:58: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 15 May 2016 00:57:24: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 15 May 2016 00:57:24: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... MACS2_treat_pileup.bdg
INFO @ Sun, 15 May 2016 00:57:24: #3 Write bedGraph files for control lambda (after scaling if necessary)... MACS2_control_lambda.bdg
INFO @ Sun, 15 May 2016 00:57:24: #3 Pileup will be based on sequencing depth in treatment.
INFO @ Sun, 15 May 2016 00:57:24: #3 Call peaks for each chromosome...
INFO @ Sun, 15 May 2016 00:58:18: #4 Write output xls file... MACS2_peaks.xls
INFO @ Sun, 15 May 2016 00:58:19: #4 Write peak in narrowPeak format file... MACS2_peaks.narrowPeak
INFO @ Sun, 15 May 2016 00:58:19: #4 Write summits bed file... MACS2_summits.bed
INFO @ Sun, 15 May 2016 00:58:19: Done!