Additional Files:

• GalGal_test_for_MACS2.1.0_peaks.xls
• GalGal_test_for_MACS2.1.0_treat_pileup.bdg.clipped

Messages from MACS:

INFO  @ Mon, 01 Jun 2015 13:38:32: 
# Command line: callpeak -t /mnt/fls01-data01/galaxy/production/database/files/003/dataset_3746.dat -c /mnt/fls01-data01/galaxy/production/database/files/003/dataset_3745.dat --format=BED --name=GalGal_test_for_MACS2.1.0 --bw=300 --gsize=775000000.0 --nomodel --extsize=243 --qvalue=0.05 -B --SPMR --mfold 5 50 --keep-dup 1
# ARGUMENTS LIST:
# name = GalGal_test_for_MACS2.1.0
# format = BED
# ChIP-seq file = ['/mnt/fls01-data01/galaxy/production/database/files/003/dataset_3746.dat']
# control file = ['/mnt/fls01-data01/galaxy/production/database/files/003/dataset_3745.dat']
# effective genome size = 7.75e+08
# 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
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 01 Jun 2015 13:38:32: #1 read tag files... 
INFO  @ Mon, 01 Jun 2015 13:38:32: #1 read treatment tags... 
INFO  @ Mon, 01 Jun 2015 13:38:32: #1.2 read input tags... 
INFO  @ Mon, 01 Jun 2015 13:38:33: #1 tag size is determined as 50 bps 
INFO  @ Mon, 01 Jun 2015 13:38:33: #1 tag size = 50 
INFO  @ Mon, 01 Jun 2015 13:38:33: #1  total tags in treatment: 250 
INFO  @ Mon, 01 Jun 2015 13:38:33: #1 user defined the maximum tags... 
INFO  @ Mon, 01 Jun 2015 13:38:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Mon, 01 Jun 2015 13:38:33: #1  tags after filtering in treatment: 248 
INFO  @ Mon, 01 Jun 2015 13:38:33: #1  Redundant rate of treatment: 0.01 
INFO  @ Mon, 01 Jun 2015 13:38:33: #1  total tags in control: 250 
INFO  @ Mon, 01 Jun 2015 13:38:33: #1 user defined the maximum tags... 
INFO  @ Mon, 01 Jun 2015 13:38:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Mon, 01 Jun 2015 13:38:33: #1  tags after filtering in control: 248 
INFO  @ Mon, 01 Jun 2015 13:38:33: #1  Redundant rate of control: 0.01 
INFO  @ Mon, 01 Jun 2015 13:38:33: #1 finished! 
INFO  @ Mon, 01 Jun 2015 13:38:33: #2 Build Peak Model... 
INFO  @ Mon, 01 Jun 2015 13:38:33: #2 Skipped... 
INFO  @ Mon, 01 Jun 2015 13:38:33: #2 Use 243 as fragment length 
INFO  @ Mon, 01 Jun 2015 13:38:33: #3 Call peaks... 
INFO  @ Mon, 01 Jun 2015 13:38:33: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 01 Jun 2015 13:38:33: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 01 Jun 2015 13:38:33: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... GalGal_test_for_MACS2.1.0_treat_pileup.bdg 
INFO  @ Mon, 01 Jun 2015 13:38:33: #3   Write bedGraph files for control lambda (after scaling if necessary)... GalGal_test_for_MACS2.1.0_control_lambda.bdg 
INFO  @ Mon, 01 Jun 2015 13:38:33: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 01 Jun 2015 13:38:33: #3 Call peaks for each chromosome... 
INFO  @ Mon, 01 Jun 2015 13:38:33: #4 Write output xls file... GalGal_test_for_MACS2.1.0_peaks.xls 
INFO  @ Mon, 01 Jun 2015 13:38:33: #4 Write peak in narrowPeak format file... GalGal_test_for_MACS2.1.0_peaks.narrowPeak 
INFO  @ Mon, 01 Jun 2015 13:38:33: #4 Write summits bed file... GalGal_test_for_MACS2.1.0_summits.bed 
INFO  @ Mon, 01 Jun 2015 13:38:33: Done!