macs2---使用记录

-- (base) [yangjy@GSCG01 dum]$ macs2 callpeak -c  Control.merge.rmdup.bam -t H2Aub1.merge.rmdup.bam -f BAM -B -g mm -n H2Aub1
INFO  @ Wed, 03 Feb 2021 12:22:13:
# Command line: callpeak -c Control.merge.rmdup.bam -t H2Aub1.merge.rmdup.bam -f BAM -B -g mm -n H2Aub1
# ARGUMENTS LIST:
# name = H2Aub1
# format = BAM
# ChIP-seq file = ['H2Aub1.merge.rmdup.bam']
# control file = ['Control.merge.rmdup.bam']
# effective genome size = 1.87e+09
# band width = 300
# model fold = [5, 50]
# qvalue cutoff = 5.00e-02
# The maximum gap between significant sites is assigned as the read length/tag size.
# The minimum length of peaks is assigned as the predicted fragment length "d".
# 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 off

处理进程

INFO  @ Wed, 03 Feb 2021 12:22:13: #1 read tag files...  
INFO  @ Wed, 03 Feb 2021 12:22:13: #1 read treatment tags...    读取 实验组
INFO  @ Wed, 03 Feb 2021 12:22:15:  1000000
INFO  @ Wed, 03 Feb 2021 12:22:16:  2000000
INFO  @ Wed, 03 Feb 2021 12:22:18:  3000000
INFO  @ Wed, 03 Feb 2021 12:22:19:  4000000
INFO  @ Wed, 03 Feb 2021 12:22:21:  5000000
INFO  @ Wed, 03 Feb 2021 12:22:22:  6000000
INFO  @ Wed, 03 Feb 2021 12:22:24:  7000000
INFO  @ Wed, 03 Feb 2021 12:22:25:  8000000
INFO  @ Wed, 03 Feb 2021 12:22:27:  9000000
INFO  @ Wed, 03 Feb 2021 12:22:28:  10000000
INFO  @ Wed, 03 Feb 2021 12:22:30:  11000000
INFO  @ Wed, 03 Feb 2021 12:22:32:  12000000
INFO  @ Wed, 03 Feb 2021 12:22:33:  13000000
INFO  @ Wed, 03 Feb 2021 12:22:35:  14000000
INFO  @ Wed, 03 Feb 2021 12:22:36:  15000000
INFO  @ Wed, 03 Feb 2021 12:22:38:  16000000
INFO  @ Wed, 03 Feb 2021 12:22:39:  17000000
INFO  @ Wed, 03 Feb 2021 12:22:41: 17515747 reads have been read.

INFO  @ Wed, 03 Feb 2021 12:22:41: #1.2 read input tags...   *读取 对照组
INFO  @ Wed, 03 Feb 2021 12:22:42:  1000000
INFO  @ Wed, 03 Feb 2021 12:22:44:  2000000
INFO  @ Wed, 03 Feb 2021 12:22:45:  3000000
INFO  @ Wed, 03 Feb 2021 12:22:47:  4000000
INFO  @ Wed, 03 Feb 2021 12:22:48:  5000000
INFO  @ Wed, 03 Feb 2021 12:22:50:  6000000
INFO  @ Wed, 03 Feb 2021 12:22:51:  7000000
INFO  @ Wed, 03 Feb 2021 12:22:52:  8000000
INFO  @ Wed, 03 Feb 2021 12:22:54:  9000000
INFO  @ Wed, 03 Feb 2021 12:22:55:  10000000
INFO  @ Wed, 03 Feb 2021 12:22:57:  11000000
INFO  @ Wed, 03 Feb 2021 12:22:58:  12000000
INFO  @ Wed, 03 Feb 2021 12:23:01: 12331048 reads have been read.

INFO  @ Wed, 03 Feb 2021 12:23:01: #1 tag size is determined as 49 bps   
INFO  @ Wed, 03 Feb 2021 12:23:01: #1 tag size = 49.0
INFO  @ Wed, 03 Feb 2021 12:23:01: #1  total tags in treatment: 17515747
INFO  @ Wed, 03 Feb 2021 12:23:01: #1 user defined the maximum tags...
INFO  @ Wed, 03 Feb 2021 12:23:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO  @ Wed, 03 Feb 2021 12:23:01: #1  tags after filtering in treatment: 17515746
INFO  @ Wed, 03 Feb 2021 12:23:01: #1  Redundant rate of treatment: 0.00
INFO  @ Wed, 03 Feb 2021 12:23:01: #1  total tags in control: 12331048
INFO  @ Wed, 03 Feb 2021 12:23:01: #1 user defined the maximum tags...
INFO  @ Wed, 03 Feb 2021 12:23:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO  @ Wed, 03 Feb 2021 12:23:01: #1  tags after filtering in control: 12331048
INFO  @ Wed, 03 Feb 2021 12:23:01: #1  Redundant rate of control: 0.00
INFO  @ Wed, 03 Feb 2021 12:23:01: #1 finished!   # 完成
INFO  @ Wed, 03 Feb 2021 12:23:01: #2 Build Peak Model... # 建立模型
INFO  @ Wed, 03 Feb 2021 12:23:01: #2 looking for paired plus/minus strand peaks...
INFO  @ Wed, 03 Feb 2021 12:23:03: #2 number of paired peaks: 4584  # 
INFO  @ Wed, 03 Feb 2021 12:23:03: start model_add_line...
INFO  @ Wed, 03 Feb 2021 12:23:03: start X-correlation...
INFO  @ Wed, 03 Feb 2021 12:23:03: end of X-cor
INFO  @ Wed, 03 Feb 2021 12:23:03: #2 finished!
INFO  @ Wed, 03 Feb 2021 12:23:03: #2 predicted fragment length is 83 bps
INFO  @ Wed, 03 Feb 2021 12:23:03: #2 alternative fragment length(s) may be 83 bps
INFO  @ Wed, 03 Feb 2021 12:23:03: #2.2 Generate R script for model : H2Aub1_model.r
WARNING @ Wed, 03 Feb 2021 12:23:03: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem!
WARNING @ Wed, 03 Feb 2021 12:23:03: #2 You may need to consider one of the other alternative d(s): 83
WARNING @ Wed, 03 Feb 2021 12:23:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing.
INFO  @ Wed, 03 Feb 2021 12:23:03: #3 Call peaks...
INFO  @ Wed, 03 Feb 2021 12:23:03: #3 Pre-compute pvalue-qvalue table...
INFO  @ Wed, 03 Feb 2021 12:23:48: #3 In the peak calling step, the following will be performed simultaneously:
INFO  @ Wed, 03 Feb 2021 12:23:48: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... H2Aub1_treat_pileup.bdg
INFO  @ Wed, 03 Feb 2021 12:23:48: #3   Write bedGraph files for control lambda (after scaling if necessary)... H2Aub1_control_lambda.bdg
INFO  @ Wed, 03 Feb 2021 12:23:48: #3   Pileup will be based on sequencing depth in control.
INFO  @ Wed, 03 Feb 2021 12:23:48: #3 Call peaks for each chromosome...
INFO  @ Wed, 03 Feb 2021 12:24:34: #4 Write output xls file... H2Aub1_peaks.xls
INFO  @ Wed, 03 Feb 2021 12:24:34: #4 Write peak in narrowPeak format file... H2Aub1_peaks.narrowPeak
INFO  @ Wed, 03 Feb 2021 12:24:34: #4 Write summits bed file... H2Aub1_summits.bed
INFO  @ Wed, 03 Feb 2021 12:24:34: Done!
[1]+  Done                    macs2 callpeak -c Control.merge.rmdup.bam -t H2Aub1.merge.rmdup.bam -f BAM -B -g mm -n H2Aub1 2> H2Aub1.macs2.log