Job ID = 2002180 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,895,798 reads read : 21,895,798 reads written : 21,895,798 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:07:38 21895798 reads; of these: 21895798 (100.00%) were unpaired; of these: 734598 (3.35%) aligned 0 times 15526232 (70.91%) aligned exactly 1 time 5634968 (25.74%) aligned >1 times 96.65% overall alignment rate Time searching: 00:07:39 Overall time: 00:07:39 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1604564 / 21161200 = 0.0758 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 11:41:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 11:41:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:41:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:41:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 11:41:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:41:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:41:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 11:41:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:41:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:41:15: 1000000 INFO @ Fri, 05 Jul 2019 11:41:16: 1000000 INFO @ Fri, 05 Jul 2019 11:41:16: 1000000 INFO @ Fri, 05 Jul 2019 11:41:22: 2000000 INFO @ Fri, 05 Jul 2019 11:41:23: 2000000 INFO @ Fri, 05 Jul 2019 11:41:24: 2000000 INFO @ Fri, 05 Jul 2019 11:41:28: 3000000 INFO @ Fri, 05 Jul 2019 11:41:29: 3000000 INFO @ Fri, 05 Jul 2019 11:41:33: 3000000 INFO @ Fri, 05 Jul 2019 11:41:35: 4000000 INFO @ Fri, 05 Jul 2019 11:41:36: 4000000 INFO @ Fri, 05 Jul 2019 11:41:41: 4000000 INFO @ Fri, 05 Jul 2019 11:41:42: 5000000 INFO @ Fri, 05 Jul 2019 11:41:43: 5000000 INFO @ Fri, 05 Jul 2019 11:41:48: 6000000 INFO @ Fri, 05 Jul 2019 11:41:49: 6000000 INFO @ Fri, 05 Jul 2019 11:41:50: 5000000 INFO @ Fri, 05 Jul 2019 11:41:55: 7000000 INFO @ Fri, 05 Jul 2019 11:41:56: 7000000 INFO @ Fri, 05 Jul 2019 11:41:58: 6000000 INFO @ Fri, 05 Jul 2019 11:42:02: 8000000 INFO @ Fri, 05 Jul 2019 11:42:03: 8000000 INFO @ Fri, 05 Jul 2019 11:42:06: 7000000 INFO @ Fri, 05 Jul 2019 11:42:08: 9000000 INFO @ Fri, 05 Jul 2019 11:42:09: 9000000 INFO @ Fri, 05 Jul 2019 11:42:15: 8000000 INFO @ Fri, 05 Jul 2019 11:42:15: 10000000 INFO @ Fri, 05 Jul 2019 11:42:16: 10000000 INFO @ Fri, 05 Jul 2019 11:42:21: 11000000 INFO @ Fri, 05 Jul 2019 11:42:22: 11000000 INFO @ Fri, 05 Jul 2019 11:42:23: 9000000 INFO @ Fri, 05 Jul 2019 11:42:28: 12000000 INFO @ Fri, 05 Jul 2019 11:42:29: 12000000 INFO @ Fri, 05 Jul 2019 11:42:31: 10000000 INFO @ Fri, 05 Jul 2019 11:42:34: 13000000 INFO @ Fri, 05 Jul 2019 11:42:35: 13000000 INFO @ Fri, 05 Jul 2019 11:42:39: 11000000 INFO @ Fri, 05 Jul 2019 11:42:41: 14000000 INFO @ Fri, 05 Jul 2019 11:42:42: 14000000 INFO @ Fri, 05 Jul 2019 11:42:47: 12000000 INFO @ Fri, 05 Jul 2019 11:42:48: 15000000 INFO @ Fri, 05 Jul 2019 11:42:49: 15000000 INFO @ Fri, 05 Jul 2019 11:42:54: 16000000 INFO @ Fri, 05 Jul 2019 11:42:55: 13000000 INFO @ Fri, 05 Jul 2019 11:42:55: 16000000 INFO @ Fri, 05 Jul 2019 11:43:01: 17000000 INFO @ Fri, 05 Jul 2019 11:43:02: 17000000 INFO @ Fri, 05 Jul 2019 11:43:03: 14000000 INFO @ Fri, 05 Jul 2019 11:43:07: 18000000 INFO @ Fri, 05 Jul 2019 11:43:08: 18000000 INFO @ Fri, 05 Jul 2019 11:43:11: 15000000 INFO @ Fri, 05 Jul 2019 11:43:14: 19000000 INFO @ Fri, 05 Jul 2019 11:43:15: 19000000 INFO @ Fri, 05 Jul 2019 11:43:18: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:43:18: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:43:18: #1 total tags in treatment: 19556636 INFO @ Fri, 05 Jul 2019 11:43:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:43:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 11:43:19: #1 tags after filtering in treatment: 19556505 INFO @ Fri, 05 Jul 2019 11:43:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:43:19: #1 finished! INFO @ Fri, 05 Jul 2019 11:43:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:43:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:43:19: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:43:19: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:43:19: #1 total tags in treatment: 19556636 INFO @ Fri, 05 Jul 2019 11:43:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:43:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 11:43:19: 16000000 INFO @ Fri, 05 Jul 2019 11:43:20: #1 tags after filtering in treatment: 19556505 INFO @ Fri, 05 Jul 2019 11:43:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:43:20: #1 finished! INFO @ Fri, 05 Jul 2019 11:43:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:43:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:43:22: #2 number of paired peaks: 37005 INFO @ Fri, 05 Jul 2019 11:43:22: start model_add_line... INFO @ Fri, 05 Jul 2019 11:43:22: start X-correlation... INFO @ Fri, 05 Jul 2019 11:43:22: end of X-cor INFO @ Fri, 05 Jul 2019 11:43:22: #2 finished! INFO @ Fri, 05 Jul 2019 11:43:22: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 11:43:22: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 05 Jul 2019 11:43:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.10_model.r INFO @ Fri, 05 Jul 2019 11:43:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:43:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:43:23: #2 number of paired peaks: 37005 INFO @ Fri, 05 Jul 2019 11:43:23: start model_add_line... INFO @ Fri, 05 Jul 2019 11:43:23: start X-correlation... INFO @ Fri, 05 Jul 2019 11:43:23: end of X-cor INFO @ Fri, 05 Jul 2019 11:43:23: #2 finished! INFO @ Fri, 05 Jul 2019 11:43:23: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 11:43:23: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 05 Jul 2019 11:43:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.20_model.r INFO @ Fri, 05 Jul 2019 11:43:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:43:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:43:27: 17000000 INFO @ Fri, 05 Jul 2019 11:43:35: 18000000 INFO @ Fri, 05 Jul 2019 11:43:43: 19000000 INFO @ Fri, 05 Jul 2019 11:43:48: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:43:48: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:43:48: #1 total tags in treatment: 19556636 INFO @ Fri, 05 Jul 2019 11:43:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:43:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 11:43:48: #1 tags after filtering in treatment: 19556505 INFO @ Fri, 05 Jul 2019 11:43:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:43:48: #1 finished! INFO @ Fri, 05 Jul 2019 11:43:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:43:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:43:52: #2 number of paired peaks: 37005 INFO @ Fri, 05 Jul 2019 11:43:52: start model_add_line... INFO @ Fri, 05 Jul 2019 11:43:52: start X-correlation... INFO @ Fri, 05 Jul 2019 11:43:52: end of X-cor INFO @ Fri, 05 Jul 2019 11:43:52: #2 finished! INFO @ Fri, 05 Jul 2019 11:43:52: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 11:43:52: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 05 Jul 2019 11:43:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.05_model.r INFO @ Fri, 05 Jul 2019 11:43:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:43:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:44:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:44:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:44:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:44:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:44:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:44:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:44:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:44:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.20_summits.bed INFO @ Fri, 05 Jul 2019 11:44:57: Done! INFO @ Fri, 05 Jul 2019 11:44:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.10_summits.bed INFO @ Fri, 05 Jul 2019 11:44:57: Done! pass1 - making usageList (53 chroms): 4 millis pass2 - checking and writing primary data (13769 records, 4 fields): 20 millis pass1 - making usageList (79 chroms): 7 millis pass2 - checking and writing primary data (22914 records, 4 fields): 32 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:45:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:45:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:45:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210277/ERX210277.05_summits.bed INFO @ Fri, 05 Jul 2019 11:45:26: Done! pass1 - making usageList (106 chroms): 12 millis pass2 - checking and writing primary data (33206 records, 4 fields): 45 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。