Job ID = 2002156 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,687,549 reads read : 25,687,549 reads written : 25,687,549 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:21:12 25687549 reads; of these: 25687549 (100.00%) were unpaired; of these: 464619 (1.81%) aligned 0 times 20215876 (78.70%) aligned exactly 1 time 5007054 (19.49%) aligned >1 times 98.19% overall alignment rate Time searching: 00:21:15 Overall time: 00:21:15 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 12 files... [bam_rmdupse_core] 511288 / 25222930 = 0.0203 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 11:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.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 11:26:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:26:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.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 11:26:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:26:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.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 11:26:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:26:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:26:26: 1000000 INFO @ Fri, 05 Jul 2019 11:26:27: 1000000 INFO @ Fri, 05 Jul 2019 11:26:27: 1000000 INFO @ Fri, 05 Jul 2019 11:26:35: 2000000 INFO @ Fri, 05 Jul 2019 11:26:38: 2000000 INFO @ Fri, 05 Jul 2019 11:26:38: 2000000 INFO @ Fri, 05 Jul 2019 11:26:44: 3000000 INFO @ Fri, 05 Jul 2019 11:26:49: 3000000 INFO @ Fri, 05 Jul 2019 11:26:49: 3000000 INFO @ Fri, 05 Jul 2019 11:26:53: 4000000 INFO @ Fri, 05 Jul 2019 11:27:00: 4000000 INFO @ Fri, 05 Jul 2019 11:27:00: 4000000 INFO @ Fri, 05 Jul 2019 11:27:02: 5000000 INFO @ Fri, 05 Jul 2019 11:27:11: 5000000 INFO @ Fri, 05 Jul 2019 11:27:11: 6000000 INFO @ Fri, 05 Jul 2019 11:27:12: 5000000 INFO @ Fri, 05 Jul 2019 11:27:20: 7000000 INFO @ Fri, 05 Jul 2019 11:27:22: 6000000 INFO @ Fri, 05 Jul 2019 11:27:23: 6000000 INFO @ Fri, 05 Jul 2019 11:27:29: 8000000 INFO @ Fri, 05 Jul 2019 11:27:33: 7000000 INFO @ Fri, 05 Jul 2019 11:27:34: 7000000 INFO @ Fri, 05 Jul 2019 11:27:38: 9000000 INFO @ Fri, 05 Jul 2019 11:27:44: 8000000 INFO @ Fri, 05 Jul 2019 11:27:44: 8000000 INFO @ Fri, 05 Jul 2019 11:27:47: 10000000 INFO @ Fri, 05 Jul 2019 11:27:54: 9000000 INFO @ Fri, 05 Jul 2019 11:27:56: 9000000 INFO @ Fri, 05 Jul 2019 11:27:57: 11000000 INFO @ Fri, 05 Jul 2019 11:28:05: 10000000 INFO @ Fri, 05 Jul 2019 11:28:06: 12000000 INFO @ Fri, 05 Jul 2019 11:28:07: 10000000 INFO @ Fri, 05 Jul 2019 11:28:15: 13000000 INFO @ Fri, 05 Jul 2019 11:28:16: 11000000 INFO @ Fri, 05 Jul 2019 11:28:18: 11000000 INFO @ Fri, 05 Jul 2019 11:28:24: 14000000 INFO @ Fri, 05 Jul 2019 11:28:27: 12000000 INFO @ Fri, 05 Jul 2019 11:28:28: 12000000 INFO @ Fri, 05 Jul 2019 11:28:33: 15000000 INFO @ Fri, 05 Jul 2019 11:28:37: 13000000 INFO @ Fri, 05 Jul 2019 11:28:39: 13000000 INFO @ Fri, 05 Jul 2019 11:28:42: 16000000 INFO @ Fri, 05 Jul 2019 11:28:48: 14000000 INFO @ Fri, 05 Jul 2019 11:28:50: 14000000 INFO @ Fri, 05 Jul 2019 11:28:50: 17000000 INFO @ Fri, 05 Jul 2019 11:28:59: 15000000 INFO @ Fri, 05 Jul 2019 11:28:59: 18000000 INFO @ Fri, 05 Jul 2019 11:29:01: 15000000 INFO @ Fri, 05 Jul 2019 11:29:07: 19000000 INFO @ Fri, 05 Jul 2019 11:29:09: 16000000 INFO @ Fri, 05 Jul 2019 11:29:12: 16000000 INFO @ Fri, 05 Jul 2019 11:29:15: 20000000 INFO @ Fri, 05 Jul 2019 11:29:19: 17000000 INFO @ Fri, 05 Jul 2019 11:29:23: 17000000 INFO @ Fri, 05 Jul 2019 11:29:24: 21000000 INFO @ Fri, 05 Jul 2019 11:29:30: 18000000 INFO @ Fri, 05 Jul 2019 11:29:33: 18000000 INFO @ Fri, 05 Jul 2019 11:29:33: 22000000 INFO @ Fri, 05 Jul 2019 11:29:41: 19000000 INFO @ Fri, 05 Jul 2019 11:29:42: 23000000 INFO @ Fri, 05 Jul 2019 11:29:43: 19000000 INFO @ Fri, 05 Jul 2019 11:29:50: 24000000 INFO @ Fri, 05 Jul 2019 11:29:51: 20000000 INFO @ Fri, 05 Jul 2019 11:29:53: 20000000 INFO @ Fri, 05 Jul 2019 11:29:57: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:29:57: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:29:57: #1 total tags in treatment: 24711642 INFO @ Fri, 05 Jul 2019 11:29:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:29:57: #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 11:29:57: #1 tags after filtering in treatment: 24711456 INFO @ Fri, 05 Jul 2019 11:29:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:29:57: #1 finished! INFO @ Fri, 05 Jul 2019 11:29:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:29:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:30:02: 21000000 INFO @ Fri, 05 Jul 2019 11:30:04: 21000000 INFO @ Fri, 05 Jul 2019 11:30:04: #2 number of paired peaks: 125958 INFO @ Fri, 05 Jul 2019 11:30:04: start model_add_line... INFO @ Fri, 05 Jul 2019 11:30:05: start X-correlation... INFO @ Fri, 05 Jul 2019 11:30:05: end of X-cor INFO @ Fri, 05 Jul 2019 11:30:05: #2 finished! INFO @ Fri, 05 Jul 2019 11:30:05: #2 predicted fragment length is 254 bps INFO @ Fri, 05 Jul 2019 11:30:05: #2 alternative fragment length(s) may be 254 bps INFO @ Fri, 05 Jul 2019 11:30:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.20_model.r INFO @ Fri, 05 Jul 2019 11:30:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:30:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:30:12: 22000000 INFO @ Fri, 05 Jul 2019 11:30:15: 22000000 INFO @ Fri, 05 Jul 2019 11:30:22: 23000000 INFO @ Fri, 05 Jul 2019 11:30:25: 23000000 INFO @ Fri, 05 Jul 2019 11:30:32: 24000000 INFO @ Fri, 05 Jul 2019 11:30:35: 24000000 INFO @ Fri, 05 Jul 2019 11:30:39: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:30:39: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:30:39: #1 total tags in treatment: 24711642 INFO @ Fri, 05 Jul 2019 11:30:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:30:39: #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 11:30:40: #1 tags after filtering in treatment: 24711456 INFO @ Fri, 05 Jul 2019 11:30:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:30:40: #1 finished! INFO @ Fri, 05 Jul 2019 11:30:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:30:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:30:43: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:30:43: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:30:43: #1 total tags in treatment: 24711642 INFO @ Fri, 05 Jul 2019 11:30:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:30:43: #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 11:30:43: #1 tags after filtering in treatment: 24711456 INFO @ Fri, 05 Jul 2019 11:30:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:30:43: #1 finished! INFO @ Fri, 05 Jul 2019 11:30:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:30:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:30:47: #2 number of paired peaks: 125958 INFO @ Fri, 05 Jul 2019 11:30:47: start model_add_line... INFO @ Fri, 05 Jul 2019 11:30:47: start X-correlation... INFO @ Fri, 05 Jul 2019 11:30:47: end of X-cor INFO @ Fri, 05 Jul 2019 11:30:47: #2 finished! INFO @ Fri, 05 Jul 2019 11:30:47: #2 predicted fragment length is 254 bps INFO @ Fri, 05 Jul 2019 11:30:47: #2 alternative fragment length(s) may be 254 bps INFO @ Fri, 05 Jul 2019 11:30:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.05_model.r INFO @ Fri, 05 Jul 2019 11:30:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:30:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:30:50: #2 number of paired peaks: 125958 INFO @ Fri, 05 Jul 2019 11:30:50: start model_add_line... INFO @ Fri, 05 Jul 2019 11:30:51: start X-correlation... INFO @ Fri, 05 Jul 2019 11:30:51: end of X-cor INFO @ Fri, 05 Jul 2019 11:30:51: #2 finished! INFO @ Fri, 05 Jul 2019 11:30:51: #2 predicted fragment length is 254 bps INFO @ Fri, 05 Jul 2019 11:30:51: #2 alternative fragment length(s) may be 254 bps INFO @ Fri, 05 Jul 2019 11:30:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.10_model.r INFO @ Fri, 05 Jul 2019 11:30:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:30:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:31:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:32:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:32:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:32:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:32:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.20_summits.bed INFO @ Fri, 05 Jul 2019 11:32:08: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (411 records, 4 fields): 5 millis INFO @ Fri, 05 Jul 2019 11:32:09: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:32:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:32:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:32:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.05_summits.bed INFO @ Fri, 05 Jul 2019 11:32:53: Done! pass1 - making usageList (95 chroms): 9 millis pass2 - checking and writing primary data (27470 records, 4 fields): 73 millis INFO @ Fri, 05 Jul 2019 11:32:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:32:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:32:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX1120745/ERX1120745.10_summits.bed INFO @ Fri, 05 Jul 2019 11:32:54: Done! pass1 - making usageList (51 chroms): 3 millis pass2 - checking and writing primary data (4572 records, 4 fields): 13 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。