Job ID = 2001700 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,748,853 reads read : 28,748,853 reads written : 28,748,853 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:11:04 28748853 reads; of these: 28748853 (100.00%) were unpaired; of these: 618260 (2.15%) aligned 0 times 21370212 (74.33%) aligned exactly 1 time 6760381 (23.52%) aligned >1 times 97.85% overall alignment rate Time searching: 00:11:06 Overall time: 00:11:07 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] 1962382 / 28130593 = 0.0698 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 09:22:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.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 09:22:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:22:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:22:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.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 09:22:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:22:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:22:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.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 09:22:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:22:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:22:38: 1000000 INFO @ Fri, 05 Jul 2019 09:22:39: 1000000 INFO @ Fri, 05 Jul 2019 09:22:39: 1000000 INFO @ Fri, 05 Jul 2019 09:22:45: 2000000 INFO @ Fri, 05 Jul 2019 09:22:46: 2000000 INFO @ Fri, 05 Jul 2019 09:22:46: 2000000 INFO @ Fri, 05 Jul 2019 09:22:52: 3000000 INFO @ Fri, 05 Jul 2019 09:22:52: 3000000 INFO @ Fri, 05 Jul 2019 09:22:53: 3000000 INFO @ Fri, 05 Jul 2019 09:22:58: 4000000 INFO @ Fri, 05 Jul 2019 09:22:58: 4000000 INFO @ Fri, 05 Jul 2019 09:23:01: 4000000 INFO @ Fri, 05 Jul 2019 09:23:05: 5000000 INFO @ Fri, 05 Jul 2019 09:23:05: 5000000 INFO @ Fri, 05 Jul 2019 09:23:08: 5000000 INFO @ Fri, 05 Jul 2019 09:23:11: 6000000 INFO @ Fri, 05 Jul 2019 09:23:12: 6000000 INFO @ Fri, 05 Jul 2019 09:23:16: 6000000 INFO @ Fri, 05 Jul 2019 09:23:18: 7000000 INFO @ Fri, 05 Jul 2019 09:23:18: 7000000 INFO @ Fri, 05 Jul 2019 09:23:23: 7000000 INFO @ Fri, 05 Jul 2019 09:23:24: 8000000 INFO @ Fri, 05 Jul 2019 09:23:25: 8000000 INFO @ Fri, 05 Jul 2019 09:23:30: 9000000 INFO @ Fri, 05 Jul 2019 09:23:31: 8000000 INFO @ Fri, 05 Jul 2019 09:23:32: 9000000 INFO @ Fri, 05 Jul 2019 09:23:37: 10000000 INFO @ Fri, 05 Jul 2019 09:23:38: 10000000 INFO @ Fri, 05 Jul 2019 09:23:39: 9000000 INFO @ Fri, 05 Jul 2019 09:23:43: 11000000 INFO @ Fri, 05 Jul 2019 09:23:45: 11000000 INFO @ Fri, 05 Jul 2019 09:23:47: 10000000 INFO @ Fri, 05 Jul 2019 09:23:49: 12000000 INFO @ Fri, 05 Jul 2019 09:23:51: 12000000 INFO @ Fri, 05 Jul 2019 09:23:54: 11000000 INFO @ Fri, 05 Jul 2019 09:23:56: 13000000 INFO @ Fri, 05 Jul 2019 09:23:58: 13000000 INFO @ Fri, 05 Jul 2019 09:24:02: 12000000 INFO @ Fri, 05 Jul 2019 09:24:02: 14000000 INFO @ Fri, 05 Jul 2019 09:24:04: 14000000 INFO @ Fri, 05 Jul 2019 09:24:09: 15000000 INFO @ Fri, 05 Jul 2019 09:24:10: 13000000 INFO @ Fri, 05 Jul 2019 09:24:11: 15000000 INFO @ Fri, 05 Jul 2019 09:24:15: 16000000 INFO @ Fri, 05 Jul 2019 09:24:17: 16000000 INFO @ Fri, 05 Jul 2019 09:24:18: 14000000 INFO @ Fri, 05 Jul 2019 09:24:22: 17000000 INFO @ Fri, 05 Jul 2019 09:24:24: 17000000 INFO @ Fri, 05 Jul 2019 09:24:25: 15000000 INFO @ Fri, 05 Jul 2019 09:24:28: 18000000 INFO @ Fri, 05 Jul 2019 09:24:30: 18000000 INFO @ Fri, 05 Jul 2019 09:24:33: 16000000 INFO @ Fri, 05 Jul 2019 09:24:34: 19000000 INFO @ Fri, 05 Jul 2019 09:24:37: 19000000 INFO @ Fri, 05 Jul 2019 09:24:41: 20000000 INFO @ Fri, 05 Jul 2019 09:24:41: 17000000 INFO @ Fri, 05 Jul 2019 09:24:44: 20000000 INFO @ Fri, 05 Jul 2019 09:24:48: 21000000 INFO @ Fri, 05 Jul 2019 09:24:49: 18000000 INFO @ Fri, 05 Jul 2019 09:24:51: 21000000 INFO @ Fri, 05 Jul 2019 09:24:55: 22000000 INFO @ Fri, 05 Jul 2019 09:24:56: 19000000 INFO @ Fri, 05 Jul 2019 09:24:58: 22000000 INFO @ Fri, 05 Jul 2019 09:25:01: 23000000 INFO @ Fri, 05 Jul 2019 09:25:04: 20000000 INFO @ Fri, 05 Jul 2019 09:25:04: 23000000 INFO @ Fri, 05 Jul 2019 09:25:08: 24000000 INFO @ Fri, 05 Jul 2019 09:25:11: 24000000 INFO @ Fri, 05 Jul 2019 09:25:12: 21000000 INFO @ Fri, 05 Jul 2019 09:25:14: 25000000 INFO @ Fri, 05 Jul 2019 09:25:18: 25000000 INFO @ Fri, 05 Jul 2019 09:25:20: 22000000 INFO @ Fri, 05 Jul 2019 09:25:21: 26000000 INFO @ Fri, 05 Jul 2019 09:25:22: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:25:22: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:25:22: #1 total tags in treatment: 26168211 INFO @ Fri, 05 Jul 2019 09:25:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:25:22: #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 09:25:23: #1 tags after filtering in treatment: 26168055 INFO @ Fri, 05 Jul 2019 09:25:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:25:23: #1 finished! INFO @ Fri, 05 Jul 2019 09:25:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:25:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:25:25: 26000000 INFO @ Fri, 05 Jul 2019 09:25:26: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:25:26: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:25:26: #1 total tags in treatment: 26168211 INFO @ Fri, 05 Jul 2019 09:25:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:25:26: #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 09:25:27: #1 tags after filtering in treatment: 26168055 INFO @ Fri, 05 Jul 2019 09:25:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:25:27: #1 finished! INFO @ Fri, 05 Jul 2019 09:25:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:25:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:25:27: 23000000 INFO @ Fri, 05 Jul 2019 09:25:28: #2 number of paired peaks: 57559 INFO @ Fri, 05 Jul 2019 09:25:28: start model_add_line... INFO @ Fri, 05 Jul 2019 09:25:28: start X-correlation... INFO @ Fri, 05 Jul 2019 09:25:28: end of X-cor INFO @ Fri, 05 Jul 2019 09:25:28: #2 finished! INFO @ Fri, 05 Jul 2019 09:25:28: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 09:25:28: #2 alternative fragment length(s) may be 2,131,286,501 bps INFO @ Fri, 05 Jul 2019 09:25:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.20_model.r INFO @ Fri, 05 Jul 2019 09:25:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:25:32: #2 number of paired peaks: 57559 INFO @ Fri, 05 Jul 2019 09:25:32: start model_add_line... INFO @ Fri, 05 Jul 2019 09:25:32: start X-correlation... INFO @ Fri, 05 Jul 2019 09:25:32: end of X-cor INFO @ Fri, 05 Jul 2019 09:25:32: #2 finished! INFO @ Fri, 05 Jul 2019 09:25:32: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 09:25:32: #2 alternative fragment length(s) may be 2,131,286,501 bps INFO @ Fri, 05 Jul 2019 09:25:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.10_model.r INFO @ Fri, 05 Jul 2019 09:25:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:25:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:25:35: 24000000 INFO @ Fri, 05 Jul 2019 09:25:43: 25000000 INFO @ Fri, 05 Jul 2019 09:25:50: 26000000 INFO @ Fri, 05 Jul 2019 09:25:52: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:25:52: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:25:52: #1 total tags in treatment: 26168211 INFO @ Fri, 05 Jul 2019 09:25:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:25:52: #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 09:25:53: #1 tags after filtering in treatment: 26168055 INFO @ Fri, 05 Jul 2019 09:25:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:25:53: #1 finished! INFO @ Fri, 05 Jul 2019 09:25:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:25:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:25:58: #2 number of paired peaks: 57559 INFO @ Fri, 05 Jul 2019 09:25:58: start model_add_line... INFO @ Fri, 05 Jul 2019 09:25:58: start X-correlation... INFO @ Fri, 05 Jul 2019 09:25:58: end of X-cor INFO @ Fri, 05 Jul 2019 09:25:58: #2 finished! INFO @ Fri, 05 Jul 2019 09:25:58: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 09:25:58: #2 alternative fragment length(s) may be 2,131,286,501 bps INFO @ Fri, 05 Jul 2019 09:25:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.05_model.r INFO @ Fri, 05 Jul 2019 09:25:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:25:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:26:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:26:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:27:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:27:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:27:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:27:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.20_summits.bed INFO @ Fri, 05 Jul 2019 09:27:31: Done! pass1 - making usageList (28 chroms): 2 millis pass2 - checking and writing primary data (109 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:27:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:27:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:27:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.10_summits.bed INFO @ Fri, 05 Jul 2019 09:27:35: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (990 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:28:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:28:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:28:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102010/ERX102010.05_summits.bed INFO @ Fri, 05 Jul 2019 09:28:02: Done! pass1 - making usageList (61 chroms): 1 millis pass2 - checking and writing primary data (4711 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。