Job ID = 2001605 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,030,748 reads read : 29,030,748 reads written : 29,030,748 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:10:37 29030748 reads; of these: 29030748 (100.00%) were unpaired; of these: 707802 (2.44%) aligned 0 times 21479840 (73.99%) aligned exactly 1 time 6843106 (23.57%) aligned >1 times 97.56% overall alignment rate Time searching: 00:10:40 Overall time: 00:10:40 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] 1956539 / 28322946 = 0.0691 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 06:25:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.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 06:25:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:25:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:25:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.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 06:25:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:25:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:25:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.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 06:25:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:25:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:25:55: 1000000 INFO @ Fri, 05 Jul 2019 06:25:55: 1000000 INFO @ Fri, 05 Jul 2019 06:25:56: 1000000 INFO @ Fri, 05 Jul 2019 06:26:01: 2000000 INFO @ Fri, 05 Jul 2019 06:26:02: 2000000 INFO @ Fri, 05 Jul 2019 06:26:03: 2000000 INFO @ Fri, 05 Jul 2019 06:26:08: 3000000 INFO @ Fri, 05 Jul 2019 06:26:09: 3000000 INFO @ Fri, 05 Jul 2019 06:26:10: 3000000 INFO @ Fri, 05 Jul 2019 06:26:14: 4000000 INFO @ Fri, 05 Jul 2019 06:26:16: 4000000 INFO @ Fri, 05 Jul 2019 06:26:17: 4000000 INFO @ Fri, 05 Jul 2019 06:26:21: 5000000 INFO @ Fri, 05 Jul 2019 06:26:23: 5000000 INFO @ Fri, 05 Jul 2019 06:26:24: 5000000 INFO @ Fri, 05 Jul 2019 06:26:27: 6000000 INFO @ Fri, 05 Jul 2019 06:26:29: 6000000 INFO @ Fri, 05 Jul 2019 06:26:30: 6000000 INFO @ Fri, 05 Jul 2019 06:26:33: 7000000 INFO @ Fri, 05 Jul 2019 06:26:36: 7000000 INFO @ Fri, 05 Jul 2019 06:26:37: 7000000 INFO @ Fri, 05 Jul 2019 06:26:40: 8000000 INFO @ Fri, 05 Jul 2019 06:26:43: 8000000 INFO @ Fri, 05 Jul 2019 06:26:44: 8000000 INFO @ Fri, 05 Jul 2019 06:26:46: 9000000 INFO @ Fri, 05 Jul 2019 06:26:50: 9000000 INFO @ Fri, 05 Jul 2019 06:26:51: 9000000 INFO @ Fri, 05 Jul 2019 06:26:53: 10000000 INFO @ Fri, 05 Jul 2019 06:26:56: 10000000 INFO @ Fri, 05 Jul 2019 06:26:57: 10000000 INFO @ Fri, 05 Jul 2019 06:26:59: 11000000 INFO @ Fri, 05 Jul 2019 06:27:03: 11000000 INFO @ Fri, 05 Jul 2019 06:27:04: 11000000 INFO @ Fri, 05 Jul 2019 06:27:05: 12000000 INFO @ Fri, 05 Jul 2019 06:27:09: 12000000 INFO @ Fri, 05 Jul 2019 06:27:11: 12000000 INFO @ Fri, 05 Jul 2019 06:27:12: 13000000 INFO @ Fri, 05 Jul 2019 06:27:16: 13000000 INFO @ Fri, 05 Jul 2019 06:27:18: 13000000 INFO @ Fri, 05 Jul 2019 06:27:18: 14000000 INFO @ Fri, 05 Jul 2019 06:27:23: 14000000 INFO @ Fri, 05 Jul 2019 06:27:24: 15000000 INFO @ Fri, 05 Jul 2019 06:27:25: 14000000 INFO @ Fri, 05 Jul 2019 06:27:30: 15000000 INFO @ Fri, 05 Jul 2019 06:27:30: 16000000 INFO @ Fri, 05 Jul 2019 06:27:31: 15000000 INFO @ Fri, 05 Jul 2019 06:27:36: 16000000 INFO @ Fri, 05 Jul 2019 06:27:37: 17000000 INFO @ Fri, 05 Jul 2019 06:27:38: 16000000 INFO @ Fri, 05 Jul 2019 06:27:43: 18000000 INFO @ Fri, 05 Jul 2019 06:27:43: 17000000 INFO @ Fri, 05 Jul 2019 06:27:45: 17000000 INFO @ Fri, 05 Jul 2019 06:27:49: 19000000 INFO @ Fri, 05 Jul 2019 06:27:50: 18000000 INFO @ Fri, 05 Jul 2019 06:27:51: 18000000 INFO @ Fri, 05 Jul 2019 06:27:55: 20000000 INFO @ Fri, 05 Jul 2019 06:27:56: 19000000 INFO @ Fri, 05 Jul 2019 06:27:58: 19000000 INFO @ Fri, 05 Jul 2019 06:28:01: 21000000 INFO @ Fri, 05 Jul 2019 06:28:03: 20000000 INFO @ Fri, 05 Jul 2019 06:28:05: 20000000 INFO @ Fri, 05 Jul 2019 06:28:08: 22000000 INFO @ Fri, 05 Jul 2019 06:28:10: 21000000 INFO @ Fri, 05 Jul 2019 06:28:12: 21000000 INFO @ Fri, 05 Jul 2019 06:28:14: 23000000 INFO @ Fri, 05 Jul 2019 06:28:16: 22000000 INFO @ Fri, 05 Jul 2019 06:28:19: 22000000 INFO @ Fri, 05 Jul 2019 06:28:20: 24000000 INFO @ Fri, 05 Jul 2019 06:28:23: 23000000 INFO @ Fri, 05 Jul 2019 06:28:25: 23000000 INFO @ Fri, 05 Jul 2019 06:28:26: 25000000 INFO @ Fri, 05 Jul 2019 06:28:29: 24000000 INFO @ Fri, 05 Jul 2019 06:28:32: 24000000 INFO @ Fri, 05 Jul 2019 06:28:33: 26000000 INFO @ Fri, 05 Jul 2019 06:28:35: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:28:35: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:28:35: #1 total tags in treatment: 26366407 INFO @ Fri, 05 Jul 2019 06:28:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:28:35: #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 06:28:36: #1 tags after filtering in treatment: 26366254 INFO @ Fri, 05 Jul 2019 06:28:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:28:36: #1 finished! INFO @ Fri, 05 Jul 2019 06:28:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:28:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:28:36: 25000000 INFO @ Fri, 05 Jul 2019 06:28:39: 25000000 INFO @ Fri, 05 Jul 2019 06:28:41: #2 number of paired peaks: 60199 INFO @ Fri, 05 Jul 2019 06:28:41: start model_add_line... INFO @ Fri, 05 Jul 2019 06:28:42: start X-correlation... INFO @ Fri, 05 Jul 2019 06:28:42: end of X-cor INFO @ Fri, 05 Jul 2019 06:28:42: #2 finished! INFO @ Fri, 05 Jul 2019 06:28:42: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 06:28:42: #2 alternative fragment length(s) may be 3,134,501 bps INFO @ Fri, 05 Jul 2019 06:28:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.10_model.r INFO @ Fri, 05 Jul 2019 06:28:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:28:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:28:43: 26000000 INFO @ Fri, 05 Jul 2019 06:28:46: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:28:46: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:28:46: #1 total tags in treatment: 26366407 INFO @ Fri, 05 Jul 2019 06:28:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:28:46: #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 06:28:46: 26000000 INFO @ Fri, 05 Jul 2019 06:28:46: #1 tags after filtering in treatment: 26366254 INFO @ Fri, 05 Jul 2019 06:28:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:28:46: #1 finished! INFO @ Fri, 05 Jul 2019 06:28:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:28:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:28:49: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:28:49: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:28:49: #1 total tags in treatment: 26366407 INFO @ Fri, 05 Jul 2019 06:28:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:28:49: #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 06:28:49: #1 tags after filtering in treatment: 26366254 INFO @ Fri, 05 Jul 2019 06:28:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:28:49: #1 finished! INFO @ Fri, 05 Jul 2019 06:28:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:28:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:28:52: #2 number of paired peaks: 60199 INFO @ Fri, 05 Jul 2019 06:28:52: start model_add_line... INFO @ Fri, 05 Jul 2019 06:28:52: start X-correlation... INFO @ Fri, 05 Jul 2019 06:28:52: end of X-cor INFO @ Fri, 05 Jul 2019 06:28:52: #2 finished! INFO @ Fri, 05 Jul 2019 06:28:52: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 06:28:52: #2 alternative fragment length(s) may be 3,134,501 bps INFO @ Fri, 05 Jul 2019 06:28:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.05_model.r INFO @ Fri, 05 Jul 2019 06:28:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:28:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:28:55: #2 number of paired peaks: 60199 INFO @ Fri, 05 Jul 2019 06:28:55: start model_add_line... INFO @ Fri, 05 Jul 2019 06:28:55: start X-correlation... INFO @ Fri, 05 Jul 2019 06:28:55: end of X-cor INFO @ Fri, 05 Jul 2019 06:28:55: #2 finished! INFO @ Fri, 05 Jul 2019 06:28:55: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 06:28:55: #2 alternative fragment length(s) may be 3,134,501 bps INFO @ Fri, 05 Jul 2019 06:28:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.20_model.r INFO @ Fri, 05 Jul 2019 06:28:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:28:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:30:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:30:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:30:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:30:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.10_peaks.xls INFO @ Fri, 05 Jul 2019 06:30:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:30:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.10_summits.bed INFO @ Fri, 05 Jul 2019 06:30:47: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (1598 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:31:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:31:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:31:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.05_summits.bed INFO @ Fri, 05 Jul 2019 06:31:00: Done! pass1 - making usageList (74 chroms): 2 millis pass2 - checking and writing primary data (6438 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:31:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:31:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:31:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101932/ERX101932.20_summits.bed INFO @ Fri, 05 Jul 2019 06:31:07: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (208 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。