Job ID = 2002126 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,242,778 reads read : 29,242,778 reads written : 29,242,778 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: 00:10:40 29242778 reads; of these: 29242778 (100.00%) were unpaired; of these: 644276 (2.20%) aligned 0 times 21638486 (74.00%) aligned exactly 1 time 6960016 (23.80%) aligned >1 times 97.80% overall alignment rate Time searching: 00:10:43 Overall time: 00:10:43 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] 2191074 / 28598502 = 0.0766 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 10:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.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 10:14:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:14:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.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 10:14:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:14:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.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 10:14:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:14:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:14:42: 1000000 INFO @ Fri, 05 Jul 2019 10:14:43: 1000000 INFO @ Fri, 05 Jul 2019 10:14:43: 1000000 INFO @ Fri, 05 Jul 2019 10:14:49: 2000000 INFO @ Fri, 05 Jul 2019 10:14:52: 2000000 INFO @ Fri, 05 Jul 2019 10:14:52: 2000000 INFO @ Fri, 05 Jul 2019 10:14:56: 3000000 INFO @ Fri, 05 Jul 2019 10:15:00: 3000000 INFO @ Fri, 05 Jul 2019 10:15:00: 3000000 INFO @ Fri, 05 Jul 2019 10:15:03: 4000000 INFO @ Fri, 05 Jul 2019 10:15:09: 4000000 INFO @ Fri, 05 Jul 2019 10:15:09: 4000000 INFO @ Fri, 05 Jul 2019 10:15:10: 5000000 INFO @ Fri, 05 Jul 2019 10:15:17: 5000000 INFO @ Fri, 05 Jul 2019 10:15:17: 5000000 INFO @ Fri, 05 Jul 2019 10:15:17: 6000000 INFO @ Fri, 05 Jul 2019 10:15:24: 7000000 INFO @ Fri, 05 Jul 2019 10:15:25: 6000000 INFO @ Fri, 05 Jul 2019 10:15:26: 6000000 INFO @ Fri, 05 Jul 2019 10:15:31: 8000000 INFO @ Fri, 05 Jul 2019 10:15:34: 7000000 INFO @ Fri, 05 Jul 2019 10:15:34: 7000000 INFO @ Fri, 05 Jul 2019 10:15:39: 9000000 INFO @ Fri, 05 Jul 2019 10:15:42: 8000000 INFO @ Fri, 05 Jul 2019 10:15:42: 8000000 INFO @ Fri, 05 Jul 2019 10:15:46: 10000000 INFO @ Fri, 05 Jul 2019 10:15:50: 9000000 INFO @ Fri, 05 Jul 2019 10:15:50: 9000000 INFO @ Fri, 05 Jul 2019 10:15:53: 11000000 INFO @ Fri, 05 Jul 2019 10:15:59: 10000000 INFO @ Fri, 05 Jul 2019 10:15:59: 10000000 INFO @ Fri, 05 Jul 2019 10:16:00: 12000000 INFO @ Fri, 05 Jul 2019 10:16:07: 13000000 INFO @ Fri, 05 Jul 2019 10:16:07: 11000000 INFO @ Fri, 05 Jul 2019 10:16:07: 11000000 INFO @ Fri, 05 Jul 2019 10:16:14: 14000000 INFO @ Fri, 05 Jul 2019 10:16:15: 12000000 INFO @ Fri, 05 Jul 2019 10:16:15: 12000000 INFO @ Fri, 05 Jul 2019 10:16:21: 15000000 INFO @ Fri, 05 Jul 2019 10:16:24: 13000000 INFO @ Fri, 05 Jul 2019 10:16:24: 13000000 INFO @ Fri, 05 Jul 2019 10:16:28: 16000000 INFO @ Fri, 05 Jul 2019 10:16:32: 14000000 INFO @ Fri, 05 Jul 2019 10:16:32: 14000000 INFO @ Fri, 05 Jul 2019 10:16:35: 17000000 INFO @ Fri, 05 Jul 2019 10:16:40: 15000000 INFO @ Fri, 05 Jul 2019 10:16:40: 15000000 INFO @ Fri, 05 Jul 2019 10:16:42: 18000000 INFO @ Fri, 05 Jul 2019 10:16:49: 16000000 INFO @ Fri, 05 Jul 2019 10:16:49: 16000000 INFO @ Fri, 05 Jul 2019 10:16:50: 19000000 INFO @ Fri, 05 Jul 2019 10:16:57: 20000000 INFO @ Fri, 05 Jul 2019 10:16:57: 17000000 INFO @ Fri, 05 Jul 2019 10:16:57: 17000000 INFO @ Fri, 05 Jul 2019 10:17:04: 21000000 INFO @ Fri, 05 Jul 2019 10:17:05: 18000000 INFO @ Fri, 05 Jul 2019 10:17:05: 18000000 INFO @ Fri, 05 Jul 2019 10:17:11: 22000000 INFO @ Fri, 05 Jul 2019 10:17:13: 19000000 INFO @ Fri, 05 Jul 2019 10:17:14: 19000000 INFO @ Fri, 05 Jul 2019 10:17:18: 23000000 INFO @ Fri, 05 Jul 2019 10:17:21: 20000000 INFO @ Fri, 05 Jul 2019 10:17:22: 20000000 INFO @ Fri, 05 Jul 2019 10:17:25: 24000000 INFO @ Fri, 05 Jul 2019 10:17:30: 21000000 INFO @ Fri, 05 Jul 2019 10:17:30: 21000000 INFO @ Fri, 05 Jul 2019 10:17:32: 25000000 INFO @ Fri, 05 Jul 2019 10:17:38: 22000000 INFO @ Fri, 05 Jul 2019 10:17:38: 22000000 INFO @ Fri, 05 Jul 2019 10:17:40: 26000000 INFO @ Fri, 05 Jul 2019 10:17:43: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:17:43: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:17:43: #1 total tags in treatment: 26407428 INFO @ Fri, 05 Jul 2019 10:17:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:17:43: #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 10:17:43: #1 tags after filtering in treatment: 26407277 INFO @ Fri, 05 Jul 2019 10:17:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:17:43: #1 finished! INFO @ Fri, 05 Jul 2019 10:17:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:17:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:17:46: 23000000 INFO @ Fri, 05 Jul 2019 10:17:47: 23000000 INFO @ Fri, 05 Jul 2019 10:17:49: #2 number of paired peaks: 61281 INFO @ Fri, 05 Jul 2019 10:17:49: start model_add_line... INFO @ Fri, 05 Jul 2019 10:17:49: start X-correlation... INFO @ Fri, 05 Jul 2019 10:17:49: end of X-cor INFO @ Fri, 05 Jul 2019 10:17:49: #2 finished! INFO @ Fri, 05 Jul 2019 10:17:49: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 10:17:49: #2 alternative fragment length(s) may be 3,135,503 bps INFO @ Fri, 05 Jul 2019 10:17:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.05_model.r INFO @ Fri, 05 Jul 2019 10:17:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:17:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:17:53: 24000000 INFO @ Fri, 05 Jul 2019 10:17:55: 24000000 INFO @ Fri, 05 Jul 2019 10:18:00: 25000000 INFO @ Fri, 05 Jul 2019 10:18:04: 25000000 INFO @ Fri, 05 Jul 2019 10:18:09: 26000000 INFO @ Fri, 05 Jul 2019 10:18:12: 26000000 INFO @ Fri, 05 Jul 2019 10:18:12: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:18:12: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:18:12: #1 total tags in treatment: 26407428 INFO @ Fri, 05 Jul 2019 10:18:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:18:12: #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 10:18:13: #1 tags after filtering in treatment: 26407277 INFO @ Fri, 05 Jul 2019 10:18:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:18:13: #1 finished! INFO @ Fri, 05 Jul 2019 10:18:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:18:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:18:16: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:18:16: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:18:16: #1 total tags in treatment: 26407428 INFO @ Fri, 05 Jul 2019 10:18:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:18:16: #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 10:18:16: #1 tags after filtering in treatment: 26407277 INFO @ Fri, 05 Jul 2019 10:18:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:18:16: #1 finished! INFO @ Fri, 05 Jul 2019 10:18:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:18:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:18:18: #2 number of paired peaks: 61281 INFO @ Fri, 05 Jul 2019 10:18:18: start model_add_line... INFO @ Fri, 05 Jul 2019 10:18:19: start X-correlation... INFO @ Fri, 05 Jul 2019 10:18:19: end of X-cor INFO @ Fri, 05 Jul 2019 10:18:19: #2 finished! INFO @ Fri, 05 Jul 2019 10:18:19: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 10:18:19: #2 alternative fragment length(s) may be 3,135,503 bps INFO @ Fri, 05 Jul 2019 10:18:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.10_model.r INFO @ Fri, 05 Jul 2019 10:18:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:18:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:18:22: #2 number of paired peaks: 61281 INFO @ Fri, 05 Jul 2019 10:18:22: start model_add_line... INFO @ Fri, 05 Jul 2019 10:18:22: start X-correlation... INFO @ Fri, 05 Jul 2019 10:18:22: end of X-cor INFO @ Fri, 05 Jul 2019 10:18:22: #2 finished! INFO @ Fri, 05 Jul 2019 10:18:22: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 10:18:22: #2 alternative fragment length(s) may be 3,135,503 bps INFO @ Fri, 05 Jul 2019 10:18:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.20_model.r INFO @ Fri, 05 Jul 2019 10:18:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:18:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:19:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:19:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:19:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:19:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:19:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:19:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.05_summits.bed INFO @ Fri, 05 Jul 2019 10:19:53: Done! pass1 - making usageList (76 chroms): 22 millis pass2 - checking and writing primary data (6789 records, 4 fields): 140 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:20:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:20:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:20:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.10_summits.bed INFO @ Fri, 05 Jul 2019 10:20:23: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (1775 records, 4 fields): 8 millis INFO @ Fri, 05 Jul 2019 10:20:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.20_peaks.xls INFO @ Fri, 05 Jul 2019 10:20:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:20:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102028/ERX102028.20_summits.bed INFO @ Fri, 05 Jul 2019 10:20:26: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (186 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。