Job ID = 11632712 sra ファイルのダウンロード中... Completed: 1086700K bytes transferred in 13 seconds (644020K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 70150438 spots for /home/okishinya/chipatlas/results/rn6/SRX3782471/SRR6826289.sra Written 70150438 spots for /home/okishinya/chipatlas/results/rn6/SRX3782471/SRR6826289.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:00:01 Multiseed full-index search: 00:32:18 70150438 reads; of these: 70150438 (100.00%) were unpaired; of these: 4177922 (5.96%) aligned 0 times 52119479 (74.30%) aligned exactly 1 time 13853037 (19.75%) aligned >1 times 94.04% overall alignment rate Time searching: 00:32:23 Overall time: 00:32:23 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 20 files... [bam_rmdupse_core] 8312788 / 65972516 = 0.1260 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, 15 Feb 2019 08:22:09: # Command line: callpeak -t SRX3782471.bam -f BAM -g 2.15e9 -n SRX3782471.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782471.10 # format = BAM # ChIP-seq file = ['SRX3782471.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, 15 Feb 2019 08:22:09: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:22:09: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:22:09: # Command line: callpeak -t SRX3782471.bam -f BAM -g 2.15e9 -n SRX3782471.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782471.05 # format = BAM # ChIP-seq file = ['SRX3782471.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, 15 Feb 2019 08:22:09: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:22:09: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:22:09: # Command line: callpeak -t SRX3782471.bam -f BAM -g 2.15e9 -n SRX3782471.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782471.20 # format = BAM # ChIP-seq file = ['SRX3782471.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, 15 Feb 2019 08:22:09: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:22:09: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:22:16: 1000000 INFO @ Fri, 15 Feb 2019 08:22:16: 1000000 INFO @ Fri, 15 Feb 2019 08:22:16: 1000000 INFO @ Fri, 15 Feb 2019 08:22:23: 2000000 INFO @ Fri, 15 Feb 2019 08:22:23: 2000000 INFO @ Fri, 15 Feb 2019 08:22:23: 2000000 INFO @ Fri, 15 Feb 2019 08:22:29: 3000000 INFO @ Fri, 15 Feb 2019 08:22:31: 3000000 INFO @ Fri, 15 Feb 2019 08:22:31: 3000000 INFO @ Fri, 15 Feb 2019 08:22:36: 4000000 INFO @ Fri, 15 Feb 2019 08:22:38: 4000000 INFO @ Fri, 15 Feb 2019 08:22:38: 4000000 INFO @ Fri, 15 Feb 2019 08:22:43: 5000000 INFO @ Fri, 15 Feb 2019 08:22:45: 5000000 INFO @ Fri, 15 Feb 2019 08:22:45: 5000000 INFO @ Fri, 15 Feb 2019 08:22:50: 6000000 INFO @ Fri, 15 Feb 2019 08:22:52: 6000000 INFO @ Fri, 15 Feb 2019 08:22:52: 6000000 INFO @ Fri, 15 Feb 2019 08:22:56: 7000000 INFO @ Fri, 15 Feb 2019 08:23:00: 7000000 INFO @ Fri, 15 Feb 2019 08:23:00: 7000000 INFO @ Fri, 15 Feb 2019 08:23:03: 8000000 INFO @ Fri, 15 Feb 2019 08:23:07: 8000000 INFO @ Fri, 15 Feb 2019 08:23:07: 8000000 INFO @ Fri, 15 Feb 2019 08:23:10: 9000000 INFO @ Fri, 15 Feb 2019 08:23:14: 9000000 INFO @ Fri, 15 Feb 2019 08:23:14: 9000000 INFO @ Fri, 15 Feb 2019 08:23:16: 10000000 INFO @ Fri, 15 Feb 2019 08:23:21: 10000000 INFO @ Fri, 15 Feb 2019 08:23:21: 10000000 INFO @ Fri, 15 Feb 2019 08:23:23: 11000000 INFO @ Fri, 15 Feb 2019 08:23:29: 11000000 INFO @ Fri, 15 Feb 2019 08:23:29: 11000000 INFO @ Fri, 15 Feb 2019 08:23:30: 12000000 INFO @ Fri, 15 Feb 2019 08:23:37: 13000000 INFO @ Fri, 15 Feb 2019 08:23:37: 12000000 INFO @ Fri, 15 Feb 2019 08:23:37: 12000000 INFO @ Fri, 15 Feb 2019 08:23:45: 14000000 INFO @ Fri, 15 Feb 2019 08:23:46: 13000000 INFO @ Fri, 15 Feb 2019 08:23:46: 13000000 INFO @ Fri, 15 Feb 2019 08:23:54: 15000000 INFO @ Fri, 15 Feb 2019 08:23:55: 14000000 INFO @ Fri, 15 Feb 2019 08:23:55: 14000000 INFO @ Fri, 15 Feb 2019 08:24:02: 16000000 INFO @ Fri, 15 Feb 2019 08:24:04: 15000000 INFO @ Fri, 15 Feb 2019 08:24:04: 15000000 INFO @ Fri, 15 Feb 2019 08:24:11: 17000000 INFO @ Fri, 15 Feb 2019 08:24:13: 16000000 INFO @ Fri, 15 Feb 2019 08:24:13: 16000000 INFO @ Fri, 15 Feb 2019 08:24:19: 18000000 INFO @ Fri, 15 Feb 2019 08:24:22: 17000000 INFO @ Fri, 15 Feb 2019 08:24:22: 17000000 INFO @ Fri, 15 Feb 2019 08:24:28: 19000000 INFO @ Fri, 15 Feb 2019 08:24:31: 18000000 INFO @ Fri, 15 Feb 2019 08:24:31: 18000000 INFO @ Fri, 15 Feb 2019 08:24:36: 20000000 INFO @ Fri, 15 Feb 2019 08:24:39: 19000000 INFO @ Fri, 15 Feb 2019 08:24:39: 19000000 INFO @ Fri, 15 Feb 2019 08:24:45: 21000000 INFO @ Fri, 15 Feb 2019 08:24:48: 20000000 INFO @ Fri, 15 Feb 2019 08:24:48: 20000000 INFO @ Fri, 15 Feb 2019 08:24:53: 22000000 INFO @ Fri, 15 Feb 2019 08:24:57: 21000000 INFO @ Fri, 15 Feb 2019 08:24:57: 21000000 INFO @ Fri, 15 Feb 2019 08:25:02: 23000000 INFO @ Fri, 15 Feb 2019 08:25:06: 22000000 INFO @ Fri, 15 Feb 2019 08:25:06: 22000000 INFO @ Fri, 15 Feb 2019 08:25:10: 24000000 INFO @ Fri, 15 Feb 2019 08:25:15: 23000000 INFO @ Fri, 15 Feb 2019 08:25:15: 23000000 INFO @ Fri, 15 Feb 2019 08:25:18: 25000000 INFO @ Fri, 15 Feb 2019 08:25:24: 24000000 INFO @ Fri, 15 Feb 2019 08:25:24: 24000000 INFO @ Fri, 15 Feb 2019 08:25:27: 26000000 INFO @ Fri, 15 Feb 2019 08:25:32: 25000000 INFO @ Fri, 15 Feb 2019 08:25:32: 25000000 INFO @ Fri, 15 Feb 2019 08:25:35: 27000000 INFO @ Fri, 15 Feb 2019 08:25:41: 26000000 INFO @ Fri, 15 Feb 2019 08:25:41: 26000000 INFO @ Fri, 15 Feb 2019 08:25:43: 28000000 INFO @ Fri, 15 Feb 2019 08:25:50: 27000000 INFO @ Fri, 15 Feb 2019 08:25:50: 27000000 INFO @ Fri, 15 Feb 2019 08:25:51: 29000000 INFO @ Fri, 15 Feb 2019 08:25:59: 30000000 INFO @ Fri, 15 Feb 2019 08:25:59: 28000000 INFO @ Fri, 15 Feb 2019 08:25:59: 28000000 INFO @ Fri, 15 Feb 2019 08:26:07: 31000000 INFO @ Fri, 15 Feb 2019 08:26:08: 29000000 INFO @ Fri, 15 Feb 2019 08:26:08: 29000000 INFO @ Fri, 15 Feb 2019 08:26:14: 32000000 INFO @ Fri, 15 Feb 2019 08:26:18: 30000000 INFO @ Fri, 15 Feb 2019 08:26:18: 30000000 INFO @ Fri, 15 Feb 2019 08:26:22: 33000000 INFO @ Fri, 15 Feb 2019 08:26:27: 31000000 INFO @ Fri, 15 Feb 2019 08:26:27: 31000000 INFO @ Fri, 15 Feb 2019 08:26:30: 34000000 INFO @ Fri, 15 Feb 2019 08:26:36: 32000000 INFO @ Fri, 15 Feb 2019 08:26:36: 32000000 INFO @ Fri, 15 Feb 2019 08:26:38: 35000000 INFO @ Fri, 15 Feb 2019 08:26:45: 33000000 INFO @ Fri, 15 Feb 2019 08:26:45: 33000000 INFO @ Fri, 15 Feb 2019 08:26:45: 36000000 INFO @ Fri, 15 Feb 2019 08:26:53: 37000000 INFO @ Fri, 15 Feb 2019 08:26:54: 34000000 INFO @ Fri, 15 Feb 2019 08:26:54: 34000000 INFO @ Fri, 15 Feb 2019 08:27:00: 38000000 INFO @ Fri, 15 Feb 2019 08:27:02: 35000000 INFO @ Fri, 15 Feb 2019 08:27:03: 35000000 INFO @ Fri, 15 Feb 2019 08:27:08: 39000000 INFO @ Fri, 15 Feb 2019 08:27:10: 36000000 INFO @ Fri, 15 Feb 2019 08:27:12: 36000000 INFO @ Fri, 15 Feb 2019 08:27:16: 40000000 INFO @ Fri, 15 Feb 2019 08:27:19: 37000000 INFO @ Fri, 15 Feb 2019 08:27:21: 37000000 INFO @ Fri, 15 Feb 2019 08:27:25: 41000000 INFO @ Fri, 15 Feb 2019 08:27:26: 38000000 INFO @ Fri, 15 Feb 2019 08:27:31: 38000000 INFO @ Fri, 15 Feb 2019 08:27:34: 42000000 INFO @ Fri, 15 Feb 2019 08:27:35: 39000000 INFO @ Fri, 15 Feb 2019 08:27:40: 39000000 INFO @ Fri, 15 Feb 2019 08:27:44: 40000000 INFO @ Fri, 15 Feb 2019 08:27:45: 43000000 INFO @ Fri, 15 Feb 2019 08:27:50: 40000000 INFO @ Fri, 15 Feb 2019 08:27:54: 41000000 INFO @ Fri, 15 Feb 2019 08:27:55: 44000000 INFO @ Fri, 15 Feb 2019 08:27:59: 41000000 INFO @ Fri, 15 Feb 2019 08:28:03: 42000000 INFO @ Fri, 15 Feb 2019 08:28:06: 45000000 INFO @ Fri, 15 Feb 2019 08:28:08: 42000000 INFO @ Fri, 15 Feb 2019 08:28:12: 43000000 INFO @ Fri, 15 Feb 2019 08:28:16: 46000000 INFO @ Fri, 15 Feb 2019 08:28:17: 43000000 INFO @ Fri, 15 Feb 2019 08:28:21: 44000000 INFO @ Fri, 15 Feb 2019 08:28:27: 44000000 INFO @ Fri, 15 Feb 2019 08:28:27: 47000000 INFO @ Fri, 15 Feb 2019 08:28:31: 45000000 INFO @ Fri, 15 Feb 2019 08:28:35: 45000000 INFO @ Fri, 15 Feb 2019 08:28:37: 48000000 INFO @ Fri, 15 Feb 2019 08:28:39: 46000000 INFO @ Fri, 15 Feb 2019 08:28:44: 46000000 INFO @ Fri, 15 Feb 2019 08:28:47: 49000000 INFO @ Fri, 15 Feb 2019 08:28:48: 47000000 INFO @ Fri, 15 Feb 2019 08:28:53: 47000000 INFO @ Fri, 15 Feb 2019 08:28:58: 48000000 INFO @ Fri, 15 Feb 2019 08:28:58: 50000000 INFO @ Fri, 15 Feb 2019 08:29:02: 48000000 INFO @ Fri, 15 Feb 2019 08:29:07: 49000000 INFO @ Fri, 15 Feb 2019 08:29:08: 51000000 INFO @ Fri, 15 Feb 2019 08:29:11: 49000000 INFO @ Fri, 15 Feb 2019 08:29:16: 50000000 INFO @ Fri, 15 Feb 2019 08:29:19: 52000000 INFO @ Fri, 15 Feb 2019 08:29:21: 50000000 INFO @ Fri, 15 Feb 2019 08:29:25: 51000000 INFO @ Fri, 15 Feb 2019 08:29:30: 53000000 INFO @ Fri, 15 Feb 2019 08:29:30: 51000000 INFO @ Fri, 15 Feb 2019 08:29:35: 52000000 INFO @ Fri, 15 Feb 2019 08:29:39: 52000000 INFO @ Fri, 15 Feb 2019 08:29:40: 54000000 INFO @ Fri, 15 Feb 2019 08:29:44: 53000000 INFO @ Fri, 15 Feb 2019 08:29:49: 53000000 INFO @ Fri, 15 Feb 2019 08:29:51: 55000000 INFO @ Fri, 15 Feb 2019 08:29:53: 54000000 INFO @ Fri, 15 Feb 2019 08:29:58: 54000000 INFO @ Fri, 15 Feb 2019 08:30:02: 56000000 INFO @ Fri, 15 Feb 2019 08:30:02: 55000000 INFO @ Fri, 15 Feb 2019 08:30:07: 55000000 INFO @ Fri, 15 Feb 2019 08:30:11: 56000000 INFO @ Fri, 15 Feb 2019 08:30:11: 57000000 INFO @ Fri, 15 Feb 2019 08:30:15: 56000000 INFO @ Fri, 15 Feb 2019 08:30:17: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 08:30:17: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 08:30:17: #1 total tags in treatment: 57659728 INFO @ Fri, 15 Feb 2019 08:30:17: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:30:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 08:30:19: #1 tags after filtering in treatment: 57659640 INFO @ Fri, 15 Feb 2019 08:30:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 08:30:19: #1 finished! INFO @ Fri, 15 Feb 2019 08:30:19: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:30:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:30:19: 57000000 INFO @ Fri, 15 Feb 2019 08:30:25: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 08:30:25: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 08:30:25: #1 total tags in treatment: 57659728 INFO @ Fri, 15 Feb 2019 08:30:25: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:30:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 08:30:25: 57000000 INFO @ Fri, 15 Feb 2019 08:30:26: #1 tags after filtering in treatment: 57659640 INFO @ Fri, 15 Feb 2019 08:30:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 08:30:26: #1 finished! INFO @ Fri, 15 Feb 2019 08:30:26: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:30:26: #2 number of paired peaks: 46830 INFO @ Fri, 15 Feb 2019 08:30:26: start model_add_line... INFO @ Fri, 15 Feb 2019 08:30:27: start X-correlation... INFO @ Fri, 15 Feb 2019 08:30:28: end of X-cor INFO @ Fri, 15 Feb 2019 08:30:28: #2 finished! INFO @ Fri, 15 Feb 2019 08:30:28: #2 predicted fragment length is 366 bps INFO @ Fri, 15 Feb 2019 08:30:28: #2 alternative fragment length(s) may be 366 bps INFO @ Fri, 15 Feb 2019 08:30:28: #2.2 Generate R script for model : SRX3782471.20_model.r INFO @ Fri, 15 Feb 2019 08:30:28: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:30:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:30:31: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 08:30:31: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 08:30:31: #1 total tags in treatment: 57659728 INFO @ Fri, 15 Feb 2019 08:30:31: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:30:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 08:30:32: #1 tags after filtering in treatment: 57659640 INFO @ Fri, 15 Feb 2019 08:30:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 08:30:32: #1 finished! INFO @ Fri, 15 Feb 2019 08:30:32: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:30:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:30:33: #2 number of paired peaks: 46830 INFO @ Fri, 15 Feb 2019 08:30:33: start model_add_line... INFO @ Fri, 15 Feb 2019 08:30:34: start X-correlation... INFO @ Fri, 15 Feb 2019 08:30:34: end of X-cor INFO @ Fri, 15 Feb 2019 08:30:34: #2 finished! INFO @ Fri, 15 Feb 2019 08:30:34: #2 predicted fragment length is 366 bps INFO @ Fri, 15 Feb 2019 08:30:34: #2 alternative fragment length(s) may be 366 bps INFO @ Fri, 15 Feb 2019 08:30:34: #2.2 Generate R script for model : SRX3782471.05_model.r INFO @ Fri, 15 Feb 2019 08:30:34: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:30:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:30:40: #2 number of paired peaks: 46830 INFO @ Fri, 15 Feb 2019 08:30:40: start model_add_line... INFO @ Fri, 15 Feb 2019 08:30:41: start X-correlation... INFO @ Fri, 15 Feb 2019 08:30:41: end of X-cor INFO @ Fri, 15 Feb 2019 08:30:41: #2 finished! INFO @ Fri, 15 Feb 2019 08:30:41: #2 predicted fragment length is 366 bps INFO @ Fri, 15 Feb 2019 08:30:41: #2 alternative fragment length(s) may be 366 bps INFO @ Fri, 15 Feb 2019 08:30:41: #2.2 Generate R script for model : SRX3782471.10_model.r INFO @ Fri, 15 Feb 2019 08:30:41: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:30:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:33:16: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:33:19: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:33:32: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:34:55: #4 Write output xls file... SRX3782471.20_peaks.xls INFO @ Fri, 15 Feb 2019 08:34:55: #4 Write peak in narrowPeak format file... SRX3782471.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:34:55: #4 Write summits bed file... SRX3782471.20_summits.bed INFO @ Fri, 15 Feb 2019 08:34:55: Done! pass1 - making usageList (66 chroms): 4 millis pass2 - checking and writing primary data (10427 records, 4 fields): 59 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 08:34:57: #4 Write output xls file... SRX3782471.05_peaks.xls INFO @ Fri, 15 Feb 2019 08:34:57: #4 Write peak in narrowPeak format file... SRX3782471.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:34:57: #4 Write summits bed file... SRX3782471.05_summits.bed INFO @ Fri, 15 Feb 2019 08:34:57: Done! pass1 - making usageList (109 chroms): 6 millis pass2 - checking and writing primary data (19877 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 08:35:08: #4 Write output xls file... SRX3782471.10_peaks.xls INFO @ Fri, 15 Feb 2019 08:35:08: #4 Write peak in narrowPeak format file... SRX3782471.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:35:09: #4 Write summits bed file... SRX3782471.10_summits.bed INFO @ Fri, 15 Feb 2019 08:35:09: Done! pass1 - making usageList (90 chroms): 6 millis pass2 - checking and writing primary data (14401 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。