Job ID = 11632686 sra ファイルのダウンロード中... Completed: 1138220K bytes transferred in 12 seconds (739618K 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 74984132 spots for /home/okishinya/chipatlas/results/rn6/SRX3782446/SRR6826264.sra Written 74984132 spots for /home/okishinya/chipatlas/results/rn6/SRX3782446/SRR6826264.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:27:29 74984132 reads; of these: 74984132 (100.00%) were unpaired; of these: 4681357 (6.24%) aligned 0 times 60157059 (80.23%) aligned exactly 1 time 10145716 (13.53%) aligned >1 times 93.76% overall alignment rate Time searching: 00:27:32 Overall time: 00:27:32 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] 10784847 / 70302775 = 0.1534 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 07:02:44: # Command line: callpeak -t SRX3782446.bam -f BAM -g 2.15e9 -n SRX3782446.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782446.20 # format = BAM # ChIP-seq file = ['SRX3782446.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 07:02:44: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:02:44: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:02:44: # Command line: callpeak -t SRX3782446.bam -f BAM -g 2.15e9 -n SRX3782446.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782446.05 # format = BAM # ChIP-seq file = ['SRX3782446.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 07:02:44: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:02:44: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:02:44: # Command line: callpeak -t SRX3782446.bam -f BAM -g 2.15e9 -n SRX3782446.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782446.10 # format = BAM # ChIP-seq file = ['SRX3782446.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 07:02:44: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:02:44: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:02:51: 1000000 INFO @ Fri, 15 Feb 2019 07:02:51: 1000000 INFO @ Fri, 15 Feb 2019 07:02:51: 1000000 INFO @ Fri, 15 Feb 2019 07:02:57: 2000000 INFO @ Fri, 15 Feb 2019 07:02:58: 2000000 INFO @ Fri, 15 Feb 2019 07:02:58: 2000000 INFO @ Fri, 15 Feb 2019 07:03:03: 3000000 INFO @ Fri, 15 Feb 2019 07:03:05: 3000000 INFO @ Fri, 15 Feb 2019 07:03:05: 3000000 INFO @ Fri, 15 Feb 2019 07:03:10: 4000000 INFO @ Fri, 15 Feb 2019 07:03:12: 4000000 INFO @ Fri, 15 Feb 2019 07:03:12: 4000000 INFO @ Fri, 15 Feb 2019 07:03:16: 5000000 INFO @ Fri, 15 Feb 2019 07:03:19: 5000000 INFO @ Fri, 15 Feb 2019 07:03:19: 5000000 INFO @ Fri, 15 Feb 2019 07:03:22: 6000000 INFO @ Fri, 15 Feb 2019 07:03:25: 6000000 INFO @ Fri, 15 Feb 2019 07:03:25: 6000000 INFO @ Fri, 15 Feb 2019 07:03:28: 7000000 INFO @ Fri, 15 Feb 2019 07:03:32: 7000000 INFO @ Fri, 15 Feb 2019 07:03:32: 7000000 INFO @ Fri, 15 Feb 2019 07:03:35: 8000000 INFO @ Fri, 15 Feb 2019 07:03:39: 8000000 INFO @ Fri, 15 Feb 2019 07:03:39: 8000000 INFO @ Fri, 15 Feb 2019 07:03:41: 9000000 INFO @ Fri, 15 Feb 2019 07:03:46: 9000000 INFO @ Fri, 15 Feb 2019 07:03:46: 9000000 INFO @ Fri, 15 Feb 2019 07:03:48: 10000000 INFO @ Fri, 15 Feb 2019 07:03:52: 10000000 INFO @ Fri, 15 Feb 2019 07:03:53: 10000000 INFO @ Fri, 15 Feb 2019 07:03:54: 11000000 INFO @ Fri, 15 Feb 2019 07:03:59: 11000000 INFO @ Fri, 15 Feb 2019 07:04:00: 11000000 INFO @ Fri, 15 Feb 2019 07:04:01: 12000000 INFO @ Fri, 15 Feb 2019 07:04:06: 12000000 INFO @ Fri, 15 Feb 2019 07:04:07: 12000000 INFO @ Fri, 15 Feb 2019 07:04:08: 13000000 INFO @ Fri, 15 Feb 2019 07:04:13: 13000000 INFO @ Fri, 15 Feb 2019 07:04:14: 13000000 INFO @ Fri, 15 Feb 2019 07:04:15: 14000000 INFO @ Fri, 15 Feb 2019 07:04:20: 14000000 INFO @ Fri, 15 Feb 2019 07:04:20: 14000000 INFO @ Fri, 15 Feb 2019 07:04:22: 15000000 INFO @ Fri, 15 Feb 2019 07:04:27: 15000000 INFO @ Fri, 15 Feb 2019 07:04:28: 15000000 INFO @ Fri, 15 Feb 2019 07:04:29: 16000000 INFO @ Fri, 15 Feb 2019 07:04:34: 16000000 INFO @ Fri, 15 Feb 2019 07:04:34: 16000000 INFO @ Fri, 15 Feb 2019 07:04:36: 17000000 INFO @ Fri, 15 Feb 2019 07:04:41: 17000000 INFO @ Fri, 15 Feb 2019 07:04:41: 17000000 INFO @ Fri, 15 Feb 2019 07:04:43: 18000000 INFO @ Fri, 15 Feb 2019 07:04:48: 18000000 INFO @ Fri, 15 Feb 2019 07:04:48: 18000000 INFO @ Fri, 15 Feb 2019 07:04:49: 19000000 INFO @ Fri, 15 Feb 2019 07:04:55: 19000000 INFO @ Fri, 15 Feb 2019 07:04:55: 19000000 INFO @ Fri, 15 Feb 2019 07:04:55: 20000000 INFO @ Fri, 15 Feb 2019 07:05:01: 20000000 INFO @ Fri, 15 Feb 2019 07:05:02: 21000000 INFO @ Fri, 15 Feb 2019 07:05:02: 20000000 INFO @ Fri, 15 Feb 2019 07:05:08: 22000000 INFO @ Fri, 15 Feb 2019 07:05:08: 21000000 INFO @ Fri, 15 Feb 2019 07:05:09: 21000000 INFO @ Fri, 15 Feb 2019 07:05:15: 23000000 INFO @ Fri, 15 Feb 2019 07:05:15: 22000000 INFO @ Fri, 15 Feb 2019 07:05:16: 22000000 INFO @ Fri, 15 Feb 2019 07:05:21: 23000000 INFO @ Fri, 15 Feb 2019 07:05:21: 24000000 INFO @ Fri, 15 Feb 2019 07:05:23: 23000000 INFO @ Fri, 15 Feb 2019 07:05:28: 24000000 INFO @ Fri, 15 Feb 2019 07:05:28: 25000000 INFO @ Fri, 15 Feb 2019 07:05:30: 24000000 INFO @ Fri, 15 Feb 2019 07:05:35: 26000000 INFO @ Fri, 15 Feb 2019 07:05:35: 25000000 INFO @ Fri, 15 Feb 2019 07:05:37: 25000000 INFO @ Fri, 15 Feb 2019 07:05:41: 27000000 INFO @ Fri, 15 Feb 2019 07:05:42: 26000000 INFO @ Fri, 15 Feb 2019 07:05:44: 26000000 INFO @ Fri, 15 Feb 2019 07:05:48: 28000000 INFO @ Fri, 15 Feb 2019 07:05:48: 27000000 INFO @ Fri, 15 Feb 2019 07:05:51: 27000000 INFO @ Fri, 15 Feb 2019 07:05:54: 29000000 INFO @ Fri, 15 Feb 2019 07:05:55: 28000000 INFO @ Fri, 15 Feb 2019 07:05:57: 28000000 INFO @ Fri, 15 Feb 2019 07:06:01: 30000000 INFO @ Fri, 15 Feb 2019 07:06:02: 29000000 INFO @ Fri, 15 Feb 2019 07:06:04: 29000000 INFO @ Fri, 15 Feb 2019 07:06:08: 31000000 INFO @ Fri, 15 Feb 2019 07:06:09: 30000000 INFO @ Fri, 15 Feb 2019 07:06:11: 30000000 INFO @ Fri, 15 Feb 2019 07:06:15: 32000000 INFO @ Fri, 15 Feb 2019 07:06:16: 31000000 INFO @ Fri, 15 Feb 2019 07:06:18: 31000000 INFO @ Fri, 15 Feb 2019 07:06:21: 33000000 INFO @ Fri, 15 Feb 2019 07:06:22: 32000000 INFO @ Fri, 15 Feb 2019 07:06:25: 32000000 INFO @ Fri, 15 Feb 2019 07:06:28: 34000000 INFO @ Fri, 15 Feb 2019 07:06:29: 33000000 INFO @ Fri, 15 Feb 2019 07:06:32: 33000000 INFO @ Fri, 15 Feb 2019 07:06:35: 35000000 INFO @ Fri, 15 Feb 2019 07:06:36: 34000000 INFO @ Fri, 15 Feb 2019 07:06:39: 34000000 INFO @ Fri, 15 Feb 2019 07:06:41: 36000000 INFO @ Fri, 15 Feb 2019 07:06:42: 35000000 INFO @ Fri, 15 Feb 2019 07:06:46: 35000000 INFO @ Fri, 15 Feb 2019 07:06:48: 37000000 INFO @ Fri, 15 Feb 2019 07:06:49: 36000000 INFO @ Fri, 15 Feb 2019 07:06:53: 36000000 INFO @ Fri, 15 Feb 2019 07:06:54: 38000000 INFO @ Fri, 15 Feb 2019 07:06:56: 37000000 INFO @ Fri, 15 Feb 2019 07:07:00: 37000000 INFO @ Fri, 15 Feb 2019 07:07:01: 39000000 INFO @ Fri, 15 Feb 2019 07:07:03: 38000000 INFO @ Fri, 15 Feb 2019 07:07:07: 40000000 INFO @ Fri, 15 Feb 2019 07:07:07: 38000000 INFO @ Fri, 15 Feb 2019 07:07:10: 39000000 INFO @ Fri, 15 Feb 2019 07:07:14: 41000000 INFO @ Fri, 15 Feb 2019 07:07:14: 39000000 INFO @ Fri, 15 Feb 2019 07:07:17: 40000000 INFO @ Fri, 15 Feb 2019 07:07:20: 42000000 INFO @ Fri, 15 Feb 2019 07:07:21: 40000000 INFO @ Fri, 15 Feb 2019 07:07:24: 41000000 INFO @ Fri, 15 Feb 2019 07:07:27: 43000000 INFO @ Fri, 15 Feb 2019 07:07:27: 41000000 INFO @ Fri, 15 Feb 2019 07:07:31: 42000000 INFO @ Fri, 15 Feb 2019 07:07:34: 44000000 INFO @ Fri, 15 Feb 2019 07:07:34: 42000000 INFO @ Fri, 15 Feb 2019 07:07:38: 43000000 INFO @ Fri, 15 Feb 2019 07:07:40: 45000000 INFO @ Fri, 15 Feb 2019 07:07:41: 43000000 INFO @ Fri, 15 Feb 2019 07:07:45: 44000000 INFO @ Fri, 15 Feb 2019 07:07:47: 46000000 INFO @ Fri, 15 Feb 2019 07:07:48: 44000000 INFO @ Fri, 15 Feb 2019 07:07:53: 45000000 INFO @ Fri, 15 Feb 2019 07:07:53: 47000000 INFO @ Fri, 15 Feb 2019 07:07:55: 45000000 INFO @ Fri, 15 Feb 2019 07:07:59: 48000000 INFO @ Fri, 15 Feb 2019 07:08:00: 46000000 INFO @ Fri, 15 Feb 2019 07:08:02: 46000000 INFO @ Fri, 15 Feb 2019 07:08:06: 49000000 INFO @ Fri, 15 Feb 2019 07:08:08: 47000000 INFO @ Fri, 15 Feb 2019 07:08:09: 47000000 INFO @ Fri, 15 Feb 2019 07:08:12: 50000000 INFO @ Fri, 15 Feb 2019 07:08:15: 48000000 INFO @ Fri, 15 Feb 2019 07:08:16: 48000000 INFO @ Fri, 15 Feb 2019 07:08:18: 51000000 INFO @ Fri, 15 Feb 2019 07:08:22: 49000000 INFO @ Fri, 15 Feb 2019 07:08:23: 49000000 INFO @ Fri, 15 Feb 2019 07:08:25: 52000000 INFO @ Fri, 15 Feb 2019 07:08:29: 50000000 INFO @ Fri, 15 Feb 2019 07:08:30: 50000000 INFO @ Fri, 15 Feb 2019 07:08:31: 53000000 INFO @ Fri, 15 Feb 2019 07:08:36: 51000000 INFO @ Fri, 15 Feb 2019 07:08:37: 51000000 INFO @ Fri, 15 Feb 2019 07:08:38: 54000000 INFO @ Fri, 15 Feb 2019 07:08:43: 52000000 INFO @ Fri, 15 Feb 2019 07:08:44: 52000000 INFO @ Fri, 15 Feb 2019 07:08:45: 55000000 INFO @ Fri, 15 Feb 2019 07:08:50: 53000000 INFO @ Fri, 15 Feb 2019 07:08:50: 53000000 INFO @ Fri, 15 Feb 2019 07:08:51: 56000000 INFO @ Fri, 15 Feb 2019 07:08:57: 54000000 INFO @ Fri, 15 Feb 2019 07:08:57: 54000000 INFO @ Fri, 15 Feb 2019 07:08:57: 57000000 INFO @ Fri, 15 Feb 2019 07:09:04: 55000000 INFO @ Fri, 15 Feb 2019 07:09:04: 58000000 INFO @ Fri, 15 Feb 2019 07:09:04: 55000000 INFO @ Fri, 15 Feb 2019 07:09:11: 56000000 INFO @ Fri, 15 Feb 2019 07:09:11: 59000000 INFO @ Fri, 15 Feb 2019 07:09:11: 56000000 INFO @ Fri, 15 Feb 2019 07:09:15: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:09:15: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:09:15: #1 total tags in treatment: 59517928 INFO @ Fri, 15 Feb 2019 07:09:15: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:09:15: #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 07:09:16: #1 tags after filtering in treatment: 59517792 INFO @ Fri, 15 Feb 2019 07:09:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:09:16: #1 finished! INFO @ Fri, 15 Feb 2019 07:09:16: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:09:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:09:18: 57000000 INFO @ Fri, 15 Feb 2019 07:09:18: 57000000 INFO @ Fri, 15 Feb 2019 07:09:24: 58000000 INFO @ Fri, 15 Feb 2019 07:09:24: 58000000 INFO @ Fri, 15 Feb 2019 07:09:29: #2 number of paired peaks: 141404 INFO @ Fri, 15 Feb 2019 07:09:29: start model_add_line... INFO @ Fri, 15 Feb 2019 07:09:31: 59000000 INFO @ Fri, 15 Feb 2019 07:09:31: 59000000 INFO @ Fri, 15 Feb 2019 07:09:31: start X-correlation... INFO @ Fri, 15 Feb 2019 07:09:31: end of X-cor INFO @ Fri, 15 Feb 2019 07:09:31: #2 finished! INFO @ Fri, 15 Feb 2019 07:09:31: #2 predicted fragment length is 312 bps INFO @ Fri, 15 Feb 2019 07:09:31: #2 alternative fragment length(s) may be 312 bps INFO @ Fri, 15 Feb 2019 07:09:31: #2.2 Generate R script for model : SRX3782446.10_model.r INFO @ Fri, 15 Feb 2019 07:09:31: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:09:35: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:09:35: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:09:35: #1 total tags in treatment: 59517928 INFO @ Fri, 15 Feb 2019 07:09:35: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:09:35: #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 07:09:35: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:09:35: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:09:35: #1 total tags in treatment: 59517928 INFO @ Fri, 15 Feb 2019 07:09:35: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:09:35: #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 07:09:36: #1 tags after filtering in treatment: 59517792 INFO @ Fri, 15 Feb 2019 07:09:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:09:36: #1 finished! INFO @ Fri, 15 Feb 2019 07:09:36: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:09:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:09:36: #1 tags after filtering in treatment: 59517792 INFO @ Fri, 15 Feb 2019 07:09:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:09:36: #1 finished! INFO @ Fri, 15 Feb 2019 07:09:36: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:09:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:09:49: #2 number of paired peaks: 141404 INFO @ Fri, 15 Feb 2019 07:09:49: start model_add_line... INFO @ Fri, 15 Feb 2019 07:09:50: #2 number of paired peaks: 141404 INFO @ Fri, 15 Feb 2019 07:09:50: start model_add_line... INFO @ Fri, 15 Feb 2019 07:09:51: start X-correlation... INFO @ Fri, 15 Feb 2019 07:09:51: end of X-cor INFO @ Fri, 15 Feb 2019 07:09:51: #2 finished! INFO @ Fri, 15 Feb 2019 07:09:51: #2 predicted fragment length is 312 bps INFO @ Fri, 15 Feb 2019 07:09:51: #2 alternative fragment length(s) may be 312 bps INFO @ Fri, 15 Feb 2019 07:09:51: #2.2 Generate R script for model : SRX3782446.05_model.r INFO @ Fri, 15 Feb 2019 07:09:51: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:09:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:09:51: start X-correlation... INFO @ Fri, 15 Feb 2019 07:09:51: end of X-cor INFO @ Fri, 15 Feb 2019 07:09:51: #2 finished! INFO @ Fri, 15 Feb 2019 07:09:51: #2 predicted fragment length is 312 bps INFO @ Fri, 15 Feb 2019 07:09:51: #2 alternative fragment length(s) may be 312 bps INFO @ Fri, 15 Feb 2019 07:09:51: #2.2 Generate R script for model : SRX3782446.20_model.r INFO @ Fri, 15 Feb 2019 07:09:51: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:09:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:12:27: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:12:43: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:12:57: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:14:10: #4 Write output xls file... SRX3782446.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:14:10: #4 Write peak in narrowPeak format file... SRX3782446.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:14:11: #4 Write summits bed file... SRX3782446.10_summits.bed INFO @ Fri, 15 Feb 2019 07:14:11: Done! pass1 - making usageList (134 chroms): 10 millis pass2 - checking and writing primary data (51985 records, 4 fields): 66 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:14:27: #4 Write output xls file... SRX3782446.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:14:28: #4 Write peak in narrowPeak format file... SRX3782446.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:14:28: #4 Write summits bed file... SRX3782446.20_summits.bed INFO @ Fri, 15 Feb 2019 07:14:28: Done! pass1 - making usageList (105 chroms): 7 millis pass2 - checking and writing primary data (34599 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:14:42: #4 Write output xls file... SRX3782446.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:14:43: #4 Write peak in narrowPeak format file... SRX3782446.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:14:44: #4 Write summits bed file... SRX3782446.05_summits.bed INFO @ Fri, 15 Feb 2019 07:14:44: Done! pass1 - making usageList (160 chroms): 12 millis pass2 - checking and writing primary data (66006 records, 4 fields): 83 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。