Job ID = 11632703 sra ファイルのダウンロード中... Completed: 1797615K bytes transferred in 23 seconds (623403K 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 67451971 spots for /home/okishinya/chipatlas/results/rn6/SRX3782462/SRR6826280.sra Written 67451971 spots for /home/okishinya/chipatlas/results/rn6/SRX3782462/SRR6826280.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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:29:40 67451971 reads; of these: 67451971 (100.00%) were unpaired; of these: 3548007 (5.26%) aligned 0 times 48958995 (72.58%) aligned exactly 1 time 14944969 (22.16%) aligned >1 times 94.74% overall alignment rate Time searching: 00:29:44 Overall time: 00:29:44 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] 2931635 / 63903964 = 0.0459 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 07:04:11: # Command line: callpeak -t SRX3782462.bam -f BAM -g 2.15e9 -n SRX3782462.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782462.05 # format = BAM # ChIP-seq file = ['SRX3782462.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 07:04:11: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:04:11: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:04:11: # Command line: callpeak -t SRX3782462.bam -f BAM -g 2.15e9 -n SRX3782462.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782462.10 # format = BAM # ChIP-seq file = ['SRX3782462.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 07:04:11: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:04:11: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:04:11: # Command line: callpeak -t SRX3782462.bam -f BAM -g 2.15e9 -n SRX3782462.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782462.20 # format = BAM # ChIP-seq file = ['SRX3782462.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 07:04:11: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:04:11: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:04:18: 1000000 INFO @ Fri, 15 Feb 2019 07:04:18: 1000000 INFO @ Fri, 15 Feb 2019 07:04:19: 1000000 INFO @ Fri, 15 Feb 2019 07:04:25: 2000000 INFO @ Fri, 15 Feb 2019 07:04:26: 2000000 INFO @ Fri, 15 Feb 2019 07:04:26: 2000000 INFO @ Fri, 15 Feb 2019 07:04:32: 3000000 INFO @ Fri, 15 Feb 2019 07:04:33: 3000000 INFO @ Fri, 15 Feb 2019 07:04:33: 3000000 INFO @ Fri, 15 Feb 2019 07:04:38: 4000000 INFO @ Fri, 15 Feb 2019 07:04:41: 4000000 INFO @ Fri, 15 Feb 2019 07:04:41: 4000000 INFO @ Fri, 15 Feb 2019 07:04:45: 5000000 INFO @ Fri, 15 Feb 2019 07:04:49: 5000000 INFO @ Fri, 15 Feb 2019 07:04:49: 5000000 INFO @ Fri, 15 Feb 2019 07:04:52: 6000000 INFO @ Fri, 15 Feb 2019 07:04:57: 6000000 INFO @ Fri, 15 Feb 2019 07:04:57: 6000000 INFO @ Fri, 15 Feb 2019 07:04:58: 7000000 INFO @ Fri, 15 Feb 2019 07:05:05: 7000000 INFO @ Fri, 15 Feb 2019 07:05:05: 7000000 INFO @ Fri, 15 Feb 2019 07:05:05: 8000000 INFO @ Fri, 15 Feb 2019 07:05:12: 8000000 INFO @ Fri, 15 Feb 2019 07:05:12: 9000000 INFO @ Fri, 15 Feb 2019 07:05:12: 8000000 INFO @ Fri, 15 Feb 2019 07:05:19: 9000000 INFO @ Fri, 15 Feb 2019 07:05:19: 10000000 INFO @ Fri, 15 Feb 2019 07:05:19: 9000000 INFO @ Fri, 15 Feb 2019 07:05:26: 11000000 INFO @ Fri, 15 Feb 2019 07:05:26: 10000000 INFO @ Fri, 15 Feb 2019 07:05:26: 10000000 INFO @ Fri, 15 Feb 2019 07:05:33: 12000000 INFO @ Fri, 15 Feb 2019 07:05:33: 11000000 INFO @ Fri, 15 Feb 2019 07:05:33: 11000000 INFO @ Fri, 15 Feb 2019 07:05:40: 13000000 INFO @ Fri, 15 Feb 2019 07:05:40: 12000000 INFO @ Fri, 15 Feb 2019 07:05:41: 12000000 INFO @ Fri, 15 Feb 2019 07:05:47: 14000000 INFO @ Fri, 15 Feb 2019 07:05:47: 13000000 INFO @ Fri, 15 Feb 2019 07:05:47: 13000000 INFO @ Fri, 15 Feb 2019 07:05:54: 15000000 INFO @ Fri, 15 Feb 2019 07:05:54: 14000000 INFO @ Fri, 15 Feb 2019 07:05:54: 14000000 INFO @ Fri, 15 Feb 2019 07:06:01: 16000000 INFO @ Fri, 15 Feb 2019 07:06:01: 15000000 INFO @ Fri, 15 Feb 2019 07:06:02: 15000000 INFO @ Fri, 15 Feb 2019 07:06:08: 17000000 INFO @ Fri, 15 Feb 2019 07:06:08: 16000000 INFO @ Fri, 15 Feb 2019 07:06:09: 16000000 INFO @ Fri, 15 Feb 2019 07:06:14: 18000000 INFO @ Fri, 15 Feb 2019 07:06:15: 17000000 INFO @ Fri, 15 Feb 2019 07:06:17: 17000000 INFO @ Fri, 15 Feb 2019 07:06:21: 19000000 INFO @ Fri, 15 Feb 2019 07:06:22: 18000000 INFO @ Fri, 15 Feb 2019 07:06:25: 18000000 INFO @ Fri, 15 Feb 2019 07:06:28: 20000000 INFO @ Fri, 15 Feb 2019 07:06:29: 19000000 INFO @ Fri, 15 Feb 2019 07:06:32: 19000000 INFO @ Fri, 15 Feb 2019 07:06:35: 21000000 INFO @ Fri, 15 Feb 2019 07:06:36: 20000000 INFO @ Fri, 15 Feb 2019 07:06:39: 20000000 INFO @ Fri, 15 Feb 2019 07:06:42: 22000000 INFO @ Fri, 15 Feb 2019 07:06:43: 21000000 INFO @ Fri, 15 Feb 2019 07:06:46: 21000000 INFO @ Fri, 15 Feb 2019 07:06:49: 23000000 INFO @ Fri, 15 Feb 2019 07:06:50: 22000000 INFO @ Fri, 15 Feb 2019 07:06:53: 22000000 INFO @ Fri, 15 Feb 2019 07:06:56: 24000000 INFO @ Fri, 15 Feb 2019 07:06:57: 23000000 INFO @ Fri, 15 Feb 2019 07:07:00: 23000000 INFO @ Fri, 15 Feb 2019 07:07:03: 25000000 INFO @ Fri, 15 Feb 2019 07:07:04: 24000000 INFO @ Fri, 15 Feb 2019 07:07:07: 24000000 INFO @ Fri, 15 Feb 2019 07:07:10: 26000000 INFO @ Fri, 15 Feb 2019 07:07:11: 25000000 INFO @ Fri, 15 Feb 2019 07:07:14: 25000000 INFO @ Fri, 15 Feb 2019 07:07:17: 27000000 INFO @ Fri, 15 Feb 2019 07:07:18: 26000000 INFO @ Fri, 15 Feb 2019 07:07:21: 26000000 INFO @ Fri, 15 Feb 2019 07:07:24: 28000000 INFO @ Fri, 15 Feb 2019 07:07:25: 27000000 INFO @ Fri, 15 Feb 2019 07:07:28: 27000000 INFO @ Fri, 15 Feb 2019 07:07:30: 29000000 INFO @ Fri, 15 Feb 2019 07:07:31: 28000000 INFO @ Fri, 15 Feb 2019 07:07:36: 28000000 INFO @ Fri, 15 Feb 2019 07:07:37: 30000000 INFO @ Fri, 15 Feb 2019 07:07:38: 29000000 INFO @ Fri, 15 Feb 2019 07:07:44: 29000000 INFO @ Fri, 15 Feb 2019 07:07:44: 31000000 INFO @ Fri, 15 Feb 2019 07:07:45: 30000000 INFO @ Fri, 15 Feb 2019 07:07:51: 32000000 INFO @ Fri, 15 Feb 2019 07:07:51: 30000000 INFO @ Fri, 15 Feb 2019 07:07:52: 31000000 INFO @ Fri, 15 Feb 2019 07:07:58: 33000000 INFO @ Fri, 15 Feb 2019 07:07:59: 31000000 INFO @ Fri, 15 Feb 2019 07:07:59: 32000000 INFO @ Fri, 15 Feb 2019 07:08:05: 34000000 INFO @ Fri, 15 Feb 2019 07:08:06: 32000000 INFO @ Fri, 15 Feb 2019 07:08:06: 33000000 INFO @ Fri, 15 Feb 2019 07:08:12: 35000000 INFO @ Fri, 15 Feb 2019 07:08:13: 33000000 INFO @ Fri, 15 Feb 2019 07:08:13: 34000000 INFO @ Fri, 15 Feb 2019 07:08:19: 36000000 INFO @ Fri, 15 Feb 2019 07:08:20: 34000000 INFO @ Fri, 15 Feb 2019 07:08:20: 35000000 INFO @ Fri, 15 Feb 2019 07:08:25: 37000000 INFO @ Fri, 15 Feb 2019 07:08:27: 35000000 INFO @ Fri, 15 Feb 2019 07:08:27: 36000000 INFO @ Fri, 15 Feb 2019 07:08:32: 38000000 INFO @ Fri, 15 Feb 2019 07:08:34: 36000000 INFO @ Fri, 15 Feb 2019 07:08:34: 37000000 INFO @ Fri, 15 Feb 2019 07:08:39: 39000000 INFO @ Fri, 15 Feb 2019 07:08:41: 37000000 INFO @ Fri, 15 Feb 2019 07:08:41: 38000000 INFO @ Fri, 15 Feb 2019 07:08:46: 40000000 INFO @ Fri, 15 Feb 2019 07:08:48: 38000000 INFO @ Fri, 15 Feb 2019 07:08:48: 39000000 INFO @ Fri, 15 Feb 2019 07:08:53: 41000000 INFO @ Fri, 15 Feb 2019 07:08:55: 39000000 INFO @ Fri, 15 Feb 2019 07:08:55: 40000000 INFO @ Fri, 15 Feb 2019 07:09:00: 42000000 INFO @ Fri, 15 Feb 2019 07:09:02: 41000000 INFO @ Fri, 15 Feb 2019 07:09:03: 40000000 INFO @ Fri, 15 Feb 2019 07:09:07: 43000000 INFO @ Fri, 15 Feb 2019 07:09:09: 42000000 INFO @ Fri, 15 Feb 2019 07:09:10: 41000000 INFO @ Fri, 15 Feb 2019 07:09:14: 44000000 INFO @ Fri, 15 Feb 2019 07:09:16: 43000000 INFO @ Fri, 15 Feb 2019 07:09:18: 42000000 INFO @ Fri, 15 Feb 2019 07:09:21: 45000000 INFO @ Fri, 15 Feb 2019 07:09:23: 44000000 INFO @ Fri, 15 Feb 2019 07:09:25: 43000000 INFO @ Fri, 15 Feb 2019 07:09:28: 46000000 INFO @ Fri, 15 Feb 2019 07:09:30: 45000000 INFO @ Fri, 15 Feb 2019 07:09:32: 44000000 INFO @ Fri, 15 Feb 2019 07:09:35: 47000000 INFO @ Fri, 15 Feb 2019 07:09:37: 46000000 INFO @ Fri, 15 Feb 2019 07:09:39: 45000000 INFO @ Fri, 15 Feb 2019 07:09:41: 48000000 INFO @ Fri, 15 Feb 2019 07:09:44: 47000000 INFO @ Fri, 15 Feb 2019 07:09:46: 46000000 INFO @ Fri, 15 Feb 2019 07:09:48: 49000000 INFO @ Fri, 15 Feb 2019 07:09:51: 48000000 INFO @ Fri, 15 Feb 2019 07:09:53: 47000000 INFO @ Fri, 15 Feb 2019 07:09:55: 50000000 INFO @ Fri, 15 Feb 2019 07:09:58: 49000000 INFO @ Fri, 15 Feb 2019 07:10:01: 48000000 INFO @ Fri, 15 Feb 2019 07:10:02: 51000000 INFO @ Fri, 15 Feb 2019 07:10:05: 50000000 INFO @ Fri, 15 Feb 2019 07:10:07: 49000000 INFO @ Fri, 15 Feb 2019 07:10:09: 52000000 INFO @ Fri, 15 Feb 2019 07:10:12: 51000000 INFO @ Fri, 15 Feb 2019 07:10:14: 50000000 INFO @ Fri, 15 Feb 2019 07:10:16: 53000000 INFO @ Fri, 15 Feb 2019 07:10:19: 52000000 INFO @ Fri, 15 Feb 2019 07:10:22: 51000000 INFO @ Fri, 15 Feb 2019 07:10:23: 54000000 INFO @ Fri, 15 Feb 2019 07:10:26: 53000000 INFO @ Fri, 15 Feb 2019 07:10:29: 52000000 INFO @ Fri, 15 Feb 2019 07:10:30: 55000000 INFO @ Fri, 15 Feb 2019 07:10:33: 54000000 INFO @ Fri, 15 Feb 2019 07:10:37: 56000000 INFO @ Fri, 15 Feb 2019 07:10:37: 53000000 INFO @ Fri, 15 Feb 2019 07:10:40: 55000000 INFO @ Fri, 15 Feb 2019 07:10:44: 57000000 INFO @ Fri, 15 Feb 2019 07:10:45: 54000000 INFO @ Fri, 15 Feb 2019 07:10:47: 56000000 INFO @ Fri, 15 Feb 2019 07:10:51: 58000000 INFO @ Fri, 15 Feb 2019 07:10:52: 55000000 INFO @ Fri, 15 Feb 2019 07:10:54: 57000000 INFO @ Fri, 15 Feb 2019 07:10:58: 59000000 INFO @ Fri, 15 Feb 2019 07:10:59: 56000000 INFO @ Fri, 15 Feb 2019 07:11:01: 58000000 INFO @ Fri, 15 Feb 2019 07:11:05: 60000000 INFO @ Fri, 15 Feb 2019 07:11:06: 57000000 INFO @ Fri, 15 Feb 2019 07:11:08: 59000000 INFO @ Fri, 15 Feb 2019 07:11:12: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:11:12: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:11:12: #1 total tags in treatment: 60972329 INFO @ Fri, 15 Feb 2019 07:11:12: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:11:12: #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 07:11:13: 58000000 INFO @ Fri, 15 Feb 2019 07:11:13: #1 tags after filtering in treatment: 60972269 INFO @ Fri, 15 Feb 2019 07:11:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:11:13: #1 finished! INFO @ Fri, 15 Feb 2019 07:11:13: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:11:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:11:15: 60000000 INFO @ Fri, 15 Feb 2019 07:11:19: #2 number of paired peaks: 18019 INFO @ Fri, 15 Feb 2019 07:11:19: start model_add_line... INFO @ Fri, 15 Feb 2019 07:11:20: start X-correlation... INFO @ Fri, 15 Feb 2019 07:11:20: end of X-cor INFO @ Fri, 15 Feb 2019 07:11:20: #2 finished! INFO @ Fri, 15 Feb 2019 07:11:20: #2 predicted fragment length is 209 bps INFO @ Fri, 15 Feb 2019 07:11:20: #2 alternative fragment length(s) may be 209 bps INFO @ Fri, 15 Feb 2019 07:11:20: #2.2 Generate R script for model : SRX3782462.20_model.r INFO @ Fri, 15 Feb 2019 07:11:20: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:11:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:11:21: 59000000 INFO @ Fri, 15 Feb 2019 07:11:22: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:11:22: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:11:22: #1 total tags in treatment: 60972329 INFO @ Fri, 15 Feb 2019 07:11:22: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:11:22: #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 07:11:24: #1 tags after filtering in treatment: 60972269 INFO @ Fri, 15 Feb 2019 07:11:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:11:24: #1 finished! INFO @ Fri, 15 Feb 2019 07:11:24: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:11:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:11:28: 60000000 INFO @ Fri, 15 Feb 2019 07:11:29: #2 number of paired peaks: 18019 INFO @ Fri, 15 Feb 2019 07:11:29: start model_add_line... INFO @ Fri, 15 Feb 2019 07:11:30: start X-correlation... INFO @ Fri, 15 Feb 2019 07:11:30: end of X-cor INFO @ Fri, 15 Feb 2019 07:11:30: #2 finished! INFO @ Fri, 15 Feb 2019 07:11:30: #2 predicted fragment length is 209 bps INFO @ Fri, 15 Feb 2019 07:11:30: #2 alternative fragment length(s) may be 209 bps INFO @ Fri, 15 Feb 2019 07:11:30: #2.2 Generate R script for model : SRX3782462.05_model.r INFO @ Fri, 15 Feb 2019 07:11:30: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:11:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:11:35: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:11:35: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:11:35: #1 total tags in treatment: 60972329 INFO @ Fri, 15 Feb 2019 07:11:35: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:11:35: #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 07:11:36: #1 tags after filtering in treatment: 60972269 INFO @ Fri, 15 Feb 2019 07:11:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:11:36: #1 finished! INFO @ Fri, 15 Feb 2019 07:11:36: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:11:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:11:42: #2 number of paired peaks: 18019 INFO @ Fri, 15 Feb 2019 07:11:42: start model_add_line... INFO @ Fri, 15 Feb 2019 07:11:43: start X-correlation... INFO @ Fri, 15 Feb 2019 07:11:43: end of X-cor INFO @ Fri, 15 Feb 2019 07:11:43: #2 finished! INFO @ Fri, 15 Feb 2019 07:11:43: #2 predicted fragment length is 209 bps INFO @ Fri, 15 Feb 2019 07:11:43: #2 alternative fragment length(s) may be 209 bps INFO @ Fri, 15 Feb 2019 07:11:43: #2.2 Generate R script for model : SRX3782462.10_model.r INFO @ Fri, 15 Feb 2019 07:11:43: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:11:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:13:43: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:13:58: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:14:20: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:15:19: #4 Write output xls file... SRX3782462.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:15:19: #4 Write peak in narrowPeak format file... SRX3782462.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:15:19: #4 Write summits bed file... SRX3782462.20_summits.bed INFO @ Fri, 15 Feb 2019 07:15:19: Done! pass1 - making usageList (42 chroms): 7 millis pass2 - checking and writing primary data (1288 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:15:33: #4 Write output xls file... SRX3782462.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:15:33: #4 Write peak in narrowPeak format file... SRX3782462.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:15:33: #4 Write summits bed file... SRX3782462.05_summits.bed INFO @ Fri, 15 Feb 2019 07:15:33: Done! pass1 - making usageList (89 chroms): 8 millis pass2 - checking and writing primary data (14786 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:15:59: #4 Write output xls file... SRX3782462.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:15:59: #4 Write peak in narrowPeak format file... SRX3782462.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:15:59: #4 Write summits bed file... SRX3782462.10_summits.bed INFO @ Fri, 15 Feb 2019 07:15:59: Done! pass1 - making usageList (58 chroms): 9 millis pass2 - checking and writing primary data (4975 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。