Job ID = 10194833 sra ファイルのダウンロード中... Completed: 1327550K bytes transferred in 17 seconds (625281K 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... Written 65384760 spots for /home/okishinya/chipatlas/results/rn6/SRX1977123/SRR3952255.sra Written 65384760 spots total 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: 01:54:13 65384760 reads; of these: 65384760 (100.00%) were unpaired; of these: 11325751 (17.32%) aligned 0 times 29223356 (44.69%) aligned exactly 1 time 24835653 (37.98%) aligned >1 times 82.68% overall alignment rate Time searching: 01:54:18 Overall time: 01:54:18 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 24 files... [bam_rmdupse_core] 9278483 / 54059009 = 0.1716 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 @ Sat, 11 Nov 2017 03:44:01: # Command line: callpeak -t SRX1977123.bam -f BAM -g 2.15e9 -n SRX1977123.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977123.20 # format = BAM # ChIP-seq file = ['SRX1977123.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 @ Sat, 11 Nov 2017 03:44:01: # Command line: callpeak -t SRX1977123.bam -f BAM -g 2.15e9 -n SRX1977123.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977123.05 # format = BAM # ChIP-seq file = ['SRX1977123.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 @ Sat, 11 Nov 2017 03:44:01: # Command line: callpeak -t SRX1977123.bam -f BAM -g 2.15e9 -n SRX1977123.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977123.10 # format = BAM # ChIP-seq file = ['SRX1977123.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 @ Sat, 11 Nov 2017 03:44:01: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:44:01: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:44:01: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:44:01: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:44:01: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:44:01: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:44:08: 1000000 INFO @ Sat, 11 Nov 2017 03:44:08: 1000000 INFO @ Sat, 11 Nov 2017 03:44:08: 1000000 INFO @ Sat, 11 Nov 2017 03:44:14: 2000000 INFO @ Sat, 11 Nov 2017 03:44:14: 2000000 INFO @ Sat, 11 Nov 2017 03:44:15: 2000000 INFO @ Sat, 11 Nov 2017 03:44:21: 3000000 INFO @ Sat, 11 Nov 2017 03:44:21: 3000000 INFO @ Sat, 11 Nov 2017 03:44:22: 3000000 INFO @ Sat, 11 Nov 2017 03:44:28: 4000000 INFO @ Sat, 11 Nov 2017 03:44:28: 4000000 INFO @ Sat, 11 Nov 2017 03:44:29: 4000000 INFO @ Sat, 11 Nov 2017 03:44:35: 5000000 INFO @ Sat, 11 Nov 2017 03:44:35: 5000000 INFO @ Sat, 11 Nov 2017 03:44:37: 5000000 INFO @ Sat, 11 Nov 2017 03:44:42: 6000000 INFO @ Sat, 11 Nov 2017 03:44:42: 6000000 INFO @ Sat, 11 Nov 2017 03:44:44: 6000000 INFO @ Sat, 11 Nov 2017 03:44:49: 7000000 INFO @ Sat, 11 Nov 2017 03:44:49: 7000000 INFO @ Sat, 11 Nov 2017 03:44:51: 7000000 INFO @ Sat, 11 Nov 2017 03:44:56: 8000000 INFO @ Sat, 11 Nov 2017 03:44:56: 8000000 INFO @ Sat, 11 Nov 2017 03:44:58: 8000000 INFO @ Sat, 11 Nov 2017 03:45:02: 9000000 INFO @ Sat, 11 Nov 2017 03:45:02: 9000000 INFO @ Sat, 11 Nov 2017 03:45:06: 9000000 INFO @ Sat, 11 Nov 2017 03:45:09: 10000000 INFO @ Sat, 11 Nov 2017 03:45:09: 10000000 INFO @ Sat, 11 Nov 2017 03:45:13: 10000000 INFO @ Sat, 11 Nov 2017 03:45:16: 11000000 INFO @ Sat, 11 Nov 2017 03:45:16: 11000000 INFO @ Sat, 11 Nov 2017 03:45:20: 11000000 INFO @ Sat, 11 Nov 2017 03:45:23: 12000000 INFO @ Sat, 11 Nov 2017 03:45:23: 12000000 INFO @ Sat, 11 Nov 2017 03:45:27: 12000000 INFO @ Sat, 11 Nov 2017 03:45:29: 13000000 INFO @ Sat, 11 Nov 2017 03:45:30: 13000000 INFO @ Sat, 11 Nov 2017 03:45:35: 13000000 INFO @ Sat, 11 Nov 2017 03:45:36: 14000000 INFO @ Sat, 11 Nov 2017 03:45:37: 14000000 INFO @ Sat, 11 Nov 2017 03:45:42: 14000000 INFO @ Sat, 11 Nov 2017 03:45:43: 15000000 INFO @ Sat, 11 Nov 2017 03:45:44: 15000000 INFO @ Sat, 11 Nov 2017 03:45:49: 15000000 INFO @ Sat, 11 Nov 2017 03:45:50: 16000000 INFO @ Sat, 11 Nov 2017 03:45:51: 16000000 INFO @ Sat, 11 Nov 2017 03:45:56: 16000000 INFO @ Sat, 11 Nov 2017 03:45:57: 17000000 INFO @ Sat, 11 Nov 2017 03:45:58: 17000000 INFO @ Sat, 11 Nov 2017 03:46:04: 17000000 INFO @ Sat, 11 Nov 2017 03:46:04: 18000000 INFO @ Sat, 11 Nov 2017 03:46:05: 18000000 INFO @ Sat, 11 Nov 2017 03:46:11: 18000000 INFO @ Sat, 11 Nov 2017 03:46:12: 19000000 INFO @ Sat, 11 Nov 2017 03:46:12: 19000000 INFO @ Sat, 11 Nov 2017 03:46:19: 19000000 INFO @ Sat, 11 Nov 2017 03:46:19: 20000000 INFO @ Sat, 11 Nov 2017 03:46:20: 20000000 INFO @ Sat, 11 Nov 2017 03:46:26: 21000000 INFO @ Sat, 11 Nov 2017 03:46:26: 20000000 INFO @ Sat, 11 Nov 2017 03:46:27: 21000000 INFO @ Sat, 11 Nov 2017 03:46:33: 22000000 INFO @ Sat, 11 Nov 2017 03:46:33: 21000000 INFO @ Sat, 11 Nov 2017 03:46:34: 22000000 INFO @ Sat, 11 Nov 2017 03:46:40: 23000000 INFO @ Sat, 11 Nov 2017 03:46:41: 22000000 INFO @ Sat, 11 Nov 2017 03:46:42: 23000000 INFO @ Sat, 11 Nov 2017 03:46:48: 24000000 INFO @ Sat, 11 Nov 2017 03:46:48: 23000000 INFO @ Sat, 11 Nov 2017 03:46:49: 24000000 INFO @ Sat, 11 Nov 2017 03:46:55: 25000000 INFO @ Sat, 11 Nov 2017 03:46:56: 24000000 INFO @ Sat, 11 Nov 2017 03:46:56: 25000000 INFO @ Sat, 11 Nov 2017 03:47:02: 26000000 INFO @ Sat, 11 Nov 2017 03:47:03: 25000000 INFO @ Sat, 11 Nov 2017 03:47:03: 26000000 INFO @ Sat, 11 Nov 2017 03:47:09: 27000000 INFO @ Sat, 11 Nov 2017 03:47:11: 27000000 INFO @ Sat, 11 Nov 2017 03:47:11: 26000000 INFO @ Sat, 11 Nov 2017 03:47:16: 28000000 INFO @ Sat, 11 Nov 2017 03:47:18: 28000000 INFO @ Sat, 11 Nov 2017 03:47:18: 27000000 INFO @ Sat, 11 Nov 2017 03:47:24: 29000000 INFO @ Sat, 11 Nov 2017 03:47:25: 29000000 INFO @ Sat, 11 Nov 2017 03:47:26: 28000000 INFO @ Sat, 11 Nov 2017 03:47:31: 30000000 INFO @ Sat, 11 Nov 2017 03:47:33: 30000000 INFO @ Sat, 11 Nov 2017 03:47:33: 29000000 INFO @ Sat, 11 Nov 2017 03:47:38: 31000000 INFO @ Sat, 11 Nov 2017 03:47:41: 31000000 INFO @ Sat, 11 Nov 2017 03:47:41: 30000000 INFO @ Sat, 11 Nov 2017 03:47:46: 32000000 INFO @ Sat, 11 Nov 2017 03:47:48: 32000000 INFO @ Sat, 11 Nov 2017 03:47:49: 31000000 INFO @ Sat, 11 Nov 2017 03:47:53: 33000000 INFO @ Sat, 11 Nov 2017 03:47:56: 33000000 INFO @ Sat, 11 Nov 2017 03:47:57: 32000000 INFO @ Sat, 11 Nov 2017 03:48:01: 34000000 INFO @ Sat, 11 Nov 2017 03:48:03: 34000000 INFO @ Sat, 11 Nov 2017 03:48:04: 33000000 INFO @ Sat, 11 Nov 2017 03:48:08: 35000000 INFO @ Sat, 11 Nov 2017 03:48:11: 35000000 INFO @ Sat, 11 Nov 2017 03:48:12: 34000000 INFO @ Sat, 11 Nov 2017 03:48:16: 36000000 INFO @ Sat, 11 Nov 2017 03:48:18: 36000000 INFO @ Sat, 11 Nov 2017 03:48:20: 35000000 INFO @ Sat, 11 Nov 2017 03:48:23: 37000000 INFO @ Sat, 11 Nov 2017 03:48:25: 37000000 INFO @ Sat, 11 Nov 2017 03:48:27: 36000000 INFO @ Sat, 11 Nov 2017 03:48:30: 38000000 INFO @ Sat, 11 Nov 2017 03:48:32: 38000000 INFO @ Sat, 11 Nov 2017 03:48:34: 37000000 INFO @ Sat, 11 Nov 2017 03:48:37: 39000000 INFO @ Sat, 11 Nov 2017 03:48:39: 39000000 INFO @ Sat, 11 Nov 2017 03:48:41: 38000000 INFO @ Sat, 11 Nov 2017 03:48:43: 40000000 INFO @ Sat, 11 Nov 2017 03:48:46: 40000000 INFO @ Sat, 11 Nov 2017 03:48:48: 39000000 INFO @ Sat, 11 Nov 2017 03:48:50: 41000000 INFO @ Sat, 11 Nov 2017 03:48:53: 41000000 INFO @ Sat, 11 Nov 2017 03:48:55: 40000000 INFO @ Sat, 11 Nov 2017 03:48:57: 42000000 INFO @ Sat, 11 Nov 2017 03:49:01: 42000000 INFO @ Sat, 11 Nov 2017 03:49:02: 41000000 INFO @ Sat, 11 Nov 2017 03:49:04: 43000000 INFO @ Sat, 11 Nov 2017 03:49:07: 43000000 INFO @ Sat, 11 Nov 2017 03:49:09: 42000000 INFO @ Sat, 11 Nov 2017 03:49:11: 44000000 INFO @ Sat, 11 Nov 2017 03:49:14: 44000000 INFO @ Sat, 11 Nov 2017 03:49:16: 43000000 INFO @ Sat, 11 Nov 2017 03:49:17: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:49:17: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:49:17: #1 total tags in treatment: 44780526 INFO @ Sat, 11 Nov 2017 03:49:17: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:49:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 03:49:18: #1 tags after filtering in treatment: 44780475 INFO @ Sat, 11 Nov 2017 03:49:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:49:18: #1 finished! INFO @ Sat, 11 Nov 2017 03:49:18: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:49:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:49:20: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:49:20: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:49:20: #1 total tags in treatment: 44780526 INFO @ Sat, 11 Nov 2017 03:49:20: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:49:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 03:49:21: #1 tags after filtering in treatment: 44780475 INFO @ Sat, 11 Nov 2017 03:49:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:49:21: #1 finished! INFO @ Sat, 11 Nov 2017 03:49:21: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:49:23: 44000000 INFO @ Sat, 11 Nov 2017 03:49:23: #2 number of paired peaks: 30174 INFO @ Sat, 11 Nov 2017 03:49:23: start model_add_line... INFO @ Sat, 11 Nov 2017 03:49:24: start X-correlation... INFO @ Sat, 11 Nov 2017 03:49:24: end of X-cor INFO @ Sat, 11 Nov 2017 03:49:24: #2 finished! INFO @ Sat, 11 Nov 2017 03:49:24: #2 predicted fragment length is 146 bps INFO @ Sat, 11 Nov 2017 03:49:24: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 11 Nov 2017 03:49:24: #2.2 Generate R script for model : SRX1977123.20_model.r INFO @ Sat, 11 Nov 2017 03:49:24: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:49:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:49:26: #2 number of paired peaks: 30174 INFO @ Sat, 11 Nov 2017 03:49:26: start model_add_line... INFO @ Sat, 11 Nov 2017 03:49:27: start X-correlation... INFO @ Sat, 11 Nov 2017 03:49:27: end of X-cor INFO @ Sat, 11 Nov 2017 03:49:27: #2 finished! INFO @ Sat, 11 Nov 2017 03:49:27: #2 predicted fragment length is 146 bps INFO @ Sat, 11 Nov 2017 03:49:27: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 11 Nov 2017 03:49:27: #2.2 Generate R script for model : SRX1977123.10_model.r INFO @ Sat, 11 Nov 2017 03:49:27: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:49:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:49:29: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:49:29: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:49:29: #1 total tags in treatment: 44780526 INFO @ Sat, 11 Nov 2017 03:49:29: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:49:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 03:49:30: #1 tags after filtering in treatment: 44780475 INFO @ Sat, 11 Nov 2017 03:49:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:49:30: #1 finished! INFO @ Sat, 11 Nov 2017 03:49:30: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:49:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:49:36: #2 number of paired peaks: 30174 INFO @ Sat, 11 Nov 2017 03:49:36: start model_add_line... INFO @ Sat, 11 Nov 2017 03:49:36: start X-correlation... INFO @ Sat, 11 Nov 2017 03:49:36: end of X-cor INFO @ Sat, 11 Nov 2017 03:49:36: #2 finished! INFO @ Sat, 11 Nov 2017 03:49:36: #2 predicted fragment length is 146 bps INFO @ Sat, 11 Nov 2017 03:49:36: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 11 Nov 2017 03:49:36: #2.2 Generate R script for model : SRX1977123.05_model.r INFO @ Sat, 11 Nov 2017 03:49:36: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:49:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:51:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:51:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:51:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:52:33: #4 Write output xls file... SRX1977123.10_peaks.xls INFO @ Sat, 11 Nov 2017 03:52:33: #4 Write peak in narrowPeak format file... SRX1977123.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:52:33: #4 Write summits bed file... SRX1977123.10_summits.bed INFO @ Sat, 11 Nov 2017 03:52:33: Done! pass1 - making usageList (158 chroms): 6 millis pass2 - checking and writing primary data (24612 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:52:38: #4 Write output xls file... SRX1977123.20_peaks.xls INFO @ Sat, 11 Nov 2017 03:52:38: #4 Write peak in narrowPeak format file... SRX1977123.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:52:38: #4 Write summits bed file... SRX1977123.20_summits.bed INFO @ Sat, 11 Nov 2017 03:52:38: Done! pass1 - making usageList (79 chroms): 1 millis pass2 - checking and writing primary data (5419 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:52:40: #4 Write output xls file... SRX1977123.05_peaks.xls INFO @ Sat, 11 Nov 2017 03:52:41: #4 Write peak in narrowPeak format file... SRX1977123.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:52:41: #4 Write summits bed file... SRX1977123.05_summits.bed INFO @ Sat, 11 Nov 2017 03:52:42: Done! pass1 - making usageList (225 chroms): 14 millis pass2 - checking and writing primary data (73125 records, 4 fields): 89 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。