Job ID = 10194806 sra ファイルのダウンロード中... Completed: 1591382K bytes transferred in 21 seconds (604150K 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 59201101 spots for /home/okishinya/chipatlas/results/rn6/SRX1819032/SRR3624108.sra Written 59201101 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: 00:46:59 59201101 reads; of these: 59201101 (100.00%) were unpaired; of these: 4845310 (8.18%) aligned 0 times 40702402 (68.75%) aligned exactly 1 time 13653389 (23.06%) aligned >1 times 91.82% overall alignment rate Time searching: 00:47:04 Overall time: 00:47:04 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 16 files... [bam_rmdupse_core] 9388119 / 54355791 = 0.1727 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, 10 Nov 2017 22:44:39: # Command line: callpeak -t SRX1819032.bam -f BAM -g 2.15e9 -n SRX1819032.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1819032.05 # format = BAM # ChIP-seq file = ['SRX1819032.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, 10 Nov 2017 22:44:39: # Command line: callpeak -t SRX1819032.bam -f BAM -g 2.15e9 -n SRX1819032.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1819032.10 # format = BAM # ChIP-seq file = ['SRX1819032.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, 10 Nov 2017 22:44:39: # Command line: callpeak -t SRX1819032.bam -f BAM -g 2.15e9 -n SRX1819032.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1819032.20 # format = BAM # ChIP-seq file = ['SRX1819032.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, 10 Nov 2017 22:44:39: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:44:39: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:44:39: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:44:39: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:44:39: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:44:39: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:44:48: 1000000 INFO @ Fri, 10 Nov 2017 22:44:49: 1000000 INFO @ Fri, 10 Nov 2017 22:44:49: 1000000 INFO @ Fri, 10 Nov 2017 22:44:56: 2000000 INFO @ Fri, 10 Nov 2017 22:45:01: 2000000 INFO @ Fri, 10 Nov 2017 22:45:01: 2000000 INFO @ Fri, 10 Nov 2017 22:45:04: 3000000 INFO @ Fri, 10 Nov 2017 22:45:09: 3000000 INFO @ Fri, 10 Nov 2017 22:45:09: 3000000 INFO @ Fri, 10 Nov 2017 22:45:12: 4000000 INFO @ Fri, 10 Nov 2017 22:45:18: 4000000 INFO @ Fri, 10 Nov 2017 22:45:18: 4000000 INFO @ Fri, 10 Nov 2017 22:45:20: 5000000 INFO @ Fri, 10 Nov 2017 22:45:27: 5000000 INFO @ Fri, 10 Nov 2017 22:45:27: 5000000 INFO @ Fri, 10 Nov 2017 22:45:29: 6000000 INFO @ Fri, 10 Nov 2017 22:45:36: 6000000 INFO @ Fri, 10 Nov 2017 22:45:36: 6000000 INFO @ Fri, 10 Nov 2017 22:45:38: 7000000 INFO @ Fri, 10 Nov 2017 22:45:45: 7000000 INFO @ Fri, 10 Nov 2017 22:45:47: 8000000 INFO @ Fri, 10 Nov 2017 22:45:48: 7000000 INFO @ Fri, 10 Nov 2017 22:45:53: 8000000 INFO @ Fri, 10 Nov 2017 22:45:56: 9000000 INFO @ Fri, 10 Nov 2017 22:46:01: 8000000 INFO @ Fri, 10 Nov 2017 22:46:01: 9000000 INFO @ Fri, 10 Nov 2017 22:46:05: 10000000 INFO @ Fri, 10 Nov 2017 22:46:10: 10000000 INFO @ Fri, 10 Nov 2017 22:46:12: 9000000 INFO @ Fri, 10 Nov 2017 22:46:13: 11000000 INFO @ Fri, 10 Nov 2017 22:46:19: 11000000 INFO @ Fri, 10 Nov 2017 22:46:22: 10000000 INFO @ Fri, 10 Nov 2017 22:46:23: 12000000 INFO @ Fri, 10 Nov 2017 22:46:27: 12000000 INFO @ Fri, 10 Nov 2017 22:46:32: 13000000 INFO @ Fri, 10 Nov 2017 22:46:33: 11000000 INFO @ Fri, 10 Nov 2017 22:46:35: 13000000 INFO @ Fri, 10 Nov 2017 22:46:40: 14000000 INFO @ Fri, 10 Nov 2017 22:46:44: 14000000 INFO @ Fri, 10 Nov 2017 22:46:45: 12000000 INFO @ Fri, 10 Nov 2017 22:46:49: 15000000 INFO @ Fri, 10 Nov 2017 22:46:52: 15000000 INFO @ Fri, 10 Nov 2017 22:46:56: 13000000 INFO @ Fri, 10 Nov 2017 22:46:57: 16000000 INFO @ Fri, 10 Nov 2017 22:47:00: 16000000 INFO @ Fri, 10 Nov 2017 22:47:05: 17000000 INFO @ Fri, 10 Nov 2017 22:47:07: 14000000 INFO @ Fri, 10 Nov 2017 22:47:09: 17000000 INFO @ Fri, 10 Nov 2017 22:47:14: 18000000 INFO @ Fri, 10 Nov 2017 22:47:17: 18000000 INFO @ Fri, 10 Nov 2017 22:47:18: 15000000 INFO @ Fri, 10 Nov 2017 22:47:23: 19000000 INFO @ Fri, 10 Nov 2017 22:47:26: 19000000 INFO @ Fri, 10 Nov 2017 22:47:30: 16000000 INFO @ Fri, 10 Nov 2017 22:47:32: 20000000 INFO @ Fri, 10 Nov 2017 22:47:35: 20000000 INFO @ Fri, 10 Nov 2017 22:47:41: 21000000 INFO @ Fri, 10 Nov 2017 22:47:41: 17000000 INFO @ Fri, 10 Nov 2017 22:47:44: 21000000 INFO @ Fri, 10 Nov 2017 22:47:50: 22000000 INFO @ Fri, 10 Nov 2017 22:47:52: 18000000 INFO @ Fri, 10 Nov 2017 22:47:52: 22000000 INFO @ Fri, 10 Nov 2017 22:47:58: 23000000 INFO @ Fri, 10 Nov 2017 22:48:01: 23000000 INFO @ Fri, 10 Nov 2017 22:48:03: 19000000 INFO @ Fri, 10 Nov 2017 22:48:06: 24000000 INFO @ Fri, 10 Nov 2017 22:48:10: 24000000 INFO @ Fri, 10 Nov 2017 22:48:14: 25000000 INFO @ Fri, 10 Nov 2017 22:48:15: 20000000 INFO @ Fri, 10 Nov 2017 22:48:19: 25000000 INFO @ Fri, 10 Nov 2017 22:48:23: 26000000 INFO @ Fri, 10 Nov 2017 22:48:27: 21000000 INFO @ Fri, 10 Nov 2017 22:48:28: 26000000 INFO @ Fri, 10 Nov 2017 22:48:31: 27000000 INFO @ Fri, 10 Nov 2017 22:48:37: 27000000 INFO @ Fri, 10 Nov 2017 22:48:39: 22000000 INFO @ Fri, 10 Nov 2017 22:48:40: 28000000 INFO @ Fri, 10 Nov 2017 22:48:46: 28000000 INFO @ Fri, 10 Nov 2017 22:48:49: 29000000 INFO @ Fri, 10 Nov 2017 22:48:50: 23000000 INFO @ Fri, 10 Nov 2017 22:48:55: 29000000 INFO @ Fri, 10 Nov 2017 22:48:58: 30000000 INFO @ Fri, 10 Nov 2017 22:49:01: 24000000 INFO @ Fri, 10 Nov 2017 22:49:04: 30000000 INFO @ Fri, 10 Nov 2017 22:49:07: 31000000 INFO @ Fri, 10 Nov 2017 22:49:12: 25000000 INFO @ Fri, 10 Nov 2017 22:49:13: 31000000 INFO @ Fri, 10 Nov 2017 22:49:15: 32000000 INFO @ Fri, 10 Nov 2017 22:49:23: 26000000 INFO @ Fri, 10 Nov 2017 22:49:25: 32000000 INFO @ Fri, 10 Nov 2017 22:49:27: 33000000 INFO @ Fri, 10 Nov 2017 22:49:34: 33000000 INFO @ Fri, 10 Nov 2017 22:49:35: 27000000 INFO @ Fri, 10 Nov 2017 22:49:36: 34000000 INFO @ Fri, 10 Nov 2017 22:49:44: 34000000 INFO @ Fri, 10 Nov 2017 22:49:46: 28000000 INFO @ Fri, 10 Nov 2017 22:49:47: 35000000 INFO @ Fri, 10 Nov 2017 22:49:54: 35000000 INFO @ Fri, 10 Nov 2017 22:49:58: 36000000 INFO @ Fri, 10 Nov 2017 22:49:58: 29000000 INFO @ Fri, 10 Nov 2017 22:50:03: 36000000 INFO @ Fri, 10 Nov 2017 22:50:08: 37000000 INFO @ Fri, 10 Nov 2017 22:50:11: 30000000 INFO @ Fri, 10 Nov 2017 22:50:13: 37000000 INFO @ Fri, 10 Nov 2017 22:50:19: 38000000 INFO @ Fri, 10 Nov 2017 22:50:23: 38000000 INFO @ Fri, 10 Nov 2017 22:50:26: 31000000 INFO @ Fri, 10 Nov 2017 22:50:27: 39000000 INFO @ Fri, 10 Nov 2017 22:50:34: 39000000 INFO @ Fri, 10 Nov 2017 22:50:36: 40000000 INFO @ Fri, 10 Nov 2017 22:50:40: 32000000 INFO @ Fri, 10 Nov 2017 22:50:45: 40000000 INFO @ Fri, 10 Nov 2017 22:50:45: 41000000 INFO @ Fri, 10 Nov 2017 22:50:52: 33000000 INFO @ Fri, 10 Nov 2017 22:50:53: 42000000 INFO @ Fri, 10 Nov 2017 22:50:56: 41000000 INFO @ Fri, 10 Nov 2017 22:51:02: 43000000 INFO @ Fri, 10 Nov 2017 22:51:05: 34000000 INFO @ Fri, 10 Nov 2017 22:51:06: 42000000 INFO @ Fri, 10 Nov 2017 22:51:10: 44000000 INFO @ Fri, 10 Nov 2017 22:51:16: 43000000 INFO @ Fri, 10 Nov 2017 22:51:17: 35000000 INFO @ Fri, 10 Nov 2017 22:51:19: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 22:51:19: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 22:51:19: #1 total tags in treatment: 44967672 INFO @ Fri, 10 Nov 2017 22:51:19: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:51:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:51:21: #1 tags after filtering in treatment: 44967609 INFO @ Fri, 10 Nov 2017 22:51:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:51:21: #1 finished! INFO @ Fri, 10 Nov 2017 22:51:21: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:51:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:51:26: #2 number of paired peaks: 9919 INFO @ Fri, 10 Nov 2017 22:51:26: start model_add_line... INFO @ Fri, 10 Nov 2017 22:51:27: start X-correlation... INFO @ Fri, 10 Nov 2017 22:51:27: end of X-cor INFO @ Fri, 10 Nov 2017 22:51:27: #2 finished! INFO @ Fri, 10 Nov 2017 22:51:27: #2 predicted fragment length is 204 bps INFO @ Fri, 10 Nov 2017 22:51:27: #2 alternative fragment length(s) may be 53,204 bps INFO @ Fri, 10 Nov 2017 22:51:27: #2.2 Generate R script for model : SRX1819032.05_model.r INFO @ Fri, 10 Nov 2017 22:51:27: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:51:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:51:27: 44000000 INFO @ Fri, 10 Nov 2017 22:51:31: 36000000 INFO @ Fri, 10 Nov 2017 22:51:38: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 22:51:38: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 22:51:38: #1 total tags in treatment: 44967672 INFO @ Fri, 10 Nov 2017 22:51:38: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:51:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:51:39: #1 tags after filtering in treatment: 44967609 INFO @ Fri, 10 Nov 2017 22:51:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:51:39: #1 finished! INFO @ Fri, 10 Nov 2017 22:51:39: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:51:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:51:43: 37000000 INFO @ Fri, 10 Nov 2017 22:51:44: #2 number of paired peaks: 9919 INFO @ Fri, 10 Nov 2017 22:51:44: start model_add_line... INFO @ Fri, 10 Nov 2017 22:51:45: start X-correlation... INFO @ Fri, 10 Nov 2017 22:51:45: end of X-cor INFO @ Fri, 10 Nov 2017 22:51:45: #2 finished! INFO @ Fri, 10 Nov 2017 22:51:45: #2 predicted fragment length is 204 bps INFO @ Fri, 10 Nov 2017 22:51:45: #2 alternative fragment length(s) may be 53,204 bps INFO @ Fri, 10 Nov 2017 22:51:45: #2.2 Generate R script for model : SRX1819032.10_model.r INFO @ Fri, 10 Nov 2017 22:51:45: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:51:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:51:54: 38000000 INFO @ Fri, 10 Nov 2017 22:52:07: 39000000 INFO @ Fri, 10 Nov 2017 22:52:20: 40000000 INFO @ Fri, 10 Nov 2017 22:52:35: 41000000 INFO @ Fri, 10 Nov 2017 22:52:48: 42000000 INFO @ Fri, 10 Nov 2017 22:53:01: 43000000 INFO @ Fri, 10 Nov 2017 22:53:13: 44000000 INFO @ Fri, 10 Nov 2017 22:53:24: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 22:53:24: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 22:53:24: #1 total tags in treatment: 44967672 INFO @ Fri, 10 Nov 2017 22:53:24: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:53:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:53:26: #1 tags after filtering in treatment: 44967609 INFO @ Fri, 10 Nov 2017 22:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:53:26: #1 finished! INFO @ Fri, 10 Nov 2017 22:53:26: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:53:31: #2 number of paired peaks: 9919 INFO @ Fri, 10 Nov 2017 22:53:31: start model_add_line... INFO @ Fri, 10 Nov 2017 22:53:32: start X-correlation... INFO @ Fri, 10 Nov 2017 22:53:32: end of X-cor INFO @ Fri, 10 Nov 2017 22:53:32: #2 finished! INFO @ Fri, 10 Nov 2017 22:53:32: #2 predicted fragment length is 204 bps INFO @ Fri, 10 Nov 2017 22:53:32: #2 alternative fragment length(s) may be 53,204 bps INFO @ Fri, 10 Nov 2017 22:53:32: #2.2 Generate R script for model : SRX1819032.20_model.r INFO @ Fri, 10 Nov 2017 22:53:32: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:53:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:53:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:53:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:55:06: #4 Write output xls file... SRX1819032.10_peaks.xls INFO @ Fri, 10 Nov 2017 22:55:06: #4 Write peak in narrowPeak format file... SRX1819032.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:55:06: #4 Write summits bed file... SRX1819032.10_summits.bed INFO @ Fri, 10 Nov 2017 22:55:06: Done! pass1 - making usageList (46 chroms): 2 millis pass2 - checking and writing primary data (2732 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:55:15: #4 Write output xls file... SRX1819032.05_peaks.xls INFO @ Fri, 10 Nov 2017 22:55:15: #4 Write peak in narrowPeak format file... SRX1819032.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:55:15: #4 Write summits bed file... SRX1819032.05_summits.bed INFO @ Fri, 10 Nov 2017 22:55:15: Done! pass1 - making usageList (65 chroms): 4 millis pass2 - checking and writing primary data (6521 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:55:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:57:03: #4 Write output xls file... SRX1819032.20_peaks.xls INFO @ Fri, 10 Nov 2017 22:57:03: #4 Write peak in narrowPeak format file... SRX1819032.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:57:03: #4 Write summits bed file... SRX1819032.20_summits.bed INFO @ Fri, 10 Nov 2017 22:57:03: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (801 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。