Job ID = 10194907 sra ファイルのダウンロード中... Completed: 294043K bytes transferred in 20 seconds (119529K bits/sec), in 1 file. Completed: 287867K bytes transferred in 19 seconds (122550K bits/sec), in 1 file. Completed: 400593K bytes transferred in 23 seconds (141884K bits/sec), in 1 file. Completed: 394816K bytes transferred in 26 seconds (121851K bits/sec), in 1 file. Completed: 394153K bytes transferred in 23 seconds (138050K bits/sec), in 1 file. Completed: 389259K bytes transferred in 22 seconds (144377K 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 6751748 spots for /home/okishinya/chipatlas/results/rn6/SRX2202902/SRR4319957.sra Written 6751748 spots total Written 6927481 spots for /home/okishinya/chipatlas/results/rn6/SRX2202902/SRR4319956.sra Written 6927481 spots total Written 8553822 spots for /home/okishinya/chipatlas/results/rn6/SRX2202902/SRR4319961.sra Written 8553822 spots total Written 8649859 spots for /home/okishinya/chipatlas/results/rn6/SRX2202902/SRR4319960.sra Written 8649859 spots total Written 8610082 spots for /home/okishinya/chipatlas/results/rn6/SRX2202902/SRR4319959.sra Written 8610082 spots total Written 8788246 spots for /home/okishinya/chipatlas/results/rn6/SRX2202902/SRR4319958.sra Written 8788246 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 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: 01:27:36 48281238 reads; of these: 48281238 (100.00%) were unpaired; of these: 4010193 (8.31%) aligned 0 times 28982121 (60.03%) aligned exactly 1 time 15288924 (31.67%) aligned >1 times 91.69% overall alignment rate Time searching: 01:27:39 Overall time: 01:27:39 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] 6761084 / 44271045 = 0.1527 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 23:46:54: # Command line: callpeak -t SRX2202902.bam -f BAM -g 2.15e9 -n SRX2202902.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202902.10 # format = BAM # ChIP-seq file = ['SRX2202902.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 23:46:54: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:46:54: # Command line: callpeak -t SRX2202902.bam -f BAM -g 2.15e9 -n SRX2202902.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202902.05 # format = BAM # ChIP-seq file = ['SRX2202902.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 23:46:54: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:46:54: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:46:54: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:46:54: # Command line: callpeak -t SRX2202902.bam -f BAM -g 2.15e9 -n SRX2202902.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202902.20 # format = BAM # ChIP-seq file = ['SRX2202902.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 23:46:54: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:46:54: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:47:10: 1000000 INFO @ Fri, 10 Nov 2017 23:47:10: 1000000 INFO @ Fri, 10 Nov 2017 23:47:14: 1000000 INFO @ Fri, 10 Nov 2017 23:47:25: 2000000 INFO @ Fri, 10 Nov 2017 23:47:25: 2000000 INFO @ Fri, 10 Nov 2017 23:47:37: 2000000 INFO @ Fri, 10 Nov 2017 23:47:38: 3000000 INFO @ Fri, 10 Nov 2017 23:47:38: 3000000 INFO @ Fri, 10 Nov 2017 23:47:52: 4000000 INFO @ Fri, 10 Nov 2017 23:47:52: 4000000 INFO @ Fri, 10 Nov 2017 23:47:59: 3000000 INFO @ Fri, 10 Nov 2017 23:48:05: 5000000 INFO @ Fri, 10 Nov 2017 23:48:05: 5000000 INFO @ Fri, 10 Nov 2017 23:48:18: 6000000 INFO @ Fri, 10 Nov 2017 23:48:18: 6000000 INFO @ Fri, 10 Nov 2017 23:48:19: 4000000 INFO @ Fri, 10 Nov 2017 23:48:31: 7000000 INFO @ Fri, 10 Nov 2017 23:48:31: 7000000 INFO @ Fri, 10 Nov 2017 23:48:40: 5000000 INFO @ Fri, 10 Nov 2017 23:48:43: 8000000 INFO @ Fri, 10 Nov 2017 23:48:43: 8000000 INFO @ Fri, 10 Nov 2017 23:48:57: 9000000 INFO @ Fri, 10 Nov 2017 23:48:57: 9000000 INFO @ Fri, 10 Nov 2017 23:49:01: 6000000 INFO @ Fri, 10 Nov 2017 23:49:11: 10000000 INFO @ Fri, 10 Nov 2017 23:49:11: 10000000 INFO @ Fri, 10 Nov 2017 23:49:22: 7000000 INFO @ Fri, 10 Nov 2017 23:49:32: 11000000 INFO @ Fri, 10 Nov 2017 23:49:33: 11000000 INFO @ Fri, 10 Nov 2017 23:49:44: 8000000 INFO @ Fri, 10 Nov 2017 23:49:54: 12000000 INFO @ Fri, 10 Nov 2017 23:49:55: 12000000 INFO @ Fri, 10 Nov 2017 23:50:06: 9000000 INFO @ Fri, 10 Nov 2017 23:50:16: 13000000 INFO @ Fri, 10 Nov 2017 23:50:17: 13000000 INFO @ Fri, 10 Nov 2017 23:50:27: 10000000 INFO @ Fri, 10 Nov 2017 23:50:38: 14000000 INFO @ Fri, 10 Nov 2017 23:50:39: 14000000 INFO @ Fri, 10 Nov 2017 23:50:49: 11000000 INFO @ Fri, 10 Nov 2017 23:50:59: 15000000 INFO @ Fri, 10 Nov 2017 23:51:01: 15000000 INFO @ Fri, 10 Nov 2017 23:51:12: 12000000 INFO @ Fri, 10 Nov 2017 23:51:22: 16000000 INFO @ Fri, 10 Nov 2017 23:51:23: 16000000 INFO @ Fri, 10 Nov 2017 23:51:34: 13000000 INFO @ Fri, 10 Nov 2017 23:51:44: 17000000 INFO @ Fri, 10 Nov 2017 23:51:45: 17000000 INFO @ Fri, 10 Nov 2017 23:51:56: 14000000 INFO @ Fri, 10 Nov 2017 23:52:05: 18000000 INFO @ Fri, 10 Nov 2017 23:52:07: 18000000 INFO @ Fri, 10 Nov 2017 23:52:17: 15000000 INFO @ Fri, 10 Nov 2017 23:52:27: 19000000 INFO @ Fri, 10 Nov 2017 23:52:29: 19000000 INFO @ Fri, 10 Nov 2017 23:52:39: 16000000 INFO @ Fri, 10 Nov 2017 23:52:49: 20000000 INFO @ Fri, 10 Nov 2017 23:52:51: 20000000 INFO @ Fri, 10 Nov 2017 23:53:01: 17000000 INFO @ Fri, 10 Nov 2017 23:53:11: 21000000 INFO @ Fri, 10 Nov 2017 23:53:12: 21000000 INFO @ Fri, 10 Nov 2017 23:53:23: 18000000 INFO @ Fri, 10 Nov 2017 23:53:33: 22000000 INFO @ Fri, 10 Nov 2017 23:53:34: 22000000 INFO @ Fri, 10 Nov 2017 23:53:46: 19000000 INFO @ Fri, 10 Nov 2017 23:53:56: 23000000 INFO @ Fri, 10 Nov 2017 23:53:56: 23000000 INFO @ Fri, 10 Nov 2017 23:54:08: 20000000 INFO @ Fri, 10 Nov 2017 23:54:18: 24000000 INFO @ Fri, 10 Nov 2017 23:54:18: 24000000 INFO @ Fri, 10 Nov 2017 23:54:30: 21000000 INFO @ Fri, 10 Nov 2017 23:54:39: 25000000 INFO @ Fri, 10 Nov 2017 23:54:40: 25000000 INFO @ Fri, 10 Nov 2017 23:54:53: 22000000 INFO @ Fri, 10 Nov 2017 23:55:00: 26000000 INFO @ Fri, 10 Nov 2017 23:55:03: 26000000 INFO @ Fri, 10 Nov 2017 23:55:16: 23000000 INFO @ Fri, 10 Nov 2017 23:55:21: 27000000 INFO @ Fri, 10 Nov 2017 23:55:26: 27000000 INFO @ Fri, 10 Nov 2017 23:55:39: 24000000 INFO @ Fri, 10 Nov 2017 23:55:43: 28000000 INFO @ Fri, 10 Nov 2017 23:55:46: 28000000 INFO @ Fri, 10 Nov 2017 23:56:00: 29000000 INFO @ Fri, 10 Nov 2017 23:56:01: 25000000 INFO @ Fri, 10 Nov 2017 23:56:04: 29000000 INFO @ Fri, 10 Nov 2017 23:56:13: 30000000 INFO @ Fri, 10 Nov 2017 23:56:23: 26000000 INFO @ Fri, 10 Nov 2017 23:56:26: 31000000 INFO @ Fri, 10 Nov 2017 23:56:27: 30000000 INFO @ Fri, 10 Nov 2017 23:56:40: 32000000 INFO @ Fri, 10 Nov 2017 23:56:45: 27000000 INFO @ Fri, 10 Nov 2017 23:56:48: 31000000 INFO @ Fri, 10 Nov 2017 23:56:53: 33000000 INFO @ Fri, 10 Nov 2017 23:57:06: 34000000 INFO @ Fri, 10 Nov 2017 23:57:07: 32000000 INFO @ Fri, 10 Nov 2017 23:57:07: 28000000 INFO @ Fri, 10 Nov 2017 23:57:19: 35000000 INFO @ Fri, 10 Nov 2017 23:57:24: 33000000 INFO @ Fri, 10 Nov 2017 23:57:25: 29000000 INFO @ Fri, 10 Nov 2017 23:57:32: 36000000 INFO @ Fri, 10 Nov 2017 23:57:41: 34000000 INFO @ Fri, 10 Nov 2017 23:57:43: 30000000 INFO @ Fri, 10 Nov 2017 23:57:44: 37000000 INFO @ Fri, 10 Nov 2017 23:57:51: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:57:51: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:57:51: #1 total tags in treatment: 37509961 INFO @ Fri, 10 Nov 2017 23:57:51: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:57:51: #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 23:57:53: #1 tags after filtering in treatment: 37509882 INFO @ Fri, 10 Nov 2017 23:57:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:57:53: #1 finished! INFO @ Fri, 10 Nov 2017 23:57:53: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:57:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:57:59: 35000000 INFO @ Fri, 10 Nov 2017 23:57:59: #2 number of paired peaks: 38068 INFO @ Fri, 10 Nov 2017 23:57:59: start model_add_line... INFO @ Fri, 10 Nov 2017 23:58:00: start X-correlation... INFO @ Fri, 10 Nov 2017 23:58:00: end of X-cor INFO @ Fri, 10 Nov 2017 23:58:00: #2 finished! INFO @ Fri, 10 Nov 2017 23:58:00: #2 predicted fragment length is 119 bps INFO @ Fri, 10 Nov 2017 23:58:00: #2 alternative fragment length(s) may be 119 bps INFO @ Fri, 10 Nov 2017 23:58:00: #2.2 Generate R script for model : SRX2202902.10_model.r INFO @ Fri, 10 Nov 2017 23:58:00: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:58:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:58:01: 31000000 INFO @ Fri, 10 Nov 2017 23:58:16: 36000000 INFO @ Fri, 10 Nov 2017 23:58:19: 32000000 INFO @ Fri, 10 Nov 2017 23:58:34: 37000000 INFO @ Fri, 10 Nov 2017 23:58:39: 33000000 INFO @ Fri, 10 Nov 2017 23:58:42: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:58:42: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:58:42: #1 total tags in treatment: 37509961 INFO @ Fri, 10 Nov 2017 23:58:42: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:58:42: #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 23:58:43: #1 tags after filtering in treatment: 37509882 INFO @ Fri, 10 Nov 2017 23:58:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:58:43: #1 finished! INFO @ Fri, 10 Nov 2017 23:58:43: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:58:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:58:50: #2 number of paired peaks: 38068 INFO @ Fri, 10 Nov 2017 23:58:50: start model_add_line... INFO @ Fri, 10 Nov 2017 23:58:51: start X-correlation... INFO @ Fri, 10 Nov 2017 23:58:51: end of X-cor INFO @ Fri, 10 Nov 2017 23:58:51: #2 finished! INFO @ Fri, 10 Nov 2017 23:58:51: #2 predicted fragment length is 119 bps INFO @ Fri, 10 Nov 2017 23:58:51: #2 alternative fragment length(s) may be 119 bps INFO @ Fri, 10 Nov 2017 23:58:51: #2.2 Generate R script for model : SRX2202902.20_model.r INFO @ Fri, 10 Nov 2017 23:58:51: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:58:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:58:57: 34000000 INFO @ Fri, 10 Nov 2017 23:59:14: 35000000 INFO @ Fri, 10 Nov 2017 23:59:32: 36000000 INFO @ Fri, 10 Nov 2017 23:59:50: 37000000 INFO @ Sat, 11 Nov 2017 00:00:00: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:00:00: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:00:00: #1 total tags in treatment: 37509961 INFO @ Sat, 11 Nov 2017 00:00:00: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:00:00: #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 00:00:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:00:01: #1 tags after filtering in treatment: 37509882 INFO @ Sat, 11 Nov 2017 00:00:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:00:01: #1 finished! INFO @ Sat, 11 Nov 2017 00:00:01: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:00:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:00:08: #2 number of paired peaks: 38068 INFO @ Sat, 11 Nov 2017 00:00:08: start model_add_line... INFO @ Sat, 11 Nov 2017 00:00:09: start X-correlation... INFO @ Sat, 11 Nov 2017 00:00:09: end of X-cor INFO @ Sat, 11 Nov 2017 00:00:09: #2 finished! INFO @ Sat, 11 Nov 2017 00:00:09: #2 predicted fragment length is 119 bps INFO @ Sat, 11 Nov 2017 00:00:09: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 11 Nov 2017 00:00:09: #2.2 Generate R script for model : SRX2202902.05_model.r INFO @ Sat, 11 Nov 2017 00:00:09: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:00:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:00:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:01:12: #4 Write output xls file... SRX2202902.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:01:13: #4 Write peak in narrowPeak format file... SRX2202902.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:01:13: #4 Write summits bed file... SRX2202902.10_summits.bed INFO @ Sat, 11 Nov 2017 00:01:13: Done! pass1 - making usageList (92 chroms): 5 millis pass2 - checking and writing primary data (16400 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:02:00: #4 Write output xls file... SRX2202902.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:02:00: #4 Write peak in narrowPeak format file... SRX2202902.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:02:00: #4 Write summits bed file... SRX2202902.20_summits.bed INFO @ Sat, 11 Nov 2017 00:02:00: Done! pass1 - making usageList (65 chroms): 3 millis pass2 - checking and writing primary data (7812 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:02:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:03:21: #4 Write output xls file... SRX2202902.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:03:21: #4 Write peak in narrowPeak format file... SRX2202902.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:03:21: #4 Write summits bed file... SRX2202902.05_summits.bed INFO @ Sat, 11 Nov 2017 00:03:22: Done! pass1 - making usageList (117 chroms): 7 millis pass2 - checking and writing primary data (23722 records, 4 fields): 46 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。