Job ID = 10194799 sra ファイルのダウンロード中... Completed: 1494021K bytes transferred in 20 seconds (584570K 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 53108331 spots for /home/okishinya/chipatlas/results/rn6/SRX1819026/SRR3624102.sra Written 53108331 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: 00:53:32 53108331 reads; of these: 53108331 (100.00%) were unpaired; of these: 3850151 (7.25%) aligned 0 times 37272904 (70.18%) aligned exactly 1 time 11985276 (22.57%) aligned >1 times 92.75% overall alignment rate Time searching: 00:53:37 Overall time: 00:53:37 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] 5536821 / 49258180 = 0.1124 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 23:56:05: # Command line: callpeak -t SRX1819026.bam -f BAM -g 2.15e9 -n SRX1819026.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1819026.20 # format = BAM # ChIP-seq file = ['SRX1819026.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 23:56:05: # Command line: callpeak -t SRX1819026.bam -f BAM -g 2.15e9 -n SRX1819026.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1819026.10 # format = BAM # ChIP-seq file = ['SRX1819026.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 23:56:05: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:56:05: # Command line: callpeak -t SRX1819026.bam -f BAM -g 2.15e9 -n SRX1819026.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1819026.05 # format = BAM # ChIP-seq file = ['SRX1819026.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 23:56:05: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:56:05: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:56:05: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:56:05: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:56:05: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:56:17: 1000000 INFO @ Fri, 10 Nov 2017 23:56:20: 1000000 INFO @ Fri, 10 Nov 2017 23:56:23: 1000000 INFO @ Fri, 10 Nov 2017 23:56:29: 2000000 INFO @ Fri, 10 Nov 2017 23:56:35: 2000000 INFO @ Fri, 10 Nov 2017 23:56:40: 2000000 INFO @ Fri, 10 Nov 2017 23:56:41: 3000000 INFO @ Fri, 10 Nov 2017 23:56:49: 3000000 INFO @ Fri, 10 Nov 2017 23:56:53: 4000000 INFO @ Fri, 10 Nov 2017 23:56:57: 3000000 INFO @ Fri, 10 Nov 2017 23:57:04: 4000000 INFO @ Fri, 10 Nov 2017 23:57:06: 5000000 INFO @ Fri, 10 Nov 2017 23:57:13: 4000000 INFO @ Fri, 10 Nov 2017 23:57:18: 6000000 INFO @ Fri, 10 Nov 2017 23:57:19: 5000000 INFO @ Fri, 10 Nov 2017 23:57:29: 5000000 INFO @ Fri, 10 Nov 2017 23:57:31: 7000000 INFO @ Fri, 10 Nov 2017 23:57:32: 6000000 INFO @ Fri, 10 Nov 2017 23:57:44: 8000000 INFO @ Fri, 10 Nov 2017 23:57:46: 6000000 INFO @ Fri, 10 Nov 2017 23:57:47: 7000000 INFO @ Fri, 10 Nov 2017 23:57:59: 9000000 INFO @ Fri, 10 Nov 2017 23:58:01: 8000000 INFO @ Fri, 10 Nov 2017 23:58:02: 7000000 INFO @ Fri, 10 Nov 2017 23:58:12: 9000000 INFO @ Fri, 10 Nov 2017 23:58:15: 10000000 INFO @ Fri, 10 Nov 2017 23:58:18: 8000000 INFO @ Fri, 10 Nov 2017 23:58:22: 10000000 INFO @ Fri, 10 Nov 2017 23:58:32: 11000000 INFO @ Fri, 10 Nov 2017 23:58:32: 11000000 INFO @ Fri, 10 Nov 2017 23:58:37: 9000000 INFO @ Fri, 10 Nov 2017 23:58:43: 12000000 INFO @ Fri, 10 Nov 2017 23:58:48: 12000000 INFO @ Fri, 10 Nov 2017 23:58:54: 13000000 INFO @ Fri, 10 Nov 2017 23:58:57: 10000000 INFO @ Fri, 10 Nov 2017 23:59:05: 13000000 INFO @ Fri, 10 Nov 2017 23:59:05: 14000000 INFO @ Fri, 10 Nov 2017 23:59:15: 11000000 INFO @ Fri, 10 Nov 2017 23:59:17: 15000000 INFO @ Fri, 10 Nov 2017 23:59:21: 14000000 INFO @ Fri, 10 Nov 2017 23:59:28: 16000000 INFO @ Fri, 10 Nov 2017 23:59:33: 12000000 INFO @ Fri, 10 Nov 2017 23:59:37: 15000000 INFO @ Fri, 10 Nov 2017 23:59:40: 17000000 INFO @ Fri, 10 Nov 2017 23:59:50: 18000000 INFO @ Fri, 10 Nov 2017 23:59:51: 13000000 INFO @ Fri, 10 Nov 2017 23:59:53: 16000000 INFO @ Sat, 11 Nov 2017 00:00:00: 19000000 INFO @ Sat, 11 Nov 2017 00:00:08: 14000000 INFO @ Sat, 11 Nov 2017 00:00:09: 17000000 INFO @ Sat, 11 Nov 2017 00:00:11: 20000000 INFO @ Sat, 11 Nov 2017 00:00:21: 21000000 INFO @ Sat, 11 Nov 2017 00:00:24: 18000000 INFO @ Sat, 11 Nov 2017 00:00:25: 15000000 INFO @ Sat, 11 Nov 2017 00:00:32: 22000000 INFO @ Sat, 11 Nov 2017 00:00:38: 19000000 INFO @ Sat, 11 Nov 2017 00:00:43: 16000000 INFO @ Sat, 11 Nov 2017 00:00:44: 23000000 INFO @ Sat, 11 Nov 2017 00:00:54: 20000000 INFO @ Sat, 11 Nov 2017 00:00:56: 24000000 INFO @ Sat, 11 Nov 2017 00:01:00: 17000000 INFO @ Sat, 11 Nov 2017 00:01:08: 25000000 INFO @ Sat, 11 Nov 2017 00:01:10: 21000000 INFO @ Sat, 11 Nov 2017 00:01:16: 18000000 INFO @ Sat, 11 Nov 2017 00:01:18: 26000000 INFO @ Sat, 11 Nov 2017 00:01:26: 22000000 INFO @ Sat, 11 Nov 2017 00:01:29: 27000000 INFO @ Sat, 11 Nov 2017 00:01:32: 19000000 INFO @ Sat, 11 Nov 2017 00:01:40: 28000000 INFO @ Sat, 11 Nov 2017 00:01:41: 23000000 INFO @ Sat, 11 Nov 2017 00:01:47: 20000000 INFO @ Sat, 11 Nov 2017 00:01:50: 29000000 INFO @ Sat, 11 Nov 2017 00:01:57: 24000000 INFO @ Sat, 11 Nov 2017 00:02:01: 30000000 INFO @ Sat, 11 Nov 2017 00:02:03: 21000000 INFO @ Sat, 11 Nov 2017 00:02:13: 31000000 INFO @ Sat, 11 Nov 2017 00:02:13: 25000000 INFO @ Sat, 11 Nov 2017 00:02:20: 22000000 INFO @ Sat, 11 Nov 2017 00:02:24: 32000000 INFO @ Sat, 11 Nov 2017 00:02:28: 26000000 INFO @ Sat, 11 Nov 2017 00:02:35: 23000000 INFO @ Sat, 11 Nov 2017 00:02:36: 33000000 INFO @ Sat, 11 Nov 2017 00:02:43: 27000000 INFO @ Sat, 11 Nov 2017 00:02:47: 34000000 INFO @ Sat, 11 Nov 2017 00:02:51: 24000000 INFO @ Sat, 11 Nov 2017 00:02:58: 28000000 INFO @ Sat, 11 Nov 2017 00:03:00: 35000000 INFO @ Sat, 11 Nov 2017 00:03:07: 25000000 INFO @ Sat, 11 Nov 2017 00:03:11: 36000000 INFO @ Sat, 11 Nov 2017 00:03:13: 29000000 INFO @ Sat, 11 Nov 2017 00:03:22: 26000000 INFO @ Sat, 11 Nov 2017 00:03:22: 37000000 INFO @ Sat, 11 Nov 2017 00:03:27: 30000000 INFO @ Sat, 11 Nov 2017 00:03:33: 38000000 INFO @ Sat, 11 Nov 2017 00:03:38: 27000000 INFO @ Sat, 11 Nov 2017 00:03:41: 31000000 INFO @ Sat, 11 Nov 2017 00:03:44: 39000000 INFO @ Sat, 11 Nov 2017 00:03:54: 28000000 INFO @ Sat, 11 Nov 2017 00:03:56: 40000000 INFO @ Sat, 11 Nov 2017 00:03:57: 32000000 INFO @ Sat, 11 Nov 2017 00:04:09: 29000000 INFO @ Sat, 11 Nov 2017 00:04:10: 41000000 INFO @ Sat, 11 Nov 2017 00:04:11: 33000000 INFO @ Sat, 11 Nov 2017 00:04:25: 34000000 INFO @ Sat, 11 Nov 2017 00:04:26: 30000000 INFO @ Sat, 11 Nov 2017 00:04:27: 42000000 INFO @ Sat, 11 Nov 2017 00:04:41: 35000000 INFO @ Sat, 11 Nov 2017 00:04:41: 31000000 INFO @ Sat, 11 Nov 2017 00:04:45: 43000000 INFO @ Sat, 11 Nov 2017 00:04:58: 36000000 INFO @ Sat, 11 Nov 2017 00:04:59: 32000000 INFO @ Sat, 11 Nov 2017 00:05:00: #1 tag size is determined as 40 bps INFO @ Sat, 11 Nov 2017 00:05:00: #1 tag size = 40 INFO @ Sat, 11 Nov 2017 00:05:00: #1 total tags in treatment: 43721359 INFO @ Sat, 11 Nov 2017 00:05:00: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:05:00: #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 00:05:02: #1 tags after filtering in treatment: 43721280 INFO @ Sat, 11 Nov 2017 00:05:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:05:02: #1 finished! INFO @ Sat, 11 Nov 2017 00:05:02: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:05:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:05:08: #2 number of paired peaks: 16501 INFO @ Sat, 11 Nov 2017 00:05:08: start model_add_line... INFO @ Sat, 11 Nov 2017 00:05:08: start X-correlation... INFO @ Sat, 11 Nov 2017 00:05:08: end of X-cor INFO @ Sat, 11 Nov 2017 00:05:08: #2 finished! INFO @ Sat, 11 Nov 2017 00:05:08: #2 predicted fragment length is 229 bps INFO @ Sat, 11 Nov 2017 00:05:08: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 11 Nov 2017 00:05:08: #2.2 Generate R script for model : SRX1819026.20_model.r INFO @ Sat, 11 Nov 2017 00:05:08: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:05:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:05:14: 37000000 INFO @ Sat, 11 Nov 2017 00:05:18: 33000000 INFO @ Sat, 11 Nov 2017 00:05:32: 38000000 INFO @ Sat, 11 Nov 2017 00:05:39: 34000000 INFO @ Sat, 11 Nov 2017 00:05:49: 39000000 INFO @ Sat, 11 Nov 2017 00:05:58: 35000000 INFO @ Sat, 11 Nov 2017 00:06:05: 40000000 INFO @ Sat, 11 Nov 2017 00:06:18: 36000000 INFO @ Sat, 11 Nov 2017 00:06:23: 41000000 INFO @ Sat, 11 Nov 2017 00:06:36: 37000000 INFO @ Sat, 11 Nov 2017 00:06:39: 42000000 INFO @ Sat, 11 Nov 2017 00:06:55: 38000000 INFO @ Sat, 11 Nov 2017 00:06:57: 43000000 INFO @ Sat, 11 Nov 2017 00:07:11: #1 tag size is determined as 40 bps INFO @ Sat, 11 Nov 2017 00:07:11: #1 tag size = 40 INFO @ Sat, 11 Nov 2017 00:07:11: #1 total tags in treatment: 43721359 INFO @ Sat, 11 Nov 2017 00:07:11: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:07:11: #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 00:07:12: #1 tags after filtering in treatment: 43721280 INFO @ Sat, 11 Nov 2017 00:07:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:07:12: #1 finished! INFO @ Sat, 11 Nov 2017 00:07:12: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:07:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:07:13: 39000000 INFO @ Sat, 11 Nov 2017 00:07:18: #2 number of paired peaks: 16501 INFO @ Sat, 11 Nov 2017 00:07:18: start model_add_line... INFO @ Sat, 11 Nov 2017 00:07:19: start X-correlation... INFO @ Sat, 11 Nov 2017 00:07:19: end of X-cor INFO @ Sat, 11 Nov 2017 00:07:19: #2 finished! INFO @ Sat, 11 Nov 2017 00:07:19: #2 predicted fragment length is 229 bps INFO @ Sat, 11 Nov 2017 00:07:19: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 11 Nov 2017 00:07:19: #2.2 Generate R script for model : SRX1819026.10_model.r INFO @ Sat, 11 Nov 2017 00:07:19: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:07:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:07:30: 40000000 INFO @ Sat, 11 Nov 2017 00:07:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:07:49: 41000000 INFO @ Sat, 11 Nov 2017 00:08:09: 42000000 INFO @ Sat, 11 Nov 2017 00:08:28: 43000000 INFO @ Sat, 11 Nov 2017 00:08:40: #1 tag size is determined as 40 bps INFO @ Sat, 11 Nov 2017 00:08:40: #1 tag size = 40 INFO @ Sat, 11 Nov 2017 00:08:40: #1 total tags in treatment: 43721359 INFO @ Sat, 11 Nov 2017 00:08:40: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:08:40: #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 00:08:42: #1 tags after filtering in treatment: 43721280 INFO @ Sat, 11 Nov 2017 00:08:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:08:42: #1 finished! INFO @ Sat, 11 Nov 2017 00:08:42: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:08:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:08:48: #2 number of paired peaks: 16501 INFO @ Sat, 11 Nov 2017 00:08:48: start model_add_line... INFO @ Sat, 11 Nov 2017 00:08:48: start X-correlation... INFO @ Sat, 11 Nov 2017 00:08:48: end of X-cor INFO @ Sat, 11 Nov 2017 00:08:48: #2 finished! INFO @ Sat, 11 Nov 2017 00:08:48: #2 predicted fragment length is 229 bps INFO @ Sat, 11 Nov 2017 00:08:48: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 11 Nov 2017 00:08:48: #2.2 Generate R script for model : SRX1819026.05_model.r INFO @ Sat, 11 Nov 2017 00:08:48: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:08:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:09:02: #4 Write output xls file... SRX1819026.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:09:02: #4 Write peak in narrowPeak format file... SRX1819026.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:09:02: #4 Write summits bed file... SRX1819026.20_summits.bed INFO @ Sat, 11 Nov 2017 00:09:02: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (1389 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:09:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:11:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:11:28: #4 Write output xls file... SRX1819026.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:11:28: #4 Write peak in narrowPeak format file... SRX1819026.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:11:28: #4 Write summits bed file... SRX1819026.10_summits.bed INFO @ Sat, 11 Nov 2017 00:11:28: Done! pass1 - making usageList (44 chroms): 3 millis pass2 - checking and writing primary data (5422 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:12:40: #4 Write output xls file... SRX1819026.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:12:41: #4 Write peak in narrowPeak format file... SRX1819026.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:12:41: #4 Write summits bed file... SRX1819026.05_summits.bed INFO @ Sat, 11 Nov 2017 00:12:41: Done! pass1 - making usageList (63 chroms): 5 millis pass2 - checking and writing primary data (13474 records, 4 fields): 28 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。