Job ID = 10194854 sra ファイルのダウンロード中... Completed: 810237K bytes transferred in 9 seconds (715786K 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 40344441 spots for /home/okishinya/chipatlas/results/rn6/SRX1977143/SRR3952275.sra Written 40344441 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:19:50 40344441 reads; of these: 40344441 (100.00%) were unpaired; of these: 5205475 (12.90%) aligned 0 times 16878172 (41.84%) aligned exactly 1 time 18260794 (45.26%) aligned >1 times 87.10% overall alignment rate Time searching: 01:19:53 Overall time: 01:19:53 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] 3909129 / 35138966 = 0.1112 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 04:20:40: # Command line: callpeak -t SRX1977143.bam -f BAM -g 2.15e9 -n SRX1977143.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977143.10 # format = BAM # ChIP-seq file = ['SRX1977143.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 04:20:40: # Command line: callpeak -t SRX1977143.bam -f BAM -g 2.15e9 -n SRX1977143.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977143.20 # format = BAM # ChIP-seq file = ['SRX1977143.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 04:20:40: #1 read tag files... INFO @ Sat, 11 Nov 2017 04:20:40: #1 read tag files... INFO @ Sat, 11 Nov 2017 04:20:40: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 04:20:40: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 04:20:40: # Command line: callpeak -t SRX1977143.bam -f BAM -g 2.15e9 -n SRX1977143.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977143.05 # format = BAM # ChIP-seq file = ['SRX1977143.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 04:20:40: #1 read tag files... INFO @ Sat, 11 Nov 2017 04:20:40: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 04:20:48: 1000000 INFO @ Sat, 11 Nov 2017 04:20:48: 1000000 INFO @ Sat, 11 Nov 2017 04:20:48: 1000000 INFO @ Sat, 11 Nov 2017 04:20:55: 2000000 INFO @ Sat, 11 Nov 2017 04:20:56: 2000000 INFO @ Sat, 11 Nov 2017 04:20:56: 2000000 INFO @ Sat, 11 Nov 2017 04:21:03: 3000000 INFO @ Sat, 11 Nov 2017 04:21:04: 3000000 INFO @ Sat, 11 Nov 2017 04:21:04: 3000000 INFO @ Sat, 11 Nov 2017 04:21:10: 4000000 INFO @ Sat, 11 Nov 2017 04:21:11: 4000000 INFO @ Sat, 11 Nov 2017 04:21:11: 4000000 INFO @ Sat, 11 Nov 2017 04:21:18: 5000000 INFO @ Sat, 11 Nov 2017 04:21:19: 5000000 INFO @ Sat, 11 Nov 2017 04:21:20: 5000000 INFO @ Sat, 11 Nov 2017 04:21:26: 6000000 INFO @ Sat, 11 Nov 2017 04:21:27: 6000000 INFO @ Sat, 11 Nov 2017 04:21:28: 6000000 INFO @ Sat, 11 Nov 2017 04:21:34: 7000000 INFO @ Sat, 11 Nov 2017 04:21:35: 7000000 INFO @ Sat, 11 Nov 2017 04:21:36: 7000000 INFO @ Sat, 11 Nov 2017 04:21:42: 8000000 INFO @ Sat, 11 Nov 2017 04:21:44: 8000000 INFO @ Sat, 11 Nov 2017 04:21:44: 8000000 INFO @ Sat, 11 Nov 2017 04:21:50: 9000000 INFO @ Sat, 11 Nov 2017 04:21:53: 9000000 INFO @ Sat, 11 Nov 2017 04:21:53: 9000000 INFO @ Sat, 11 Nov 2017 04:21:58: 10000000 INFO @ Sat, 11 Nov 2017 04:22:02: 10000000 INFO @ Sat, 11 Nov 2017 04:22:02: 10000000 INFO @ Sat, 11 Nov 2017 04:22:08: 11000000 INFO @ Sat, 11 Nov 2017 04:22:10: 11000000 INFO @ Sat, 11 Nov 2017 04:22:11: 11000000 INFO @ Sat, 11 Nov 2017 04:22:17: 12000000 INFO @ Sat, 11 Nov 2017 04:22:18: 12000000 INFO @ Sat, 11 Nov 2017 04:22:21: 12000000 INFO @ Sat, 11 Nov 2017 04:22:26: 13000000 INFO @ Sat, 11 Nov 2017 04:22:27: 13000000 INFO @ Sat, 11 Nov 2017 04:22:30: 13000000 INFO @ Sat, 11 Nov 2017 04:22:35: 14000000 INFO @ Sat, 11 Nov 2017 04:22:35: 14000000 INFO @ Sat, 11 Nov 2017 04:22:39: 14000000 INFO @ Sat, 11 Nov 2017 04:22:43: 15000000 INFO @ Sat, 11 Nov 2017 04:22:44: 15000000 INFO @ Sat, 11 Nov 2017 04:22:47: 15000000 INFO @ Sat, 11 Nov 2017 04:22:50: 16000000 INFO @ Sat, 11 Nov 2017 04:22:52: 16000000 INFO @ Sat, 11 Nov 2017 04:22:55: 16000000 INFO @ Sat, 11 Nov 2017 04:22:58: 17000000 INFO @ Sat, 11 Nov 2017 04:23:00: 17000000 INFO @ Sat, 11 Nov 2017 04:23:02: 17000000 INFO @ Sat, 11 Nov 2017 04:23:05: 18000000 INFO @ Sat, 11 Nov 2017 04:23:08: 18000000 INFO @ Sat, 11 Nov 2017 04:23:10: 18000000 INFO @ Sat, 11 Nov 2017 04:23:13: 19000000 INFO @ Sat, 11 Nov 2017 04:23:16: 19000000 INFO @ Sat, 11 Nov 2017 04:23:17: 19000000 INFO @ Sat, 11 Nov 2017 04:23:21: 20000000 INFO @ Sat, 11 Nov 2017 04:23:25: 20000000 INFO @ Sat, 11 Nov 2017 04:23:26: 20000000 INFO @ Sat, 11 Nov 2017 04:23:29: 21000000 INFO @ Sat, 11 Nov 2017 04:23:34: 21000000 INFO @ Sat, 11 Nov 2017 04:23:35: 21000000 INFO @ Sat, 11 Nov 2017 04:23:37: 22000000 INFO @ Sat, 11 Nov 2017 04:23:42: 22000000 INFO @ Sat, 11 Nov 2017 04:23:42: 22000000 INFO @ Sat, 11 Nov 2017 04:23:45: 23000000 INFO @ Sat, 11 Nov 2017 04:23:50: 23000000 INFO @ Sat, 11 Nov 2017 04:23:50: 23000000 INFO @ Sat, 11 Nov 2017 04:23:52: 24000000 INFO @ Sat, 11 Nov 2017 04:23:57: 24000000 INFO @ Sat, 11 Nov 2017 04:23:58: 24000000 INFO @ Sat, 11 Nov 2017 04:24:01: 25000000 INFO @ Sat, 11 Nov 2017 04:24:05: 25000000 INFO @ Sat, 11 Nov 2017 04:24:06: 25000000 INFO @ Sat, 11 Nov 2017 04:24:10: 26000000 INFO @ Sat, 11 Nov 2017 04:24:12: 26000000 INFO @ Sat, 11 Nov 2017 04:24:14: 26000000 INFO @ Sat, 11 Nov 2017 04:24:18: 27000000 INFO @ Sat, 11 Nov 2017 04:24:21: 27000000 INFO @ Sat, 11 Nov 2017 04:24:23: 27000000 INFO @ Sat, 11 Nov 2017 04:24:25: 28000000 INFO @ Sat, 11 Nov 2017 04:24:29: 28000000 INFO @ Sat, 11 Nov 2017 04:24:32: 28000000 INFO @ Sat, 11 Nov 2017 04:24:33: 29000000 INFO @ Sat, 11 Nov 2017 04:24:37: 29000000 INFO @ Sat, 11 Nov 2017 04:24:40: 29000000 INFO @ Sat, 11 Nov 2017 04:24:41: 30000000 INFO @ Sat, 11 Nov 2017 04:24:46: 30000000 INFO @ Sat, 11 Nov 2017 04:24:48: 31000000 INFO @ Sat, 11 Nov 2017 04:24:48: 30000000 INFO @ Sat, 11 Nov 2017 04:24:50: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 04:24:50: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 04:24:50: #1 total tags in treatment: 31229837 INFO @ Sat, 11 Nov 2017 04:24:50: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 04:24:50: #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 04:24:51: #1 tags after filtering in treatment: 31229752 INFO @ Sat, 11 Nov 2017 04:24:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 04:24:51: #1 finished! INFO @ Sat, 11 Nov 2017 04:24:51: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 04:24:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 04:24:54: 31000000 INFO @ Sat, 11 Nov 2017 04:24:55: #2 number of paired peaks: 45440 INFO @ Sat, 11 Nov 2017 04:24:55: start model_add_line... INFO @ Sat, 11 Nov 2017 04:24:56: start X-correlation... INFO @ Sat, 11 Nov 2017 04:24:56: end of X-cor INFO @ Sat, 11 Nov 2017 04:24:56: #2 finished! INFO @ Sat, 11 Nov 2017 04:24:56: #2 predicted fragment length is 159 bps INFO @ Sat, 11 Nov 2017 04:24:56: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 11 Nov 2017 04:24:56: #2.2 Generate R script for model : SRX1977143.20_model.r INFO @ Sat, 11 Nov 2017 04:24:56: #3 Call peaks... INFO @ Sat, 11 Nov 2017 04:24:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 04:24:56: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 04:24:56: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 04:24:56: #1 total tags in treatment: 31229837 INFO @ Sat, 11 Nov 2017 04:24:56: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 04:24:56: #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 04:24:57: 31000000 INFO @ Sat, 11 Nov 2017 04:24:57: #1 tags after filtering in treatment: 31229752 INFO @ Sat, 11 Nov 2017 04:24:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 04:24:57: #1 finished! INFO @ Sat, 11 Nov 2017 04:24:57: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 04:24:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 04:24:58: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 04:24:58: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 04:24:58: #1 total tags in treatment: 31229837 INFO @ Sat, 11 Nov 2017 04:24:58: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 04:24:58: #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 04:24:59: #1 tags after filtering in treatment: 31229752 INFO @ Sat, 11 Nov 2017 04:24:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 04:24:59: #1 finished! INFO @ Sat, 11 Nov 2017 04:24:59: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 04:24:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 04:25:03: #2 number of paired peaks: 45440 INFO @ Sat, 11 Nov 2017 04:25:03: start model_add_line... INFO @ Sat, 11 Nov 2017 04:25:03: start X-correlation... INFO @ Sat, 11 Nov 2017 04:25:03: end of X-cor INFO @ Sat, 11 Nov 2017 04:25:03: #2 finished! INFO @ Sat, 11 Nov 2017 04:25:03: #2 predicted fragment length is 159 bps INFO @ Sat, 11 Nov 2017 04:25:03: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 11 Nov 2017 04:25:03: #2.2 Generate R script for model : SRX1977143.05_model.r INFO @ Sat, 11 Nov 2017 04:25:03: #3 Call peaks... INFO @ Sat, 11 Nov 2017 04:25:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 04:25:05: #2 number of paired peaks: 45440 INFO @ Sat, 11 Nov 2017 04:25:05: start model_add_line... INFO @ Sat, 11 Nov 2017 04:25:05: start X-correlation... INFO @ Sat, 11 Nov 2017 04:25:05: end of X-cor INFO @ Sat, 11 Nov 2017 04:25:05: #2 finished! INFO @ Sat, 11 Nov 2017 04:25:05: #2 predicted fragment length is 159 bps INFO @ Sat, 11 Nov 2017 04:25:05: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 11 Nov 2017 04:25:05: #2.2 Generate R script for model : SRX1977143.10_model.r INFO @ Sat, 11 Nov 2017 04:25:05: #3 Call peaks... INFO @ Sat, 11 Nov 2017 04:25:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 04:26:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 04:26:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 04:26:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 04:27:11: #4 Write output xls file... SRX1977143.10_peaks.xls INFO @ Sat, 11 Nov 2017 04:27:12: #4 Write peak in narrowPeak format file... SRX1977143.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 04:27:12: #4 Write summits bed file... SRX1977143.10_summits.bed INFO @ Sat, 11 Nov 2017 04:27:12: Done! pass1 - making usageList (130 chroms): 5 millis pass2 - checking and writing primary data (19043 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 04:27:15: #4 Write output xls file... SRX1977143.20_peaks.xls INFO @ Sat, 11 Nov 2017 04:27:15: #4 Write peak in narrowPeak format file... SRX1977143.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 04:27:15: #4 Write summits bed file... SRX1977143.20_summits.bed INFO @ Sat, 11 Nov 2017 04:27:15: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (4054 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 04:27:26: #4 Write output xls file... SRX1977143.05_peaks.xls INFO @ Sat, 11 Nov 2017 04:27:26: #4 Write peak in narrowPeak format file... SRX1977143.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 04:27:27: #4 Write summits bed file... SRX1977143.05_summits.bed INFO @ Sat, 11 Nov 2017 04:27:27: Done! pass1 - making usageList (212 chroms): 11 millis pass2 - checking and writing primary data (60717 records, 4 fields): 77 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。