Job ID = 10194884 sra ファイルのダウンロード中... Completed: 326647K bytes transferred in 8 seconds (317492K bits/sec), in 1 file. Completed: 328108K bytes transferred in 8 seconds (306607K bits/sec), in 1 file. Completed: 311925K bytes transferred in 10 seconds (253017K bits/sec), in 1 file. Completed: 307685K bytes transferred in 9 seconds (262763K bits/sec), in 1 file. Completed: 362408K bytes transferred in 10 seconds (290389K bits/sec), in 1 file. Completed: 367167K bytes transferred in 10 seconds (295625K 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 7008613 spots for /home/okishinya/chipatlas/results/rn6/SRX2202879/SRR4319821.sra Written 7008613 spots total Written 7091312 spots for /home/okishinya/chipatlas/results/rn6/SRX2202879/SRR4319820.sra Written 7091312 spots total Written 7411545 spots for /home/okishinya/chipatlas/results/rn6/SRX2202879/SRR4319818.sra Written 7411545 spots total Written 7420239 spots for /home/okishinya/chipatlas/results/rn6/SRX2202879/SRR4319819.sra Written 7420239 spots total Written 8050974 spots for /home/okishinya/chipatlas/results/rn6/SRX2202879/SRR4319822.sra Written 8050974 spots total Written 8125972 spots for /home/okishinya/chipatlas/results/rn6/SRX2202879/SRR4319823.sra Written 8125972 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: 00:30:29 45108655 reads; of these: 45108655 (100.00%) were unpaired; of these: 2019030 (4.48%) aligned 0 times 33861043 (75.07%) aligned exactly 1 time 9228582 (20.46%) aligned >1 times 95.52% overall alignment rate Time searching: 00:30:33 Overall time: 00:30:33 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] 6187380 / 43089625 = 0.1436 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 18:22:08: # Command line: callpeak -t SRX2202879.bam -f BAM -g 2.15e9 -n SRX2202879.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202879.05 # format = BAM # ChIP-seq file = ['SRX2202879.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 18:22:08: # Command line: callpeak -t SRX2202879.bam -f BAM -g 2.15e9 -n SRX2202879.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202879.10 # format = BAM # ChIP-seq file = ['SRX2202879.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 18:22:08: # Command line: callpeak -t SRX2202879.bam -f BAM -g 2.15e9 -n SRX2202879.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202879.20 # format = BAM # ChIP-seq file = ['SRX2202879.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 18:22:08: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:22:08: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:22:08: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:22:08: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:22:08: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:22:08: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:22:16: 1000000 INFO @ Fri, 10 Nov 2017 18:22:17: 1000000 INFO @ Fri, 10 Nov 2017 18:22:17: 1000000 INFO @ Fri, 10 Nov 2017 18:22:22: 2000000 INFO @ Fri, 10 Nov 2017 18:22:25: 2000000 INFO @ Fri, 10 Nov 2017 18:22:25: 2000000 INFO @ Fri, 10 Nov 2017 18:22:29: 3000000 INFO @ Fri, 10 Nov 2017 18:22:34: 3000000 INFO @ Fri, 10 Nov 2017 18:22:34: 3000000 INFO @ Fri, 10 Nov 2017 18:22:35: 4000000 INFO @ Fri, 10 Nov 2017 18:22:42: 5000000 INFO @ Fri, 10 Nov 2017 18:22:43: 4000000 INFO @ Fri, 10 Nov 2017 18:22:43: 4000000 INFO @ Fri, 10 Nov 2017 18:22:48: 6000000 INFO @ Fri, 10 Nov 2017 18:22:51: 5000000 INFO @ Fri, 10 Nov 2017 18:22:51: 5000000 INFO @ Fri, 10 Nov 2017 18:22:54: 7000000 INFO @ Fri, 10 Nov 2017 18:23:00: 6000000 INFO @ Fri, 10 Nov 2017 18:23:00: 6000000 INFO @ Fri, 10 Nov 2017 18:23:01: 8000000 INFO @ Fri, 10 Nov 2017 18:23:07: 9000000 INFO @ Fri, 10 Nov 2017 18:23:08: 7000000 INFO @ Fri, 10 Nov 2017 18:23:08: 7000000 INFO @ Fri, 10 Nov 2017 18:23:13: 10000000 INFO @ Fri, 10 Nov 2017 18:23:17: 8000000 INFO @ Fri, 10 Nov 2017 18:23:17: 8000000 INFO @ Fri, 10 Nov 2017 18:23:20: 11000000 INFO @ Fri, 10 Nov 2017 18:23:25: 9000000 INFO @ Fri, 10 Nov 2017 18:23:25: 9000000 INFO @ Fri, 10 Nov 2017 18:23:26: 12000000 INFO @ Fri, 10 Nov 2017 18:23:32: 13000000 INFO @ Fri, 10 Nov 2017 18:23:34: 10000000 INFO @ Fri, 10 Nov 2017 18:23:34: 10000000 INFO @ Fri, 10 Nov 2017 18:23:39: 14000000 INFO @ Fri, 10 Nov 2017 18:23:42: 11000000 INFO @ Fri, 10 Nov 2017 18:23:42: 11000000 INFO @ Fri, 10 Nov 2017 18:23:45: 15000000 INFO @ Fri, 10 Nov 2017 18:23:51: 12000000 INFO @ Fri, 10 Nov 2017 18:23:51: 12000000 INFO @ Fri, 10 Nov 2017 18:23:52: 16000000 INFO @ Fri, 10 Nov 2017 18:23:58: 17000000 INFO @ Fri, 10 Nov 2017 18:23:59: 13000000 INFO @ Fri, 10 Nov 2017 18:23:59: 13000000 INFO @ Fri, 10 Nov 2017 18:24:04: 18000000 INFO @ Fri, 10 Nov 2017 18:24:08: 14000000 INFO @ Fri, 10 Nov 2017 18:24:08: 14000000 INFO @ Fri, 10 Nov 2017 18:24:11: 19000000 INFO @ Fri, 10 Nov 2017 18:24:16: 15000000 INFO @ Fri, 10 Nov 2017 18:24:16: 15000000 INFO @ Fri, 10 Nov 2017 18:24:17: 20000000 INFO @ Fri, 10 Nov 2017 18:24:24: 21000000 INFO @ Fri, 10 Nov 2017 18:24:25: 16000000 INFO @ Fri, 10 Nov 2017 18:24:25: 16000000 INFO @ Fri, 10 Nov 2017 18:24:30: 22000000 INFO @ Fri, 10 Nov 2017 18:24:34: 17000000 INFO @ Fri, 10 Nov 2017 18:24:34: 17000000 INFO @ Fri, 10 Nov 2017 18:24:36: 23000000 INFO @ Fri, 10 Nov 2017 18:24:42: 18000000 INFO @ Fri, 10 Nov 2017 18:24:42: 18000000 INFO @ Fri, 10 Nov 2017 18:24:43: 24000000 INFO @ Fri, 10 Nov 2017 18:24:49: 25000000 INFO @ Fri, 10 Nov 2017 18:24:51: 19000000 INFO @ Fri, 10 Nov 2017 18:24:51: 19000000 INFO @ Fri, 10 Nov 2017 18:24:56: 26000000 INFO @ Fri, 10 Nov 2017 18:24:59: 20000000 INFO @ Fri, 10 Nov 2017 18:24:59: 20000000 INFO @ Fri, 10 Nov 2017 18:25:02: 27000000 INFO @ Fri, 10 Nov 2017 18:25:08: 21000000 INFO @ Fri, 10 Nov 2017 18:25:08: 21000000 INFO @ Fri, 10 Nov 2017 18:25:08: 28000000 INFO @ Fri, 10 Nov 2017 18:25:15: 29000000 INFO @ Fri, 10 Nov 2017 18:25:16: 22000000 INFO @ Fri, 10 Nov 2017 18:25:16: 22000000 INFO @ Fri, 10 Nov 2017 18:25:21: 30000000 INFO @ Fri, 10 Nov 2017 18:25:24: 23000000 INFO @ Fri, 10 Nov 2017 18:25:24: 23000000 INFO @ Fri, 10 Nov 2017 18:25:27: 31000000 INFO @ Fri, 10 Nov 2017 18:25:31: 24000000 INFO @ Fri, 10 Nov 2017 18:25:31: 24000000 INFO @ Fri, 10 Nov 2017 18:25:34: 32000000 INFO @ Fri, 10 Nov 2017 18:25:38: 25000000 INFO @ Fri, 10 Nov 2017 18:25:38: 25000000 INFO @ Fri, 10 Nov 2017 18:25:40: 33000000 INFO @ Fri, 10 Nov 2017 18:25:44: 26000000 INFO @ Fri, 10 Nov 2017 18:25:44: 26000000 INFO @ Fri, 10 Nov 2017 18:25:47: 34000000 INFO @ Fri, 10 Nov 2017 18:25:51: 27000000 INFO @ Fri, 10 Nov 2017 18:25:51: 27000000 INFO @ Fri, 10 Nov 2017 18:25:53: 35000000 INFO @ Fri, 10 Nov 2017 18:25:57: 28000000 INFO @ Fri, 10 Nov 2017 18:25:57: 28000000 INFO @ Fri, 10 Nov 2017 18:26:00: 36000000 INFO @ Fri, 10 Nov 2017 18:26:04: 29000000 INFO @ Fri, 10 Nov 2017 18:26:04: 29000000 INFO @ Fri, 10 Nov 2017 18:26:06: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:26:06: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:26:06: #1 total tags in treatment: 36902245 INFO @ Fri, 10 Nov 2017 18:26:06: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:26:06: #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 18:26:07: #1 tags after filtering in treatment: 36902129 INFO @ Fri, 10 Nov 2017 18:26:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:26:07: #1 finished! INFO @ Fri, 10 Nov 2017 18:26:07: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:26:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:26:11: 30000000 INFO @ Fri, 10 Nov 2017 18:26:11: 30000000 INFO @ Fri, 10 Nov 2017 18:26:12: #2 number of paired peaks: 52435 INFO @ Fri, 10 Nov 2017 18:26:12: start model_add_line... INFO @ Fri, 10 Nov 2017 18:26:13: start X-correlation... INFO @ Fri, 10 Nov 2017 18:26:13: end of X-cor INFO @ Fri, 10 Nov 2017 18:26:13: #2 finished! INFO @ Fri, 10 Nov 2017 18:26:13: #2 predicted fragment length is 151 bps INFO @ Fri, 10 Nov 2017 18:26:13: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 10 Nov 2017 18:26:13: #2.2 Generate R script for model : SRX2202879.20_model.r INFO @ Fri, 10 Nov 2017 18:26:13: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:26:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:26:17: 31000000 INFO @ Fri, 10 Nov 2017 18:26:17: 31000000 INFO @ Fri, 10 Nov 2017 18:26:24: 32000000 INFO @ Fri, 10 Nov 2017 18:26:24: 32000000 INFO @ Fri, 10 Nov 2017 18:26:31: 33000000 INFO @ Fri, 10 Nov 2017 18:26:31: 33000000 INFO @ Fri, 10 Nov 2017 18:26:37: 34000000 INFO @ Fri, 10 Nov 2017 18:26:38: 34000000 INFO @ Fri, 10 Nov 2017 18:26:44: 35000000 INFO @ Fri, 10 Nov 2017 18:26:44: 35000000 INFO @ Fri, 10 Nov 2017 18:26:51: 36000000 INFO @ Fri, 10 Nov 2017 18:26:51: 36000000 INFO @ Fri, 10 Nov 2017 18:26:57: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:26:57: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:26:57: #1 total tags in treatment: 36902245 INFO @ Fri, 10 Nov 2017 18:26:57: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:26:57: #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 18:26:57: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:26:57: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:26:57: #1 total tags in treatment: 36902245 INFO @ Fri, 10 Nov 2017 18:26:57: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:26:57: #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 18:26:58: #1 tags after filtering in treatment: 36902129 INFO @ Fri, 10 Nov 2017 18:26:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:26:58: #1 finished! INFO @ Fri, 10 Nov 2017 18:26:58: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:26:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:26:58: #1 tags after filtering in treatment: 36902129 INFO @ Fri, 10 Nov 2017 18:26:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:26:58: #1 finished! INFO @ Fri, 10 Nov 2017 18:26:58: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:26:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:27:04: #2 number of paired peaks: 52435 INFO @ Fri, 10 Nov 2017 18:27:04: start model_add_line... INFO @ Fri, 10 Nov 2017 18:27:04: start X-correlation... INFO @ Fri, 10 Nov 2017 18:27:04: end of X-cor INFO @ Fri, 10 Nov 2017 18:27:04: #2 finished! INFO @ Fri, 10 Nov 2017 18:27:04: #2 predicted fragment length is 151 bps INFO @ Fri, 10 Nov 2017 18:27:04: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 10 Nov 2017 18:27:04: #2.2 Generate R script for model : SRX2202879.05_model.r INFO @ Fri, 10 Nov 2017 18:27:04: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:27:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:27:04: #2 number of paired peaks: 52435 INFO @ Fri, 10 Nov 2017 18:27:04: start model_add_line... INFO @ Fri, 10 Nov 2017 18:27:05: start X-correlation... INFO @ Fri, 10 Nov 2017 18:27:05: end of X-cor INFO @ Fri, 10 Nov 2017 18:27:05: #2 finished! INFO @ Fri, 10 Nov 2017 18:27:05: #2 predicted fragment length is 151 bps INFO @ Fri, 10 Nov 2017 18:27:05: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 10 Nov 2017 18:27:05: #2.2 Generate R script for model : SRX2202879.10_model.r INFO @ Fri, 10 Nov 2017 18:27:05: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:27:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:27:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:28:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:28:38: #4 Write output xls file... SRX2202879.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:28:38: #4 Write peak in narrowPeak format file... SRX2202879.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:28:38: #4 Write summits bed file... SRX2202879.20_summits.bed INFO @ Fri, 10 Nov 2017 18:28:38: Done! pass1 - making usageList (58 chroms): 2 millis pass2 - checking and writing primary data (8514 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:28:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:29:32: #4 Write output xls file... SRX2202879.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:29:32: #4 Write peak in narrowPeak format file... SRX2202879.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:29:33: #4 Write summits bed file... SRX2202879.05_summits.bed INFO @ Fri, 10 Nov 2017 18:29:33: Done! pass1 - making usageList (110 chroms): 5 millis pass2 - checking and writing primary data (27654 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:29:40: #4 Write output xls file... SRX2202879.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:29:40: #4 Write peak in narrowPeak format file... SRX2202879.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:29:40: #4 Write summits bed file... SRX2202879.10_summits.bed INFO @ Fri, 10 Nov 2017 18:29:40: Done! pass1 - making usageList (89 chroms): 4 millis pass2 - checking and writing primary data (17656 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。