Job ID = 10194850 sra ファイルのダウンロード中... Completed: 997575K bytes transferred in 14 seconds (574890K 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 50305607 spots for /home/okishinya/chipatlas/results/rn6/SRX1977139/SRR3952271.sra Written 50305607 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: 01:30:59 50305607 reads; of these: 50305607 (100.00%) were unpaired; of these: 8826731 (17.55%) aligned 0 times 20082685 (39.92%) aligned exactly 1 time 21396191 (42.53%) aligned >1 times 82.45% overall alignment rate Time searching: 01:31:02 Overall time: 01:31:02 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] 7808207 / 41478876 = 0.1882 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 03:30:34: # Command line: callpeak -t SRX1977139.bam -f BAM -g 2.15e9 -n SRX1977139.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977139.10 # format = BAM # ChIP-seq file = ['SRX1977139.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 03:30:34: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:30:34: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:30:34: # Command line: callpeak -t SRX1977139.bam -f BAM -g 2.15e9 -n SRX1977139.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977139.20 # format = BAM # ChIP-seq file = ['SRX1977139.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 03:30:34: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:30:34: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:30:34: # Command line: callpeak -t SRX1977139.bam -f BAM -g 2.15e9 -n SRX1977139.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977139.05 # format = BAM # ChIP-seq file = ['SRX1977139.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 03:30:34: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:30:34: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:30:41: 1000000 INFO @ Sat, 11 Nov 2017 03:30:41: 1000000 INFO @ Sat, 11 Nov 2017 03:30:41: 1000000 INFO @ Sat, 11 Nov 2017 03:30:48: 2000000 INFO @ Sat, 11 Nov 2017 03:30:49: 2000000 INFO @ Sat, 11 Nov 2017 03:30:49: 2000000 INFO @ Sat, 11 Nov 2017 03:30:55: 3000000 INFO @ Sat, 11 Nov 2017 03:30:56: 3000000 INFO @ Sat, 11 Nov 2017 03:30:56: 3000000 INFO @ Sat, 11 Nov 2017 03:31:03: 4000000 INFO @ Sat, 11 Nov 2017 03:31:04: 4000000 INFO @ Sat, 11 Nov 2017 03:31:04: 4000000 INFO @ Sat, 11 Nov 2017 03:31:10: 5000000 INFO @ Sat, 11 Nov 2017 03:31:11: 5000000 INFO @ Sat, 11 Nov 2017 03:31:11: 5000000 INFO @ Sat, 11 Nov 2017 03:31:17: 6000000 INFO @ Sat, 11 Nov 2017 03:31:19: 6000000 INFO @ Sat, 11 Nov 2017 03:31:19: 6000000 INFO @ Sat, 11 Nov 2017 03:31:24: 7000000 INFO @ Sat, 11 Nov 2017 03:31:26: 7000000 INFO @ Sat, 11 Nov 2017 03:31:27: 7000000 INFO @ Sat, 11 Nov 2017 03:31:32: 8000000 INFO @ Sat, 11 Nov 2017 03:31:34: 8000000 INFO @ Sat, 11 Nov 2017 03:31:34: 8000000 INFO @ Sat, 11 Nov 2017 03:31:40: 9000000 INFO @ Sat, 11 Nov 2017 03:31:41: 9000000 INFO @ Sat, 11 Nov 2017 03:31:42: 9000000 INFO @ Sat, 11 Nov 2017 03:31:48: 10000000 INFO @ Sat, 11 Nov 2017 03:31:49: 10000000 INFO @ Sat, 11 Nov 2017 03:31:50: 10000000 INFO @ Sat, 11 Nov 2017 03:31:56: 11000000 INFO @ Sat, 11 Nov 2017 03:31:57: 11000000 INFO @ Sat, 11 Nov 2017 03:31:58: 11000000 INFO @ Sat, 11 Nov 2017 03:32:03: 12000000 INFO @ Sat, 11 Nov 2017 03:32:04: 12000000 INFO @ Sat, 11 Nov 2017 03:32:06: 12000000 INFO @ Sat, 11 Nov 2017 03:32:11: 13000000 INFO @ Sat, 11 Nov 2017 03:32:12: 13000000 INFO @ Sat, 11 Nov 2017 03:32:14: 13000000 INFO @ Sat, 11 Nov 2017 03:32:19: 14000000 INFO @ Sat, 11 Nov 2017 03:32:20: 14000000 INFO @ Sat, 11 Nov 2017 03:32:21: 14000000 INFO @ Sat, 11 Nov 2017 03:32:27: 15000000 INFO @ Sat, 11 Nov 2017 03:32:27: 15000000 INFO @ Sat, 11 Nov 2017 03:32:28: 15000000 INFO @ Sat, 11 Nov 2017 03:32:34: 16000000 INFO @ Sat, 11 Nov 2017 03:32:35: 16000000 INFO @ Sat, 11 Nov 2017 03:32:36: 16000000 INFO @ Sat, 11 Nov 2017 03:32:42: 17000000 INFO @ Sat, 11 Nov 2017 03:32:43: 17000000 INFO @ Sat, 11 Nov 2017 03:32:43: 17000000 INFO @ Sat, 11 Nov 2017 03:32:50: 18000000 INFO @ Sat, 11 Nov 2017 03:32:50: 18000000 INFO @ Sat, 11 Nov 2017 03:32:51: 18000000 INFO @ Sat, 11 Nov 2017 03:32:58: 19000000 INFO @ Sat, 11 Nov 2017 03:32:58: 19000000 INFO @ Sat, 11 Nov 2017 03:32:59: 19000000 INFO @ Sat, 11 Nov 2017 03:33:05: 20000000 INFO @ Sat, 11 Nov 2017 03:33:06: 20000000 INFO @ Sat, 11 Nov 2017 03:33:07: 20000000 INFO @ Sat, 11 Nov 2017 03:33:12: 21000000 INFO @ Sat, 11 Nov 2017 03:33:14: 21000000 INFO @ Sat, 11 Nov 2017 03:33:16: 21000000 INFO @ Sat, 11 Nov 2017 03:33:20: 22000000 INFO @ Sat, 11 Nov 2017 03:33:22: 22000000 INFO @ Sat, 11 Nov 2017 03:33:24: 22000000 INFO @ Sat, 11 Nov 2017 03:33:27: 23000000 INFO @ Sat, 11 Nov 2017 03:33:30: 23000000 INFO @ Sat, 11 Nov 2017 03:33:32: 23000000 INFO @ Sat, 11 Nov 2017 03:33:35: 24000000 INFO @ Sat, 11 Nov 2017 03:33:38: 24000000 INFO @ Sat, 11 Nov 2017 03:33:40: 24000000 INFO @ Sat, 11 Nov 2017 03:33:42: 25000000 INFO @ Sat, 11 Nov 2017 03:33:46: 25000000 INFO @ Sat, 11 Nov 2017 03:33:48: 25000000 INFO @ Sat, 11 Nov 2017 03:33:50: 26000000 INFO @ Sat, 11 Nov 2017 03:33:53: 26000000 INFO @ Sat, 11 Nov 2017 03:33:56: 26000000 INFO @ Sat, 11 Nov 2017 03:33:58: 27000000 INFO @ Sat, 11 Nov 2017 03:34:01: 27000000 INFO @ Sat, 11 Nov 2017 03:34:03: 27000000 INFO @ Sat, 11 Nov 2017 03:34:06: 28000000 INFO @ Sat, 11 Nov 2017 03:34:09: 28000000 INFO @ Sat, 11 Nov 2017 03:34:10: 28000000 INFO @ Sat, 11 Nov 2017 03:34:14: 29000000 INFO @ Sat, 11 Nov 2017 03:34:17: 29000000 INFO @ Sat, 11 Nov 2017 03:34:18: 29000000 INFO @ Sat, 11 Nov 2017 03:34:23: 30000000 INFO @ Sat, 11 Nov 2017 03:34:25: 30000000 INFO @ Sat, 11 Nov 2017 03:34:25: 30000000 INFO @ Sat, 11 Nov 2017 03:34:31: 31000000 INFO @ Sat, 11 Nov 2017 03:34:32: 31000000 INFO @ Sat, 11 Nov 2017 03:34:33: 31000000 INFO @ Sat, 11 Nov 2017 03:34:39: 32000000 INFO @ Sat, 11 Nov 2017 03:34:40: 32000000 INFO @ Sat, 11 Nov 2017 03:34:41: 32000000 INFO @ Sat, 11 Nov 2017 03:34:47: 33000000 INFO @ Sat, 11 Nov 2017 03:34:47: 33000000 INFO @ Sat, 11 Nov 2017 03:34:49: 33000000 INFO @ Sat, 11 Nov 2017 03:34:52: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:34:52: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:34:52: #1 total tags in treatment: 33670669 INFO @ Sat, 11 Nov 2017 03:34:52: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:34:52: #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 03:34:53: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:34:53: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:34:53: #1 total tags in treatment: 33670669 INFO @ Sat, 11 Nov 2017 03:34:53: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:34:53: #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 03:34:53: #1 tags after filtering in treatment: 33670579 INFO @ Sat, 11 Nov 2017 03:34:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:34:53: #1 finished! INFO @ Sat, 11 Nov 2017 03:34:53: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:34:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:34:54: #1 tags after filtering in treatment: 33670579 INFO @ Sat, 11 Nov 2017 03:34:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:34:54: #1 finished! INFO @ Sat, 11 Nov 2017 03:34:54: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:34:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:34:54: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:34:54: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:34:54: #1 total tags in treatment: 33670669 INFO @ Sat, 11 Nov 2017 03:34:54: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:34:54: #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 03:34:55: #1 tags after filtering in treatment: 33670579 INFO @ Sat, 11 Nov 2017 03:34:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:34:55: #1 finished! INFO @ Sat, 11 Nov 2017 03:34:55: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:34:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:34:59: #2 number of paired peaks: 70951 INFO @ Sat, 11 Nov 2017 03:34:59: start model_add_line... INFO @ Sat, 11 Nov 2017 03:34:59: #2 number of paired peaks: 70951 INFO @ Sat, 11 Nov 2017 03:34:59: start model_add_line... INFO @ Sat, 11 Nov 2017 03:35:00: start X-correlation... INFO @ Sat, 11 Nov 2017 03:35:00: end of X-cor INFO @ Sat, 11 Nov 2017 03:35:00: #2 finished! INFO @ Sat, 11 Nov 2017 03:35:00: #2 predicted fragment length is 193 bps INFO @ Sat, 11 Nov 2017 03:35:00: #2 alternative fragment length(s) may be 193 bps INFO @ Sat, 11 Nov 2017 03:35:00: #2.2 Generate R script for model : SRX1977139.05_model.r INFO @ Sat, 11 Nov 2017 03:35:00: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:35:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:35:00: start X-correlation... INFO @ Sat, 11 Nov 2017 03:35:00: end of X-cor INFO @ Sat, 11 Nov 2017 03:35:00: #2 finished! INFO @ Sat, 11 Nov 2017 03:35:00: #2 predicted fragment length is 193 bps INFO @ Sat, 11 Nov 2017 03:35:00: #2 alternative fragment length(s) may be 193 bps INFO @ Sat, 11 Nov 2017 03:35:00: #2.2 Generate R script for model : SRX1977139.10_model.r INFO @ Sat, 11 Nov 2017 03:35:00: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:35:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:35:01: #2 number of paired peaks: 70951 INFO @ Sat, 11 Nov 2017 03:35:01: start model_add_line... INFO @ Sat, 11 Nov 2017 03:35:02: start X-correlation... INFO @ Sat, 11 Nov 2017 03:35:02: end of X-cor INFO @ Sat, 11 Nov 2017 03:35:02: #2 finished! INFO @ Sat, 11 Nov 2017 03:35:02: #2 predicted fragment length is 193 bps INFO @ Sat, 11 Nov 2017 03:35:02: #2 alternative fragment length(s) may be 193 bps INFO @ Sat, 11 Nov 2017 03:35:02: #2.2 Generate R script for model : SRX1977139.20_model.r INFO @ Sat, 11 Nov 2017 03:35:02: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:35:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:36:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:36:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:36:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:37:14: #4 Write output xls file... SRX1977139.10_peaks.xls INFO @ Sat, 11 Nov 2017 03:37:14: #4 Write peak in narrowPeak format file... SRX1977139.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:37:15: #4 Write summits bed file... SRX1977139.10_summits.bed INFO @ Sat, 11 Nov 2017 03:37:15: Done! pass1 - making usageList (178 chroms): 6 millis pass2 - checking and writing primary data (30534 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:37:18: #4 Write output xls file... SRX1977139.20_peaks.xls INFO @ Sat, 11 Nov 2017 03:37:18: #4 Write peak in narrowPeak format file... SRX1977139.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:37:18: #4 Write output xls file... SRX1977139.05_peaks.xls INFO @ Sat, 11 Nov 2017 03:37:18: #4 Write summits bed file... SRX1977139.20_summits.bed INFO @ Sat, 11 Nov 2017 03:37:18: Done! pass1 - making usageList (96 chroms): 2 millis pass2 - checking and writing primary data (7021 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:37:19: #4 Write peak in narrowPeak format file... SRX1977139.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:37:19: #4 Write summits bed file... SRX1977139.05_summits.bed INFO @ Sat, 11 Nov 2017 03:37:20: Done! pass1 - making usageList (267 chroms): 14 millis pass2 - checking and writing primary data (72776 records, 4 fields): 91 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。