Job ID = 10194905 sra ファイルのダウンロード中... Completed: 276929K bytes transferred in 24 seconds (93507K bits/sec), in 1 file. Completed: 270513K bytes transferred in 23 seconds (93137K bits/sec), in 1 file. Completed: 453470K bytes transferred in 28 seconds (131049K bits/sec), in 1 file. Completed: 444933K bytes transferred in 28 seconds (127911K bits/sec), in 1 file. Completed: 448563K bytes transferred in 31 seconds (115112K bits/sec), in 1 file. Completed: 441524K bytes transferred in 25 seconds (139923K 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 6410544 spots for /home/okishinya/chipatlas/results/rn6/SRX2202900/SRR4319945.sra Written 6410544 spots total Written 6594434 spots for /home/okishinya/chipatlas/results/rn6/SRX2202900/SRR4319944.sra Written 6594434 spots total Written 9804196 spots for /home/okishinya/chipatlas/results/rn6/SRX2202900/SRR4319949.sra Written 9804196 spots total Written 9799757 spots for /home/okishinya/chipatlas/results/rn6/SRX2202900/SRR4319947.sra Written 9799757 spots total Written 9944165 spots for /home/okishinya/chipatlas/results/rn6/SRX2202900/SRR4319948.sra Written 9944165 spots total Written 10056276 spots for /home/okishinya/chipatlas/results/rn6/SRX2202900/SRR4319946.sra Written 10056276 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:46:30 52609372 reads; of these: 52609372 (100.00%) were unpaired; of these: 1526597 (2.90%) aligned 0 times 35002075 (66.53%) aligned exactly 1 time 16080700 (30.57%) aligned >1 times 97.10% overall alignment rate Time searching: 01:46:33 Overall time: 01:46:33 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 24 files... [bam_rmdupse_core] 6875202 / 51082775 = 0.1346 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 00:08:33: # Command line: callpeak -t SRX2202900.bam -f BAM -g 2.15e9 -n SRX2202900.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202900.20 # format = BAM # ChIP-seq file = ['SRX2202900.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 00:08:33: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:08:33: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:08:33: # Command line: callpeak -t SRX2202900.bam -f BAM -g 2.15e9 -n SRX2202900.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202900.10 # format = BAM # ChIP-seq file = ['SRX2202900.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 00:08:33: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:08:33: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:08:33: # Command line: callpeak -t SRX2202900.bam -f BAM -g 2.15e9 -n SRX2202900.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202900.05 # format = BAM # ChIP-seq file = ['SRX2202900.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 00:08:33: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:08:33: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:08:46: 1000000 INFO @ Sat, 11 Nov 2017 00:08:46: 1000000 INFO @ Sat, 11 Nov 2017 00:08:48: 1000000 INFO @ Sat, 11 Nov 2017 00:08:59: 2000000 INFO @ Sat, 11 Nov 2017 00:09:00: 2000000 INFO @ Sat, 11 Nov 2017 00:09:03: 2000000 INFO @ Sat, 11 Nov 2017 00:09:12: 3000000 INFO @ Sat, 11 Nov 2017 00:09:14: 3000000 INFO @ Sat, 11 Nov 2017 00:09:17: 3000000 INFO @ Sat, 11 Nov 2017 00:09:25: 4000000 INFO @ Sat, 11 Nov 2017 00:09:27: 4000000 INFO @ Sat, 11 Nov 2017 00:09:31: 4000000 INFO @ Sat, 11 Nov 2017 00:09:38: 5000000 INFO @ Sat, 11 Nov 2017 00:09:40: 5000000 INFO @ Sat, 11 Nov 2017 00:09:44: 5000000 INFO @ Sat, 11 Nov 2017 00:09:52: 6000000 INFO @ Sat, 11 Nov 2017 00:09:53: 6000000 INFO @ Sat, 11 Nov 2017 00:09:57: 6000000 INFO @ Sat, 11 Nov 2017 00:10:05: 7000000 INFO @ Sat, 11 Nov 2017 00:10:06: 7000000 INFO @ Sat, 11 Nov 2017 00:10:10: 7000000 INFO @ Sat, 11 Nov 2017 00:10:17: 8000000 INFO @ Sat, 11 Nov 2017 00:10:18: 8000000 INFO @ Sat, 11 Nov 2017 00:10:24: 8000000 INFO @ Sat, 11 Nov 2017 00:10:30: 9000000 INFO @ Sat, 11 Nov 2017 00:10:31: 9000000 INFO @ Sat, 11 Nov 2017 00:10:37: 9000000 INFO @ Sat, 11 Nov 2017 00:10:42: 10000000 INFO @ Sat, 11 Nov 2017 00:10:45: 10000000 INFO @ Sat, 11 Nov 2017 00:10:50: 10000000 INFO @ Sat, 11 Nov 2017 00:10:55: 11000000 INFO @ Sat, 11 Nov 2017 00:10:58: 11000000 INFO @ Sat, 11 Nov 2017 00:11:02: 11000000 INFO @ Sat, 11 Nov 2017 00:11:07: 12000000 INFO @ Sat, 11 Nov 2017 00:11:11: 12000000 INFO @ Sat, 11 Nov 2017 00:11:14: 12000000 INFO @ Sat, 11 Nov 2017 00:11:19: 13000000 INFO @ Sat, 11 Nov 2017 00:11:24: 13000000 INFO @ Sat, 11 Nov 2017 00:11:26: 13000000 INFO @ Sat, 11 Nov 2017 00:11:31: 14000000 INFO @ Sat, 11 Nov 2017 00:11:37: 14000000 INFO @ Sat, 11 Nov 2017 00:11:37: 14000000 INFO @ Sat, 11 Nov 2017 00:11:43: 15000000 INFO @ Sat, 11 Nov 2017 00:11:48: 15000000 INFO @ Sat, 11 Nov 2017 00:11:50: 15000000 INFO @ Sat, 11 Nov 2017 00:11:56: 16000000 INFO @ Sat, 11 Nov 2017 00:12:01: 16000000 INFO @ Sat, 11 Nov 2017 00:12:04: 16000000 INFO @ Sat, 11 Nov 2017 00:12:08: 17000000 INFO @ Sat, 11 Nov 2017 00:12:12: 17000000 INFO @ Sat, 11 Nov 2017 00:12:19: 17000000 INFO @ Sat, 11 Nov 2017 00:12:20: 18000000 INFO @ Sat, 11 Nov 2017 00:12:24: 18000000 INFO @ Sat, 11 Nov 2017 00:12:33: 19000000 INFO @ Sat, 11 Nov 2017 00:12:33: 18000000 INFO @ Sat, 11 Nov 2017 00:12:37: 19000000 INFO @ Sat, 11 Nov 2017 00:12:47: 20000000 INFO @ Sat, 11 Nov 2017 00:12:49: 19000000 INFO @ Sat, 11 Nov 2017 00:12:50: 20000000 INFO @ Sat, 11 Nov 2017 00:12:59: 21000000 INFO @ Sat, 11 Nov 2017 00:13:02: 21000000 INFO @ Sat, 11 Nov 2017 00:13:03: 20000000 INFO @ Sat, 11 Nov 2017 00:13:11: 22000000 INFO @ Sat, 11 Nov 2017 00:13:15: 22000000 INFO @ Sat, 11 Nov 2017 00:13:18: 21000000 INFO @ Sat, 11 Nov 2017 00:13:24: 23000000 INFO @ Sat, 11 Nov 2017 00:13:27: 23000000 INFO @ Sat, 11 Nov 2017 00:13:33: 22000000 INFO @ Sat, 11 Nov 2017 00:13:36: 24000000 INFO @ Sat, 11 Nov 2017 00:13:40: 24000000 INFO @ Sat, 11 Nov 2017 00:13:46: 25000000 INFO @ Sat, 11 Nov 2017 00:13:47: 23000000 INFO @ Sat, 11 Nov 2017 00:13:49: 25000000 INFO @ Sat, 11 Nov 2017 00:13:55: 26000000 INFO @ Sat, 11 Nov 2017 00:13:58: 26000000 INFO @ Sat, 11 Nov 2017 00:14:01: 24000000 INFO @ Sat, 11 Nov 2017 00:14:04: 27000000 INFO @ Sat, 11 Nov 2017 00:14:06: 27000000 INFO @ Sat, 11 Nov 2017 00:14:12: 28000000 INFO @ Sat, 11 Nov 2017 00:14:14: 28000000 INFO @ Sat, 11 Nov 2017 00:14:14: 25000000 INFO @ Sat, 11 Nov 2017 00:14:21: 29000000 INFO @ Sat, 11 Nov 2017 00:14:23: 29000000 INFO @ Sat, 11 Nov 2017 00:14:28: 26000000 INFO @ Sat, 11 Nov 2017 00:14:30: 30000000 INFO @ Sat, 11 Nov 2017 00:14:31: 30000000 INFO @ Sat, 11 Nov 2017 00:14:38: 31000000 INFO @ Sat, 11 Nov 2017 00:14:39: 31000000 INFO @ Sat, 11 Nov 2017 00:14:42: 27000000 INFO @ Sat, 11 Nov 2017 00:14:47: 32000000 INFO @ Sat, 11 Nov 2017 00:14:48: 32000000 INFO @ Sat, 11 Nov 2017 00:14:56: 33000000 INFO @ Sat, 11 Nov 2017 00:14:56: 33000000 INFO @ Sat, 11 Nov 2017 00:14:56: 28000000 INFO @ Sat, 11 Nov 2017 00:15:04: 34000000 INFO @ Sat, 11 Nov 2017 00:15:04: 34000000 INFO @ Sat, 11 Nov 2017 00:15:11: 29000000 INFO @ Sat, 11 Nov 2017 00:15:13: 35000000 INFO @ Sat, 11 Nov 2017 00:15:13: 35000000 INFO @ Sat, 11 Nov 2017 00:15:21: 36000000 INFO @ Sat, 11 Nov 2017 00:15:22: 36000000 INFO @ Sat, 11 Nov 2017 00:15:25: 30000000 INFO @ Sat, 11 Nov 2017 00:15:30: 37000000 INFO @ Sat, 11 Nov 2017 00:15:31: 37000000 INFO @ Sat, 11 Nov 2017 00:15:38: 38000000 INFO @ Sat, 11 Nov 2017 00:15:38: 31000000 INFO @ Sat, 11 Nov 2017 00:15:39: 38000000 INFO @ Sat, 11 Nov 2017 00:15:47: 39000000 INFO @ Sat, 11 Nov 2017 00:15:49: 39000000 INFO @ Sat, 11 Nov 2017 00:15:53: 32000000 INFO @ Sat, 11 Nov 2017 00:15:56: 40000000 INFO @ Sat, 11 Nov 2017 00:15:57: 40000000 INFO @ Sat, 11 Nov 2017 00:16:04: 41000000 INFO @ Sat, 11 Nov 2017 00:16:06: 41000000 INFO @ Sat, 11 Nov 2017 00:16:07: 33000000 INFO @ Sat, 11 Nov 2017 00:16:13: 42000000 INFO @ Sat, 11 Nov 2017 00:16:16: 42000000 INFO @ Sat, 11 Nov 2017 00:16:22: 43000000 INFO @ Sat, 11 Nov 2017 00:16:22: 34000000 INFO @ Sat, 11 Nov 2017 00:16:27: 43000000 INFO @ Sat, 11 Nov 2017 00:16:30: 44000000 INFO @ Sat, 11 Nov 2017 00:16:33: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:16:33: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:16:33: #1 total tags in treatment: 44207573 INFO @ Sat, 11 Nov 2017 00:16:33: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:16:33: #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 00:16:34: #1 tags after filtering in treatment: 44207522 INFO @ Sat, 11 Nov 2017 00:16:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:16:34: #1 finished! INFO @ Sat, 11 Nov 2017 00:16:34: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:16:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:16:36: 35000000 INFO @ Sat, 11 Nov 2017 00:16:37: 44000000 INFO @ Sat, 11 Nov 2017 00:16:40: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:16:40: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:16:40: #1 total tags in treatment: 44207573 INFO @ Sat, 11 Nov 2017 00:16:40: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:16:40: #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 00:16:40: #2 number of paired peaks: 15720 INFO @ Sat, 11 Nov 2017 00:16:40: start model_add_line... INFO @ Sat, 11 Nov 2017 00:16:41: start X-correlation... INFO @ Sat, 11 Nov 2017 00:16:41: end of X-cor INFO @ Sat, 11 Nov 2017 00:16:41: #2 finished! INFO @ Sat, 11 Nov 2017 00:16:41: #2 predicted fragment length is 58 bps INFO @ Sat, 11 Nov 2017 00:16:41: #2 alternative fragment length(s) may be 58 bps INFO @ Sat, 11 Nov 2017 00:16:41: #2.2 Generate R script for model : SRX2202900.10_model.r WARNING @ Sat, 11 Nov 2017 00:16:41: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:16:41: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sat, 11 Nov 2017 00:16:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:16:41: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:16:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:16:41: #1 tags after filtering in treatment: 44207522 INFO @ Sat, 11 Nov 2017 00:16:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:16:41: #1 finished! INFO @ Sat, 11 Nov 2017 00:16:41: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:16:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:16:47: #2 number of paired peaks: 15720 INFO @ Sat, 11 Nov 2017 00:16:47: start model_add_line... INFO @ Sat, 11 Nov 2017 00:16:48: start X-correlation... INFO @ Sat, 11 Nov 2017 00:16:48: end of X-cor INFO @ Sat, 11 Nov 2017 00:16:48: #2 finished! INFO @ Sat, 11 Nov 2017 00:16:48: #2 predicted fragment length is 58 bps INFO @ Sat, 11 Nov 2017 00:16:48: #2 alternative fragment length(s) may be 58 bps INFO @ Sat, 11 Nov 2017 00:16:48: #2.2 Generate R script for model : SRX2202900.05_model.r WARNING @ Sat, 11 Nov 2017 00:16:48: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:16:48: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sat, 11 Nov 2017 00:16:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:16:48: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:16:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:16:51: 36000000 INFO @ Sat, 11 Nov 2017 00:17:06: 37000000 INFO @ Sat, 11 Nov 2017 00:17:19: 38000000 INFO @ Sat, 11 Nov 2017 00:17:32: 39000000 INFO @ Sat, 11 Nov 2017 00:17:45: 40000000 INFO @ Sat, 11 Nov 2017 00:17:58: 41000000 INFO @ Sat, 11 Nov 2017 00:18:14: 42000000 INFO @ Sat, 11 Nov 2017 00:18:30: 43000000 INFO @ Sat, 11 Nov 2017 00:18:45: 44000000 INFO @ Sat, 11 Nov 2017 00:18:50: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:18:50: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:18:50: #1 total tags in treatment: 44207573 INFO @ Sat, 11 Nov 2017 00:18:50: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:18:50: #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 00:18:51: #1 tags after filtering in treatment: 44207522 INFO @ Sat, 11 Nov 2017 00:18:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:18:51: #1 finished! INFO @ Sat, 11 Nov 2017 00:18:51: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:18:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:18:56: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:18:57: #2 number of paired peaks: 15720 INFO @ Sat, 11 Nov 2017 00:18:57: start model_add_line... INFO @ Sat, 11 Nov 2017 00:18:58: start X-correlation... INFO @ Sat, 11 Nov 2017 00:18:58: end of X-cor INFO @ Sat, 11 Nov 2017 00:18:58: #2 finished! INFO @ Sat, 11 Nov 2017 00:18:58: #2 predicted fragment length is 58 bps INFO @ Sat, 11 Nov 2017 00:18:58: #2 alternative fragment length(s) may be 58 bps INFO @ Sat, 11 Nov 2017 00:18:58: #2.2 Generate R script for model : SRX2202900.20_model.r WARNING @ Sat, 11 Nov 2017 00:18:58: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:18:58: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sat, 11 Nov 2017 00:18:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:18:58: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:18:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:19:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:20:16: #4 Write output xls file... SRX2202900.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:20:16: #4 Write peak in narrowPeak format file... SRX2202900.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:20:16: #4 Write summits bed file... SRX2202900.10_summits.bed INFO @ Sat, 11 Nov 2017 00:20:16: Done! pass1 - making usageList (56 chroms): 2 millis pass2 - checking and writing primary data (1753 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:20:27: #4 Write output xls file... SRX2202900.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:20:28: #4 Write peak in narrowPeak format file... SRX2202900.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:20:28: #4 Write summits bed file... SRX2202900.05_summits.bed INFO @ Sat, 11 Nov 2017 00:20:28: Done! pass1 - making usageList (69 chroms): 3 millis pass2 - checking and writing primary data (6900 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:21:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:22:42: #4 Write output xls file... SRX2202900.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:22:42: #4 Write peak in narrowPeak format file... SRX2202900.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:22:42: #4 Write summits bed file... SRX2202900.20_summits.bed INFO @ Sat, 11 Nov 2017 00:22:42: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (776 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。