Job ID = 10194844 sra ファイルのダウンロード中... Completed: 1469805K bytes transferred in 33 seconds (362794K 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 73639336 spots for /home/okishinya/chipatlas/results/rn6/SRX1977133/SRR3952265.sra Written 73639336 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 02:08:52 73639336 reads; of these: 73639336 (100.00%) were unpaired; of these: 13565832 (18.42%) aligned 0 times 31274371 (42.47%) aligned exactly 1 time 28799133 (39.11%) aligned >1 times 81.58% overall alignment rate Time searching: 02:08:55 Overall time: 02:08:55 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 28 files... [bam_rmdupse_core] 6396914 / 60073504 = 0.1065 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 04:15:29: # Command line: callpeak -t SRX1977133.bam -f BAM -g 2.15e9 -n SRX1977133.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977133.20 # format = BAM # ChIP-seq file = ['SRX1977133.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 04:15:29: #1 read tag files... INFO @ Sat, 11 Nov 2017 04:15:29: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 04:15:29: # Command line: callpeak -t SRX1977133.bam -f BAM -g 2.15e9 -n SRX1977133.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977133.05 # format = BAM # ChIP-seq file = ['SRX1977133.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 04:15:29: #1 read tag files... INFO @ Sat, 11 Nov 2017 04:15:29: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 04:15:29: # Command line: callpeak -t SRX1977133.bam -f BAM -g 2.15e9 -n SRX1977133.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977133.10 # format = BAM # ChIP-seq file = ['SRX1977133.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 04:15:29: #1 read tag files... INFO @ Sat, 11 Nov 2017 04:15:29: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 04:15:35: 1000000 INFO @ Sat, 11 Nov 2017 04:15:36: 1000000 INFO @ Sat, 11 Nov 2017 04:15:36: 1000000 INFO @ Sat, 11 Nov 2017 04:15:42: 2000000 INFO @ Sat, 11 Nov 2017 04:15:42: 2000000 INFO @ Sat, 11 Nov 2017 04:15:43: 2000000 INFO @ Sat, 11 Nov 2017 04:15:48: 3000000 INFO @ Sat, 11 Nov 2017 04:15:49: 3000000 INFO @ Sat, 11 Nov 2017 04:15:49: 3000000 INFO @ Sat, 11 Nov 2017 04:15:54: 4000000 INFO @ Sat, 11 Nov 2017 04:15:55: 4000000 INFO @ Sat, 11 Nov 2017 04:15:56: 4000000 INFO @ Sat, 11 Nov 2017 04:16:01: 5000000 INFO @ Sat, 11 Nov 2017 04:16:02: 5000000 INFO @ Sat, 11 Nov 2017 04:16:03: 5000000 INFO @ Sat, 11 Nov 2017 04:16:07: 6000000 INFO @ Sat, 11 Nov 2017 04:16:09: 6000000 INFO @ Sat, 11 Nov 2017 04:16:10: 6000000 INFO @ Sat, 11 Nov 2017 04:16:13: 7000000 INFO @ Sat, 11 Nov 2017 04:16:16: 7000000 INFO @ Sat, 11 Nov 2017 04:16:17: 7000000 INFO @ Sat, 11 Nov 2017 04:16:20: 8000000 INFO @ Sat, 11 Nov 2017 04:16:23: 8000000 INFO @ Sat, 11 Nov 2017 04:16:24: 8000000 INFO @ Sat, 11 Nov 2017 04:16:26: 9000000 INFO @ Sat, 11 Nov 2017 04:16:30: 9000000 INFO @ Sat, 11 Nov 2017 04:16:32: 9000000 INFO @ Sat, 11 Nov 2017 04:16:32: 10000000 INFO @ Sat, 11 Nov 2017 04:16:37: 10000000 INFO @ Sat, 11 Nov 2017 04:16:38: 11000000 INFO @ Sat, 11 Nov 2017 04:16:38: 10000000 INFO @ Sat, 11 Nov 2017 04:16:44: 11000000 INFO @ Sat, 11 Nov 2017 04:16:44: 12000000 INFO @ Sat, 11 Nov 2017 04:16:45: 11000000 INFO @ Sat, 11 Nov 2017 04:16:51: 13000000 INFO @ Sat, 11 Nov 2017 04:16:51: 12000000 INFO @ Sat, 11 Nov 2017 04:16:52: 12000000 INFO @ Sat, 11 Nov 2017 04:16:57: 14000000 INFO @ Sat, 11 Nov 2017 04:16:58: 13000000 INFO @ Sat, 11 Nov 2017 04:16:59: 13000000 INFO @ Sat, 11 Nov 2017 04:17:03: 15000000 INFO @ Sat, 11 Nov 2017 04:17:05: 14000000 INFO @ Sat, 11 Nov 2017 04:17:06: 14000000 INFO @ Sat, 11 Nov 2017 04:17:09: 16000000 INFO @ Sat, 11 Nov 2017 04:17:12: 15000000 INFO @ Sat, 11 Nov 2017 04:17:13: 15000000 INFO @ Sat, 11 Nov 2017 04:17:16: 17000000 INFO @ Sat, 11 Nov 2017 04:17:19: 16000000 INFO @ Sat, 11 Nov 2017 04:17:20: 16000000 INFO @ Sat, 11 Nov 2017 04:17:22: 18000000 INFO @ Sat, 11 Nov 2017 04:17:26: 17000000 INFO @ Sat, 11 Nov 2017 04:17:27: 17000000 INFO @ Sat, 11 Nov 2017 04:17:28: 19000000 INFO @ Sat, 11 Nov 2017 04:17:33: 18000000 INFO @ Sat, 11 Nov 2017 04:17:34: 18000000 INFO @ Sat, 11 Nov 2017 04:17:34: 20000000 INFO @ Sat, 11 Nov 2017 04:17:39: 19000000 INFO @ Sat, 11 Nov 2017 04:17:41: 19000000 INFO @ Sat, 11 Nov 2017 04:17:41: 21000000 INFO @ Sat, 11 Nov 2017 04:17:46: 20000000 INFO @ Sat, 11 Nov 2017 04:17:48: 20000000 INFO @ Sat, 11 Nov 2017 04:17:48: 22000000 INFO @ Sat, 11 Nov 2017 04:17:52: 21000000 INFO @ Sat, 11 Nov 2017 04:17:54: 23000000 INFO @ Sat, 11 Nov 2017 04:17:54: 21000000 INFO @ Sat, 11 Nov 2017 04:17:58: 22000000 INFO @ Sat, 11 Nov 2017 04:18:01: 24000000 INFO @ Sat, 11 Nov 2017 04:18:01: 22000000 INFO @ Sat, 11 Nov 2017 04:18:05: 23000000 INFO @ Sat, 11 Nov 2017 04:18:07: 25000000 INFO @ Sat, 11 Nov 2017 04:18:08: 23000000 INFO @ Sat, 11 Nov 2017 04:18:11: 24000000 INFO @ Sat, 11 Nov 2017 04:18:14: 26000000 INFO @ Sat, 11 Nov 2017 04:18:15: 24000000 INFO @ Sat, 11 Nov 2017 04:18:18: 25000000 INFO @ Sat, 11 Nov 2017 04:18:20: 27000000 INFO @ Sat, 11 Nov 2017 04:18:22: 25000000 INFO @ Sat, 11 Nov 2017 04:18:24: 26000000 INFO @ Sat, 11 Nov 2017 04:18:27: 28000000 INFO @ Sat, 11 Nov 2017 04:18:28: 26000000 INFO @ Sat, 11 Nov 2017 04:18:30: 27000000 INFO @ Sat, 11 Nov 2017 04:18:34: 29000000 INFO @ Sat, 11 Nov 2017 04:18:35: 27000000 INFO @ Sat, 11 Nov 2017 04:18:37: 28000000 INFO @ Sat, 11 Nov 2017 04:18:40: 30000000 INFO @ Sat, 11 Nov 2017 04:18:42: 28000000 INFO @ Sat, 11 Nov 2017 04:18:43: 29000000 INFO @ Sat, 11 Nov 2017 04:18:47: 31000000 INFO @ Sat, 11 Nov 2017 04:18:49: 29000000 INFO @ Sat, 11 Nov 2017 04:18:50: 30000000 INFO @ Sat, 11 Nov 2017 04:18:53: 32000000 INFO @ Sat, 11 Nov 2017 04:18:55: 30000000 INFO @ Sat, 11 Nov 2017 04:18:56: 31000000 INFO @ Sat, 11 Nov 2017 04:19:00: 33000000 INFO @ Sat, 11 Nov 2017 04:19:01: 31000000 INFO @ Sat, 11 Nov 2017 04:19:03: 32000000 INFO @ Sat, 11 Nov 2017 04:19:07: 34000000 INFO @ Sat, 11 Nov 2017 04:19:08: 32000000 INFO @ Sat, 11 Nov 2017 04:19:10: 33000000 INFO @ Sat, 11 Nov 2017 04:19:13: 35000000 INFO @ Sat, 11 Nov 2017 04:19:14: 33000000 INFO @ Sat, 11 Nov 2017 04:19:16: 34000000 INFO @ Sat, 11 Nov 2017 04:19:20: 36000000 INFO @ Sat, 11 Nov 2017 04:19:20: 34000000 INFO @ Sat, 11 Nov 2017 04:19:23: 35000000 INFO @ Sat, 11 Nov 2017 04:19:27: 37000000 INFO @ Sat, 11 Nov 2017 04:19:27: 35000000 INFO @ Sat, 11 Nov 2017 04:19:29: 36000000 INFO @ Sat, 11 Nov 2017 04:19:33: 36000000 INFO @ Sat, 11 Nov 2017 04:19:33: 38000000 INFO @ Sat, 11 Nov 2017 04:19:36: 37000000 INFO @ Sat, 11 Nov 2017 04:19:40: 37000000 INFO @ Sat, 11 Nov 2017 04:19:40: 39000000 INFO @ Sat, 11 Nov 2017 04:19:43: 38000000 INFO @ Sat, 11 Nov 2017 04:19:46: 38000000 INFO @ Sat, 11 Nov 2017 04:19:47: 40000000 INFO @ Sat, 11 Nov 2017 04:19:49: 39000000 INFO @ Sat, 11 Nov 2017 04:19:53: 39000000 INFO @ Sat, 11 Nov 2017 04:19:53: 41000000 INFO @ Sat, 11 Nov 2017 04:19:55: 40000000 INFO @ Sat, 11 Nov 2017 04:20:00: 40000000 INFO @ Sat, 11 Nov 2017 04:20:00: 42000000 INFO @ Sat, 11 Nov 2017 04:20:02: 41000000 INFO @ Sat, 11 Nov 2017 04:20:07: 41000000 INFO @ Sat, 11 Nov 2017 04:20:07: 43000000 INFO @ Sat, 11 Nov 2017 04:20:08: 42000000 INFO @ Sat, 11 Nov 2017 04:20:13: 44000000 INFO @ Sat, 11 Nov 2017 04:20:14: 42000000 INFO @ Sat, 11 Nov 2017 04:20:14: 43000000 INFO @ Sat, 11 Nov 2017 04:20:20: 45000000 INFO @ Sat, 11 Nov 2017 04:20:20: 43000000 INFO @ Sat, 11 Nov 2017 04:20:21: 44000000 INFO @ Sat, 11 Nov 2017 04:20:26: 46000000 INFO @ Sat, 11 Nov 2017 04:20:27: 45000000 INFO @ Sat, 11 Nov 2017 04:20:27: 44000000 INFO @ Sat, 11 Nov 2017 04:20:33: 47000000 INFO @ Sat, 11 Nov 2017 04:20:33: 46000000 INFO @ Sat, 11 Nov 2017 04:20:34: 45000000 INFO @ Sat, 11 Nov 2017 04:20:39: 48000000 INFO @ Sat, 11 Nov 2017 04:20:40: 47000000 INFO @ Sat, 11 Nov 2017 04:20:41: 46000000 INFO @ Sat, 11 Nov 2017 04:20:46: 49000000 INFO @ Sat, 11 Nov 2017 04:20:46: 48000000 INFO @ Sat, 11 Nov 2017 04:20:48: 47000000 INFO @ Sat, 11 Nov 2017 04:20:52: 50000000 INFO @ Sat, 11 Nov 2017 04:20:53: 49000000 INFO @ Sat, 11 Nov 2017 04:20:54: 48000000 INFO @ Sat, 11 Nov 2017 04:20:59: 51000000 INFO @ Sat, 11 Nov 2017 04:20:59: 50000000 INFO @ Sat, 11 Nov 2017 04:21:01: 49000000 INFO @ Sat, 11 Nov 2017 04:21:05: 52000000 INFO @ Sat, 11 Nov 2017 04:21:06: 51000000 INFO @ Sat, 11 Nov 2017 04:21:08: 50000000 INFO @ Sat, 11 Nov 2017 04:21:12: 53000000 INFO @ Sat, 11 Nov 2017 04:21:12: 52000000 INFO @ Sat, 11 Nov 2017 04:21:14: 51000000 INFO @ Sat, 11 Nov 2017 04:21:16: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 04:21:16: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 04:21:16: #1 total tags in treatment: 53676590 INFO @ Sat, 11 Nov 2017 04:21:16: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 04:21:16: #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 04:21:18: #1 tags after filtering in treatment: 53676544 INFO @ Sat, 11 Nov 2017 04:21:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 04:21:18: #1 finished! INFO @ Sat, 11 Nov 2017 04:21:18: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 04:21:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 04:21:18: 53000000 INFO @ Sat, 11 Nov 2017 04:21:21: 52000000 INFO @ Sat, 11 Nov 2017 04:21:23: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 04:21:23: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 04:21:23: #1 total tags in treatment: 53676590 INFO @ Sat, 11 Nov 2017 04:21:23: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 04:21:23: #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 04:21:24: #2 number of paired peaks: 18293 INFO @ Sat, 11 Nov 2017 04:21:24: start model_add_line... INFO @ Sat, 11 Nov 2017 04:21:24: #1 tags after filtering in treatment: 53676544 INFO @ Sat, 11 Nov 2017 04:21:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 04:21:24: #1 finished! INFO @ Sat, 11 Nov 2017 04:21:24: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 04:21:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 04:21:25: start X-correlation... INFO @ Sat, 11 Nov 2017 04:21:25: end of X-cor INFO @ Sat, 11 Nov 2017 04:21:25: #2 finished! INFO @ Sat, 11 Nov 2017 04:21:25: #2 predicted fragment length is 59 bps INFO @ Sat, 11 Nov 2017 04:21:25: #2 alternative fragment length(s) may be 59 bps INFO @ Sat, 11 Nov 2017 04:21:25: #2.2 Generate R script for model : SRX1977133.05_model.r WARNING @ Sat, 11 Nov 2017 04:21:25: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 04:21:25: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sat, 11 Nov 2017 04:21:25: #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 04:21:25: #3 Call peaks... INFO @ Sat, 11 Nov 2017 04:21:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 04:21:27: 53000000 INFO @ Sat, 11 Nov 2017 04:21:30: #2 number of paired peaks: 18293 INFO @ Sat, 11 Nov 2017 04:21:30: start model_add_line... INFO @ Sat, 11 Nov 2017 04:21:31: start X-correlation... INFO @ Sat, 11 Nov 2017 04:21:31: end of X-cor INFO @ Sat, 11 Nov 2017 04:21:31: #2 finished! INFO @ Sat, 11 Nov 2017 04:21:31: #2 predicted fragment length is 59 bps INFO @ Sat, 11 Nov 2017 04:21:31: #2 alternative fragment length(s) may be 59 bps INFO @ Sat, 11 Nov 2017 04:21:31: #2.2 Generate R script for model : SRX1977133.20_model.r WARNING @ Sat, 11 Nov 2017 04:21:31: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 04:21:31: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sat, 11 Nov 2017 04:21:31: #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 04:21:31: #3 Call peaks... INFO @ Sat, 11 Nov 2017 04:21:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 04:21:32: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 04:21:32: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 04:21:32: #1 total tags in treatment: 53676590 INFO @ Sat, 11 Nov 2017 04:21:32: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 04:21:32: #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 04:21:33: #1 tags after filtering in treatment: 53676544 INFO @ Sat, 11 Nov 2017 04:21:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 04:21:33: #1 finished! INFO @ Sat, 11 Nov 2017 04:21:33: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 04:21:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 04:21:40: #2 number of paired peaks: 18293 INFO @ Sat, 11 Nov 2017 04:21:40: start model_add_line... INFO @ Sat, 11 Nov 2017 04:21:40: start X-correlation... INFO @ Sat, 11 Nov 2017 04:21:40: end of X-cor INFO @ Sat, 11 Nov 2017 04:21:40: #2 finished! INFO @ Sat, 11 Nov 2017 04:21:40: #2 predicted fragment length is 59 bps INFO @ Sat, 11 Nov 2017 04:21:40: #2 alternative fragment length(s) may be 59 bps INFO @ Sat, 11 Nov 2017 04:21:40: #2.2 Generate R script for model : SRX1977133.10_model.r WARNING @ Sat, 11 Nov 2017 04:21:40: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 04:21:40: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sat, 11 Nov 2017 04:21:40: #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 04:21:40: #3 Call peaks... INFO @ Sat, 11 Nov 2017 04:21:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 04:23:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 04:23:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 04:23:56: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 04:24:49: #4 Write output xls file... SRX1977133.05_peaks.xls INFO @ Sat, 11 Nov 2017 04:24:50: #4 Write peak in narrowPeak format file... SRX1977133.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 04:24:50: #4 Write summits bed file... SRX1977133.05_summits.bed INFO @ Sat, 11 Nov 2017 04:24:50: Done! pass1 - making usageList (197 chroms): 7 millis pass2 - checking and writing primary data (36324 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 04:24:59: #4 Write output xls file... SRX1977133.20_peaks.xls INFO @ Sat, 11 Nov 2017 04:24:59: #4 Write peak in narrowPeak format file... SRX1977133.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 04:24:59: #4 Write summits bed file... SRX1977133.20_summits.bed INFO @ Sat, 11 Nov 2017 04:24:59: Done! pass1 - making usageList (71 chroms): 1 millis pass2 - checking and writing primary data (1848 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 04:25:07: #4 Write output xls file... SRX1977133.10_peaks.xls INFO @ Sat, 11 Nov 2017 04:25:07: #4 Write peak in narrowPeak format file... SRX1977133.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 04:25:07: #4 Write summits bed file... SRX1977133.10_summits.bed INFO @ Sat, 11 Nov 2017 04:25:07: Done! pass1 - making usageList (104 chroms): 2 millis pass2 - checking and writing primary data (7820 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。