Job ID = 10194720 sra ファイルのダウンロード中... Completed: 4722221K bytes transferred in 74 seconds (519181K 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 77593626 spots for /home/okishinya/chipatlas/results/rn6/SRX1037555/SRR2039159.sra Written 77593626 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 05:19:12 77593626 reads; of these: 77593626 (100.00%) were unpaired; of these: 1724251 (2.22%) aligned 0 times 51015883 (65.75%) aligned exactly 1 time 24853492 (32.03%) aligned >1 times 97.78% overall alignment rate Time searching: 05:19:15 Overall time: 05:19:15 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 32 files... [bam_rmdupse_core] 25712933 / 75869375 = 0.3389 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 01:04:48: # Command line: callpeak -t SRX1037555.bam -f BAM -g 2.15e9 -n SRX1037555.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1037555.20 # format = BAM # ChIP-seq file = ['SRX1037555.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 01:04:48: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:04:48: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:04:48: # Command line: callpeak -t SRX1037555.bam -f BAM -g 2.15e9 -n SRX1037555.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1037555.10 # format = BAM # ChIP-seq file = ['SRX1037555.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 01:04:48: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:04:48: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:04:48: # Command line: callpeak -t SRX1037555.bam -f BAM -g 2.15e9 -n SRX1037555.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1037555.05 # format = BAM # ChIP-seq file = ['SRX1037555.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 01:04:48: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:04:48: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:05:01: 1000000 INFO @ Sat, 11 Nov 2017 01:05:03: 1000000 INFO @ Sat, 11 Nov 2017 01:05:04: 1000000 INFO @ Sat, 11 Nov 2017 01:05:18: 2000000 INFO @ Sat, 11 Nov 2017 01:05:19: 2000000 INFO @ Sat, 11 Nov 2017 01:05:19: 2000000 INFO @ Sat, 11 Nov 2017 01:05:33: 3000000 INFO @ Sat, 11 Nov 2017 01:05:35: 3000000 INFO @ Sat, 11 Nov 2017 01:05:38: 3000000 INFO @ Sat, 11 Nov 2017 01:05:45: 4000000 INFO @ Sat, 11 Nov 2017 01:05:46: 4000000 INFO @ Sat, 11 Nov 2017 01:05:51: 4000000 INFO @ Sat, 11 Nov 2017 01:05:56: 5000000 INFO @ Sat, 11 Nov 2017 01:05:58: 5000000 INFO @ Sat, 11 Nov 2017 01:06:03: 5000000 INFO @ Sat, 11 Nov 2017 01:06:07: 6000000 INFO @ Sat, 11 Nov 2017 01:06:09: 6000000 INFO @ Sat, 11 Nov 2017 01:06:16: 6000000 INFO @ Sat, 11 Nov 2017 01:06:19: 7000000 INFO @ Sat, 11 Nov 2017 01:06:20: 7000000 INFO @ Sat, 11 Nov 2017 01:06:28: 7000000 INFO @ Sat, 11 Nov 2017 01:06:30: 8000000 INFO @ Sat, 11 Nov 2017 01:06:32: 8000000 INFO @ Sat, 11 Nov 2017 01:06:40: 8000000 INFO @ Sat, 11 Nov 2017 01:06:42: 9000000 INFO @ Sat, 11 Nov 2017 01:06:44: 9000000 INFO @ Sat, 11 Nov 2017 01:06:51: 9000000 INFO @ Sat, 11 Nov 2017 01:06:53: 10000000 INFO @ Sat, 11 Nov 2017 01:06:56: 10000000 INFO @ Sat, 11 Nov 2017 01:07:03: 10000000 INFO @ Sat, 11 Nov 2017 01:07:04: 11000000 INFO @ Sat, 11 Nov 2017 01:07:07: 11000000 INFO @ Sat, 11 Nov 2017 01:07:15: 11000000 INFO @ Sat, 11 Nov 2017 01:07:16: 12000000 INFO @ Sat, 11 Nov 2017 01:07:19: 12000000 INFO @ Sat, 11 Nov 2017 01:07:26: 12000000 INFO @ Sat, 11 Nov 2017 01:07:27: 13000000 INFO @ Sat, 11 Nov 2017 01:07:30: 13000000 INFO @ Sat, 11 Nov 2017 01:07:38: 13000000 INFO @ Sat, 11 Nov 2017 01:07:38: 14000000 INFO @ Sat, 11 Nov 2017 01:07:42: 14000000 INFO @ Sat, 11 Nov 2017 01:07:50: 15000000 INFO @ Sat, 11 Nov 2017 01:07:50: 14000000 INFO @ Sat, 11 Nov 2017 01:07:54: 15000000 INFO @ Sat, 11 Nov 2017 01:08:01: 16000000 INFO @ Sat, 11 Nov 2017 01:08:01: 15000000 INFO @ Sat, 11 Nov 2017 01:08:05: 16000000 INFO @ Sat, 11 Nov 2017 01:08:12: 17000000 INFO @ Sat, 11 Nov 2017 01:08:13: 16000000 INFO @ Sat, 11 Nov 2017 01:08:17: 17000000 INFO @ Sat, 11 Nov 2017 01:08:24: 18000000 INFO @ Sat, 11 Nov 2017 01:08:25: 17000000 INFO @ Sat, 11 Nov 2017 01:08:28: 18000000 INFO @ Sat, 11 Nov 2017 01:08:35: 19000000 INFO @ Sat, 11 Nov 2017 01:08:36: 18000000 INFO @ Sat, 11 Nov 2017 01:08:40: 19000000 INFO @ Sat, 11 Nov 2017 01:08:46: 20000000 INFO @ Sat, 11 Nov 2017 01:08:48: 19000000 INFO @ Sat, 11 Nov 2017 01:08:52: 20000000 INFO @ Sat, 11 Nov 2017 01:08:57: 21000000 INFO @ Sat, 11 Nov 2017 01:09:00: 20000000 INFO @ Sat, 11 Nov 2017 01:09:03: 21000000 INFO @ Sat, 11 Nov 2017 01:09:09: 22000000 INFO @ Sat, 11 Nov 2017 01:09:13: 21000000 INFO @ Sat, 11 Nov 2017 01:09:15: 22000000 INFO @ Sat, 11 Nov 2017 01:09:20: 23000000 INFO @ Sat, 11 Nov 2017 01:09:26: 23000000 INFO @ Sat, 11 Nov 2017 01:09:26: 22000000 INFO @ Sat, 11 Nov 2017 01:09:31: 24000000 INFO @ Sat, 11 Nov 2017 01:09:37: 24000000 INFO @ Sat, 11 Nov 2017 01:09:39: 23000000 INFO @ Sat, 11 Nov 2017 01:09:43: 25000000 INFO @ Sat, 11 Nov 2017 01:09:49: 25000000 INFO @ Sat, 11 Nov 2017 01:09:52: 24000000 INFO @ Sat, 11 Nov 2017 01:09:54: 26000000 INFO @ Sat, 11 Nov 2017 01:10:00: 26000000 INFO @ Sat, 11 Nov 2017 01:10:05: 27000000 INFO @ Sat, 11 Nov 2017 01:10:05: 25000000 INFO @ Sat, 11 Nov 2017 01:10:12: 27000000 INFO @ Sat, 11 Nov 2017 01:10:16: 28000000 INFO @ Sat, 11 Nov 2017 01:10:19: 26000000 INFO @ Sat, 11 Nov 2017 01:10:23: 28000000 INFO @ Sat, 11 Nov 2017 01:10:28: 29000000 INFO @ Sat, 11 Nov 2017 01:10:32: 27000000 INFO @ Sat, 11 Nov 2017 01:10:34: 29000000 INFO @ Sat, 11 Nov 2017 01:10:39: 30000000 INFO @ Sat, 11 Nov 2017 01:10:45: 28000000 INFO @ Sat, 11 Nov 2017 01:10:46: 30000000 INFO @ Sat, 11 Nov 2017 01:10:50: 31000000 INFO @ Sat, 11 Nov 2017 01:10:57: 31000000 INFO @ Sat, 11 Nov 2017 01:10:59: 29000000 INFO @ Sat, 11 Nov 2017 01:11:02: 32000000 INFO @ Sat, 11 Nov 2017 01:11:09: 32000000 INFO @ Sat, 11 Nov 2017 01:11:12: 30000000 INFO @ Sat, 11 Nov 2017 01:11:13: 33000000 INFO @ Sat, 11 Nov 2017 01:11:20: 33000000 INFO @ Sat, 11 Nov 2017 01:11:24: 34000000 INFO @ Sat, 11 Nov 2017 01:11:25: 31000000 INFO @ Sat, 11 Nov 2017 01:11:32: 34000000 INFO @ Sat, 11 Nov 2017 01:11:36: 35000000 INFO @ Sat, 11 Nov 2017 01:11:38: 32000000 INFO @ Sat, 11 Nov 2017 01:11:44: 35000000 INFO @ Sat, 11 Nov 2017 01:11:47: 36000000 INFO @ Sat, 11 Nov 2017 01:11:51: 33000000 INFO @ Sat, 11 Nov 2017 01:11:55: 36000000 INFO @ Sat, 11 Nov 2017 01:11:59: 37000000 INFO @ Sat, 11 Nov 2017 01:12:04: 34000000 INFO @ Sat, 11 Nov 2017 01:12:07: 37000000 INFO @ Sat, 11 Nov 2017 01:12:10: 38000000 INFO @ Sat, 11 Nov 2017 01:12:17: 35000000 INFO @ Sat, 11 Nov 2017 01:12:18: 38000000 INFO @ Sat, 11 Nov 2017 01:12:22: 39000000 INFO @ Sat, 11 Nov 2017 01:12:30: 39000000 INFO @ Sat, 11 Nov 2017 01:12:30: 36000000 INFO @ Sat, 11 Nov 2017 01:12:33: 40000000 INFO @ Sat, 11 Nov 2017 01:12:41: 40000000 INFO @ Sat, 11 Nov 2017 01:12:43: 37000000 INFO @ Sat, 11 Nov 2017 01:12:45: 41000000 INFO @ Sat, 11 Nov 2017 01:12:53: 41000000 INFO @ Sat, 11 Nov 2017 01:12:56: 38000000 INFO @ Sat, 11 Nov 2017 01:12:56: 42000000 INFO @ Sat, 11 Nov 2017 01:13:04: 42000000 INFO @ Sat, 11 Nov 2017 01:13:08: 43000000 INFO @ Sat, 11 Nov 2017 01:13:09: 39000000 INFO @ Sat, 11 Nov 2017 01:13:16: 43000000 INFO @ Sat, 11 Nov 2017 01:13:19: 44000000 INFO @ Sat, 11 Nov 2017 01:13:22: 40000000 INFO @ Sat, 11 Nov 2017 01:13:28: 44000000 INFO @ Sat, 11 Nov 2017 01:13:31: 45000000 INFO @ Sat, 11 Nov 2017 01:13:35: 41000000 INFO @ Sat, 11 Nov 2017 01:13:39: 45000000 INFO @ Sat, 11 Nov 2017 01:13:42: 46000000 INFO @ Sat, 11 Nov 2017 01:13:48: 42000000 INFO @ Sat, 11 Nov 2017 01:13:51: 46000000 INFO @ Sat, 11 Nov 2017 01:13:54: 47000000 INFO @ Sat, 11 Nov 2017 01:14:01: 43000000 INFO @ Sat, 11 Nov 2017 01:14:02: 47000000 INFO @ Sat, 11 Nov 2017 01:14:05: 48000000 INFO @ Sat, 11 Nov 2017 01:14:14: 48000000 INFO @ Sat, 11 Nov 2017 01:14:14: 44000000 INFO @ Sat, 11 Nov 2017 01:14:17: 49000000 INFO @ Sat, 11 Nov 2017 01:14:25: 49000000 INFO @ Sat, 11 Nov 2017 01:14:27: 45000000 INFO @ Sat, 11 Nov 2017 01:14:28: 50000000 INFO @ Sat, 11 Nov 2017 01:14:31: #1 tag size is determined as 100 bps INFO @ Sat, 11 Nov 2017 01:14:31: #1 tag size = 100 INFO @ Sat, 11 Nov 2017 01:14:31: #1 total tags in treatment: 50156442 INFO @ Sat, 11 Nov 2017 01:14:31: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:14:31: #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 01:14:32: #1 tags after filtering in treatment: 50156363 INFO @ Sat, 11 Nov 2017 01:14:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:14:32: #1 finished! INFO @ Sat, 11 Nov 2017 01:14:32: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:14:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:14:37: 50000000 INFO @ Sat, 11 Nov 2017 01:14:39: #2 number of paired peaks: 24928 INFO @ Sat, 11 Nov 2017 01:14:39: start model_add_line... INFO @ Sat, 11 Nov 2017 01:14:39: start X-correlation... INFO @ Sat, 11 Nov 2017 01:14:40: end of X-cor INFO @ Sat, 11 Nov 2017 01:14:40: #2 finished! INFO @ Sat, 11 Nov 2017 01:14:40: #2 predicted fragment length is 103 bps INFO @ Sat, 11 Nov 2017 01:14:40: #2 alternative fragment length(s) may be 103 bps INFO @ Sat, 11 Nov 2017 01:14:40: #2.2 Generate R script for model : SRX1037555.05_model.r WARNING @ Sat, 11 Nov 2017 01:14:40: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:14:40: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Sat, 11 Nov 2017 01:14:40: #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 01:14:40: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:14:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:14:40: #1 tag size is determined as 100 bps INFO @ Sat, 11 Nov 2017 01:14:40: #1 tag size = 100 INFO @ Sat, 11 Nov 2017 01:14:40: #1 total tags in treatment: 50156442 INFO @ Sat, 11 Nov 2017 01:14:40: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:14:40: #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 01:14:40: 46000000 INFO @ Sat, 11 Nov 2017 01:14:42: #1 tags after filtering in treatment: 50156363 INFO @ Sat, 11 Nov 2017 01:14:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:14:42: #1 finished! INFO @ Sat, 11 Nov 2017 01:14:42: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:14:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:14:48: #2 number of paired peaks: 24928 INFO @ Sat, 11 Nov 2017 01:14:48: start model_add_line... INFO @ Sat, 11 Nov 2017 01:14:49: start X-correlation... INFO @ Sat, 11 Nov 2017 01:14:49: end of X-cor INFO @ Sat, 11 Nov 2017 01:14:49: #2 finished! INFO @ Sat, 11 Nov 2017 01:14:49: #2 predicted fragment length is 103 bps INFO @ Sat, 11 Nov 2017 01:14:49: #2 alternative fragment length(s) may be 103 bps INFO @ Sat, 11 Nov 2017 01:14:49: #2.2 Generate R script for model : SRX1037555.10_model.r WARNING @ Sat, 11 Nov 2017 01:14:49: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:14:49: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Sat, 11 Nov 2017 01:14:49: #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 01:14:49: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:14:53: 47000000 INFO @ Sat, 11 Nov 2017 01:15:05: 48000000 INFO @ Sat, 11 Nov 2017 01:15:18: 49000000 INFO @ Sat, 11 Nov 2017 01:15:31: 50000000 INFO @ Sat, 11 Nov 2017 01:15:33: #1 tag size is determined as 100 bps INFO @ Sat, 11 Nov 2017 01:15:33: #1 tag size = 100 INFO @ Sat, 11 Nov 2017 01:15:33: #1 total tags in treatment: 50156442 INFO @ Sat, 11 Nov 2017 01:15:33: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:15:33: #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 01:15:35: #1 tags after filtering in treatment: 50156363 INFO @ Sat, 11 Nov 2017 01:15:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:15:35: #1 finished! INFO @ Sat, 11 Nov 2017 01:15:35: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:15:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:15:41: #2 number of paired peaks: 24928 INFO @ Sat, 11 Nov 2017 01:15:41: start model_add_line... INFO @ Sat, 11 Nov 2017 01:15:42: start X-correlation... INFO @ Sat, 11 Nov 2017 01:15:42: end of X-cor INFO @ Sat, 11 Nov 2017 01:15:42: #2 finished! INFO @ Sat, 11 Nov 2017 01:15:42: #2 predicted fragment length is 103 bps INFO @ Sat, 11 Nov 2017 01:15:42: #2 alternative fragment length(s) may be 103 bps INFO @ Sat, 11 Nov 2017 01:15:42: #2.2 Generate R script for model : SRX1037555.20_model.r WARNING @ Sat, 11 Nov 2017 01:15:42: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:15:42: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Sat, 11 Nov 2017 01:15:42: #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 01:15:42: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:15:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:16:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:17:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:18:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:18:26: #4 Write output xls file... SRX1037555.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:18:26: #4 Write peak in narrowPeak format file... SRX1037555.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:18:26: #4 Write summits bed file... SRX1037555.05_summits.bed INFO @ Sat, 11 Nov 2017 01:18:26: Done! pass1 - making usageList (93 chroms): 9 millis pass2 - checking and writing primary data (12363 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:18:30: #4 Write output xls file... SRX1037555.10_peaks.xls INFO @ Sat, 11 Nov 2017 01:18:30: #4 Write peak in narrowPeak format file... SRX1037555.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:18:30: #4 Write summits bed file... SRX1037555.10_summits.bed INFO @ Sat, 11 Nov 2017 01:18:30: Done! pass1 - making usageList (59 chroms): 3 millis pass2 - checking and writing primary data (2088 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:19:24: #4 Write output xls file... SRX1037555.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:19:24: #4 Write peak in narrowPeak format file... SRX1037555.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:19:24: #4 Write summits bed file... SRX1037555.20_summits.bed INFO @ Sat, 11 Nov 2017 01:19:24: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (742 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。