Job ID = 10453669 sra ファイルのダウンロード中... Completed: 808034K bytes transferred in 23 seconds (275985K 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 47291986 spots for /home/okishinya/chipatlas/results/rn6/SRX3478274/SRR6384653.sra Written 47291986 spots total rm: cannot remove `[DSE]RX*': No such file or directory rm: cannot remove `[DSE]RR*.fastq': No such file or directory 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: 00:00:02 Multiseed full-index search: 01:28:44 47291986 reads; of these: 47291986 (100.00%) were unpaired; of these: 1094361 (2.31%) aligned 0 times 31792677 (67.23%) aligned exactly 1 time 14404948 (30.46%) aligned >1 times 97.69% overall alignment rate Time searching: 01:28:48 Overall time: 01:28:48 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] 1339604 / 46197625 = 0.0290 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 @ Thu, 08 Feb 2018 18:46:10: # Command line: callpeak -t SRX3478274.bam -f BAM -g 2.15e9 -n SRX3478274.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3478274.10 # format = BAM # ChIP-seq file = ['SRX3478274.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 @ Thu, 08 Feb 2018 18:46:10: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:46:10: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:46:10: # Command line: callpeak -t SRX3478274.bam -f BAM -g 2.15e9 -n SRX3478274.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3478274.20 # format = BAM # ChIP-seq file = ['SRX3478274.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 @ Thu, 08 Feb 2018 18:46:10: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:46:10: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:46:10: # Command line: callpeak -t SRX3478274.bam -f BAM -g 2.15e9 -n SRX3478274.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3478274.05 # format = BAM # ChIP-seq file = ['SRX3478274.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 @ Thu, 08 Feb 2018 18:46:10: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:46:10: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:46:18: 1000000 INFO @ Thu, 08 Feb 2018 18:46:23: 1000000 INFO @ Thu, 08 Feb 2018 18:46:25: 1000000 INFO @ Thu, 08 Feb 2018 18:46:26: 2000000 INFO @ Thu, 08 Feb 2018 18:46:33: 3000000 INFO @ Thu, 08 Feb 2018 18:46:36: 2000000 INFO @ Thu, 08 Feb 2018 18:46:38: 2000000 INFO @ Thu, 08 Feb 2018 18:46:41: 4000000 INFO @ Thu, 08 Feb 2018 18:46:49: 5000000 INFO @ Thu, 08 Feb 2018 18:46:50: 3000000 INFO @ Thu, 08 Feb 2018 18:46:50: 3000000 INFO @ Thu, 08 Feb 2018 18:46:57: 6000000 INFO @ Thu, 08 Feb 2018 18:47:02: 4000000 INFO @ Thu, 08 Feb 2018 18:47:03: 4000000 INFO @ Thu, 08 Feb 2018 18:47:05: 7000000 INFO @ Thu, 08 Feb 2018 18:47:12: 8000000 INFO @ Thu, 08 Feb 2018 18:47:15: 5000000 INFO @ Thu, 08 Feb 2018 18:47:15: 5000000 INFO @ Thu, 08 Feb 2018 18:47:20: 9000000 INFO @ Thu, 08 Feb 2018 18:47:27: 6000000 INFO @ Thu, 08 Feb 2018 18:47:28: 6000000 INFO @ Thu, 08 Feb 2018 18:47:28: 10000000 INFO @ Thu, 08 Feb 2018 18:47:36: 11000000 INFO @ Thu, 08 Feb 2018 18:47:40: 7000000 INFO @ Thu, 08 Feb 2018 18:47:40: 7000000 INFO @ Thu, 08 Feb 2018 18:47:44: 12000000 INFO @ Thu, 08 Feb 2018 18:47:52: 8000000 INFO @ Thu, 08 Feb 2018 18:47:52: 13000000 INFO @ Thu, 08 Feb 2018 18:47:53: 8000000 INFO @ Thu, 08 Feb 2018 18:48:00: 14000000 INFO @ Thu, 08 Feb 2018 18:48:05: 9000000 INFO @ Thu, 08 Feb 2018 18:48:06: 9000000 INFO @ Thu, 08 Feb 2018 18:48:09: 15000000 INFO @ Thu, 08 Feb 2018 18:48:16: 10000000 INFO @ Thu, 08 Feb 2018 18:48:18: 10000000 INFO @ Thu, 08 Feb 2018 18:48:19: 16000000 INFO @ Thu, 08 Feb 2018 18:48:27: 11000000 INFO @ Thu, 08 Feb 2018 18:48:28: 17000000 INFO @ Thu, 08 Feb 2018 18:48:31: 11000000 INFO @ Thu, 08 Feb 2018 18:48:37: 18000000 INFO @ Thu, 08 Feb 2018 18:48:40: 12000000 INFO @ Thu, 08 Feb 2018 18:48:46: 12000000 INFO @ Thu, 08 Feb 2018 18:48:47: 19000000 INFO @ Thu, 08 Feb 2018 18:48:53: 13000000 INFO @ Thu, 08 Feb 2018 18:48:57: 20000000 INFO @ Thu, 08 Feb 2018 18:49:02: 13000000 INFO @ Thu, 08 Feb 2018 18:49:06: 14000000 INFO @ Thu, 08 Feb 2018 18:49:07: 21000000 INFO @ Thu, 08 Feb 2018 18:49:16: 14000000 INFO @ Thu, 08 Feb 2018 18:49:17: 22000000 INFO @ Thu, 08 Feb 2018 18:49:18: 15000000 INFO @ Thu, 08 Feb 2018 18:49:26: 23000000 INFO @ Thu, 08 Feb 2018 18:49:31: 16000000 INFO @ Thu, 08 Feb 2018 18:49:31: 15000000 INFO @ Thu, 08 Feb 2018 18:49:35: 24000000 INFO @ Thu, 08 Feb 2018 18:49:43: 25000000 INFO @ Thu, 08 Feb 2018 18:49:44: 17000000 INFO @ Thu, 08 Feb 2018 18:49:44: 16000000 INFO @ Thu, 08 Feb 2018 18:49:53: 26000000 INFO @ Thu, 08 Feb 2018 18:49:56: 18000000 INFO @ Thu, 08 Feb 2018 18:50:00: 17000000 INFO @ Thu, 08 Feb 2018 18:50:02: 27000000 INFO @ Thu, 08 Feb 2018 18:50:10: 28000000 INFO @ Thu, 08 Feb 2018 18:50:10: 19000000 INFO @ Thu, 08 Feb 2018 18:50:14: 18000000 INFO @ Thu, 08 Feb 2018 18:50:19: 29000000 INFO @ Thu, 08 Feb 2018 18:50:25: 20000000 INFO @ Thu, 08 Feb 2018 18:50:27: 30000000 INFO @ Thu, 08 Feb 2018 18:50:30: 19000000 INFO @ Thu, 08 Feb 2018 18:50:36: 31000000 INFO @ Thu, 08 Feb 2018 18:50:43: 21000000 INFO @ Thu, 08 Feb 2018 18:50:45: 32000000 INFO @ Thu, 08 Feb 2018 18:50:45: 20000000 INFO @ Thu, 08 Feb 2018 18:50:53: 33000000 INFO @ Thu, 08 Feb 2018 18:51:00: 21000000 INFO @ Thu, 08 Feb 2018 18:51:01: 22000000 INFO @ Thu, 08 Feb 2018 18:51:02: 34000000 INFO @ Thu, 08 Feb 2018 18:51:10: 35000000 INFO @ Thu, 08 Feb 2018 18:51:15: 23000000 INFO @ Thu, 08 Feb 2018 18:51:15: 22000000 INFO @ Thu, 08 Feb 2018 18:51:18: 36000000 INFO @ Thu, 08 Feb 2018 18:51:26: 37000000 INFO @ Thu, 08 Feb 2018 18:51:31: 23000000 INFO @ Thu, 08 Feb 2018 18:51:31: 24000000 INFO @ Thu, 08 Feb 2018 18:51:34: 38000000 INFO @ Thu, 08 Feb 2018 18:51:42: 39000000 INFO @ Thu, 08 Feb 2018 18:51:45: 24000000 INFO @ Thu, 08 Feb 2018 18:51:48: 25000000 INFO @ Thu, 08 Feb 2018 18:51:50: 40000000 INFO @ Thu, 08 Feb 2018 18:51:58: 41000000 INFO @ Thu, 08 Feb 2018 18:52:00: 25000000 INFO @ Thu, 08 Feb 2018 18:52:03: 26000000 INFO @ Thu, 08 Feb 2018 18:52:06: 42000000 INFO @ Thu, 08 Feb 2018 18:52:15: 43000000 INFO @ Thu, 08 Feb 2018 18:52:15: 26000000 INFO @ Thu, 08 Feb 2018 18:52:21: 27000000 INFO @ Thu, 08 Feb 2018 18:52:23: 44000000 INFO @ Thu, 08 Feb 2018 18:52:30: 27000000 INFO @ Thu, 08 Feb 2018 18:52:30: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 18:52:30: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 18:52:30: #1 total tags in treatment: 44858021 INFO @ Thu, 08 Feb 2018 18:52:30: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 18:52:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 18:52:32: #1 tags after filtering in treatment: 44857951 INFO @ Thu, 08 Feb 2018 18:52:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 18:52:32: #1 finished! INFO @ Thu, 08 Feb 2018 18:52:32: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 18:52:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 18:52:37: #2 number of paired peaks: 6008 INFO @ Thu, 08 Feb 2018 18:52:37: start model_add_line... INFO @ Thu, 08 Feb 2018 18:52:37: 28000000 INFO @ Thu, 08 Feb 2018 18:52:38: start X-correlation... INFO @ Thu, 08 Feb 2018 18:52:38: end of X-cor INFO @ Thu, 08 Feb 2018 18:52:38: #2 finished! INFO @ Thu, 08 Feb 2018 18:52:38: #2 predicted fragment length is 50 bps INFO @ Thu, 08 Feb 2018 18:52:38: #2 alternative fragment length(s) may be 50,381,578 bps INFO @ Thu, 08 Feb 2018 18:52:38: #2.2 Generate R script for model : SRX3478274.10_model.r WARNING @ Thu, 08 Feb 2018 18:52:38: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Feb 2018 18:52:38: #2 You may need to consider one of the other alternative d(s): 50,381,578 WARNING @ Thu, 08 Feb 2018 18:52:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Feb 2018 18:52:38: #3 Call peaks... INFO @ Thu, 08 Feb 2018 18:52:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 18:52:45: 28000000 INFO @ Thu, 08 Feb 2018 18:52:54: 29000000 INFO @ Thu, 08 Feb 2018 18:53:00: 29000000 INFO @ Thu, 08 Feb 2018 18:53:12: 30000000 INFO @ Thu, 08 Feb 2018 18:53:15: 30000000 INFO @ Thu, 08 Feb 2018 18:53:28: 31000000 INFO @ Thu, 08 Feb 2018 18:53:31: 31000000 INFO @ Thu, 08 Feb 2018 18:53:46: 32000000 INFO @ Thu, 08 Feb 2018 18:53:46: 32000000 INFO @ Thu, 08 Feb 2018 18:53:59: 33000000 INFO @ Thu, 08 Feb 2018 18:54:02: 33000000 INFO @ Thu, 08 Feb 2018 18:54:13: 34000000 INFO @ Thu, 08 Feb 2018 18:54:17: 34000000 INFO @ Thu, 08 Feb 2018 18:54:29: 35000000 INFO @ Thu, 08 Feb 2018 18:54:33: 35000000 INFO @ Thu, 08 Feb 2018 18:54:43: 36000000 INFO @ Thu, 08 Feb 2018 18:54:49: 36000000 INFO @ Thu, 08 Feb 2018 18:54:54: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 18:55:00: 37000000 INFO @ Thu, 08 Feb 2018 18:55:05: 37000000 INFO @ Thu, 08 Feb 2018 18:55:15: 38000000 INFO @ Thu, 08 Feb 2018 18:55:20: 38000000 INFO @ Thu, 08 Feb 2018 18:55:30: 39000000 INFO @ Thu, 08 Feb 2018 18:55:34: 39000000 INFO @ Thu, 08 Feb 2018 18:55:44: 40000000 INFO @ Thu, 08 Feb 2018 18:55:50: 40000000 INFO @ Thu, 08 Feb 2018 18:56:01: 41000000 INFO @ Thu, 08 Feb 2018 18:56:05: 41000000 INFO @ Thu, 08 Feb 2018 18:56:13: #4 Write output xls file... SRX3478274.10_peaks.xls INFO @ Thu, 08 Feb 2018 18:56:13: #4 Write peak in narrowPeak format file... SRX3478274.10_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 18:56:13: #4 Write summits bed file... SRX3478274.10_summits.bed INFO @ Thu, 08 Feb 2018 18:56:13: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (1293 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 18:56:19: 42000000 INFO @ Thu, 08 Feb 2018 18:56:20: 42000000 INFO @ Thu, 08 Feb 2018 18:56:36: 43000000 INFO @ Thu, 08 Feb 2018 18:56:37: 43000000 INFO @ Thu, 08 Feb 2018 18:56:51: 44000000 INFO @ Thu, 08 Feb 2018 18:56:54: 44000000 INFO @ Thu, 08 Feb 2018 18:57:05: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 18:57:05: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 18:57:05: #1 total tags in treatment: 44858021 INFO @ Thu, 08 Feb 2018 18:57:05: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 18:57:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 18:57:07: #1 tags after filtering in treatment: 44857951 INFO @ Thu, 08 Feb 2018 18:57:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 18:57:07: #1 finished! INFO @ Thu, 08 Feb 2018 18:57:07: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 18:57:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 18:57:09: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 18:57:09: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 18:57:09: #1 total tags in treatment: 44858021 INFO @ Thu, 08 Feb 2018 18:57:09: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 18:57:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 18:57:10: #1 tags after filtering in treatment: 44857951 INFO @ Thu, 08 Feb 2018 18:57:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 18:57:10: #1 finished! INFO @ Thu, 08 Feb 2018 18:57:10: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 18:57:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 18:57:12: #2 number of paired peaks: 6008 INFO @ Thu, 08 Feb 2018 18:57:12: start model_add_line... INFO @ Thu, 08 Feb 2018 18:57:13: start X-correlation... INFO @ Thu, 08 Feb 2018 18:57:13: end of X-cor INFO @ Thu, 08 Feb 2018 18:57:13: #2 finished! INFO @ Thu, 08 Feb 2018 18:57:13: #2 predicted fragment length is 50 bps INFO @ Thu, 08 Feb 2018 18:57:13: #2 alternative fragment length(s) may be 50,381,578 bps INFO @ Thu, 08 Feb 2018 18:57:13: #2.2 Generate R script for model : SRX3478274.05_model.r WARNING @ Thu, 08 Feb 2018 18:57:13: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Feb 2018 18:57:13: #2 You may need to consider one of the other alternative d(s): 50,381,578 WARNING @ Thu, 08 Feb 2018 18:57:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Feb 2018 18:57:13: #3 Call peaks... INFO @ Thu, 08 Feb 2018 18:57:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 18:57:16: #2 number of paired peaks: 6008 INFO @ Thu, 08 Feb 2018 18:57:16: start model_add_line... INFO @ Thu, 08 Feb 2018 18:57:16: start X-correlation... INFO @ Thu, 08 Feb 2018 18:57:16: end of X-cor INFO @ Thu, 08 Feb 2018 18:57:16: #2 finished! INFO @ Thu, 08 Feb 2018 18:57:16: #2 predicted fragment length is 50 bps INFO @ Thu, 08 Feb 2018 18:57:16: #2 alternative fragment length(s) may be 50,381,578 bps INFO @ Thu, 08 Feb 2018 18:57:16: #2.2 Generate R script for model : SRX3478274.20_model.r WARNING @ Thu, 08 Feb 2018 18:57:16: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Feb 2018 18:57:16: #2 You may need to consider one of the other alternative d(s): 50,381,578 WARNING @ Thu, 08 Feb 2018 18:57:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Feb 2018 18:57:16: #3 Call peaks... INFO @ Thu, 08 Feb 2018 18:57:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 18:59:28: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 18:59:36: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 19:00:48: #4 Write output xls file... SRX3478274.05_peaks.xls INFO @ Thu, 08 Feb 2018 19:00:48: #4 Write peak in narrowPeak format file... SRX3478274.05_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 19:00:48: #4 Write summits bed file... SRX3478274.05_summits.bed INFO @ Thu, 08 Feb 2018 19:00:48: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (2335 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 19:00:58: #4 Write output xls file... SRX3478274.20_peaks.xls INFO @ Thu, 08 Feb 2018 19:00:58: #4 Write peak in narrowPeak format file... SRX3478274.20_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 19:00:58: #4 Write summits bed file... SRX3478274.20_summits.bed INFO @ Thu, 08 Feb 2018 19:00:58: Done! pass1 - making usageList (35 chroms): 2 millis pass2 - checking and writing primary data (616 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。