Job ID = 10195005 sra ファイルのダウンロード中... Completed: 3851639K bytes transferred in 35 seconds (882167K 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 111820759 spots for /home/okishinya/chipatlas/results/rn6/SRX831355/SRR1743291.sra Written 111820759 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: 00:00:00 Time loading mirror index: 00:00:02 Multiseed full-index search: 01:17:02 111820759 reads; of these: 111820759 (100.00%) were unpaired; of these: 2909019 (2.60%) aligned 0 times 82215355 (73.52%) aligned exactly 1 time 26696385 (23.87%) aligned >1 times 97.40% overall alignment rate Time searching: 01:17:05 Overall time: 01:17:05 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 48 files... [bam_rmdupse_core] 60844855 / 108911740 = 0.5587 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 @ Fri, 10 Nov 2017 20:48:05: # Command line: callpeak -t SRX831355.bam -f BAM -g 2.15e9 -n SRX831355.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX831355.05 # format = BAM # ChIP-seq file = ['SRX831355.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 @ Fri, 10 Nov 2017 20:48:05: #1 read tag files... INFO @ Fri, 10 Nov 2017 20:48:05: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 20:48:05: # Command line: callpeak -t SRX831355.bam -f BAM -g 2.15e9 -n SRX831355.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX831355.10 # format = BAM # ChIP-seq file = ['SRX831355.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 @ Fri, 10 Nov 2017 20:48:05: #1 read tag files... INFO @ Fri, 10 Nov 2017 20:48:05: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 20:48:05: # Command line: callpeak -t SRX831355.bam -f BAM -g 2.15e9 -n SRX831355.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX831355.20 # format = BAM # ChIP-seq file = ['SRX831355.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 @ Fri, 10 Nov 2017 20:48:05: #1 read tag files... INFO @ Fri, 10 Nov 2017 20:48:05: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 20:48:12: 1000000 INFO @ Fri, 10 Nov 2017 20:48:12: 1000000 INFO @ Fri, 10 Nov 2017 20:48:12: 1000000 INFO @ Fri, 10 Nov 2017 20:48:18: 2000000 INFO @ Fri, 10 Nov 2017 20:48:18: 2000000 INFO @ Fri, 10 Nov 2017 20:48:19: 2000000 INFO @ Fri, 10 Nov 2017 20:48:25: 3000000 INFO @ Fri, 10 Nov 2017 20:48:25: 3000000 INFO @ Fri, 10 Nov 2017 20:48:26: 3000000 INFO @ Fri, 10 Nov 2017 20:48:31: 4000000 INFO @ Fri, 10 Nov 2017 20:48:32: 4000000 INFO @ Fri, 10 Nov 2017 20:48:33: 4000000 INFO @ Fri, 10 Nov 2017 20:48:38: 5000000 INFO @ Fri, 10 Nov 2017 20:48:38: 5000000 INFO @ Fri, 10 Nov 2017 20:48:40: 5000000 INFO @ Fri, 10 Nov 2017 20:48:45: 6000000 INFO @ Fri, 10 Nov 2017 20:48:45: 6000000 INFO @ Fri, 10 Nov 2017 20:48:47: 6000000 INFO @ Fri, 10 Nov 2017 20:48:51: 7000000 INFO @ Fri, 10 Nov 2017 20:48:51: 7000000 INFO @ Fri, 10 Nov 2017 20:48:54: 7000000 INFO @ Fri, 10 Nov 2017 20:48:58: 8000000 INFO @ Fri, 10 Nov 2017 20:48:58: 8000000 INFO @ Fri, 10 Nov 2017 20:49:01: 8000000 INFO @ Fri, 10 Nov 2017 20:49:04: 9000000 INFO @ Fri, 10 Nov 2017 20:49:04: 9000000 INFO @ Fri, 10 Nov 2017 20:49:08: 9000000 INFO @ Fri, 10 Nov 2017 20:49:11: 10000000 INFO @ Fri, 10 Nov 2017 20:49:11: 10000000 INFO @ Fri, 10 Nov 2017 20:49:15: 10000000 INFO @ Fri, 10 Nov 2017 20:49:18: 11000000 INFO @ Fri, 10 Nov 2017 20:49:18: 11000000 INFO @ Fri, 10 Nov 2017 20:49:22: 11000000 INFO @ Fri, 10 Nov 2017 20:49:24: 12000000 INFO @ Fri, 10 Nov 2017 20:49:24: 12000000 INFO @ Fri, 10 Nov 2017 20:49:29: 12000000 INFO @ Fri, 10 Nov 2017 20:49:31: 13000000 INFO @ Fri, 10 Nov 2017 20:49:31: 13000000 INFO @ Fri, 10 Nov 2017 20:49:35: 13000000 INFO @ Fri, 10 Nov 2017 20:49:37: 14000000 INFO @ Fri, 10 Nov 2017 20:49:37: 14000000 INFO @ Fri, 10 Nov 2017 20:49:42: 14000000 INFO @ Fri, 10 Nov 2017 20:49:44: 15000000 INFO @ Fri, 10 Nov 2017 20:49:44: 15000000 INFO @ Fri, 10 Nov 2017 20:49:49: 15000000 INFO @ Fri, 10 Nov 2017 20:49:50: 16000000 INFO @ Fri, 10 Nov 2017 20:49:50: 16000000 INFO @ Fri, 10 Nov 2017 20:49:56: 16000000 INFO @ Fri, 10 Nov 2017 20:49:57: 17000000 INFO @ Fri, 10 Nov 2017 20:49:57: 17000000 INFO @ Fri, 10 Nov 2017 20:50:03: 17000000 INFO @ Fri, 10 Nov 2017 20:50:03: 18000000 INFO @ Fri, 10 Nov 2017 20:50:03: 18000000 INFO @ Fri, 10 Nov 2017 20:50:10: 18000000 INFO @ Fri, 10 Nov 2017 20:50:10: 19000000 INFO @ Fri, 10 Nov 2017 20:50:10: 19000000 INFO @ Fri, 10 Nov 2017 20:50:17: 20000000 INFO @ Fri, 10 Nov 2017 20:50:17: 20000000 INFO @ Fri, 10 Nov 2017 20:50:17: 19000000 INFO @ Fri, 10 Nov 2017 20:50:23: 21000000 INFO @ Fri, 10 Nov 2017 20:50:23: 21000000 INFO @ Fri, 10 Nov 2017 20:50:24: 20000000 INFO @ Fri, 10 Nov 2017 20:50:30: 22000000 INFO @ Fri, 10 Nov 2017 20:50:30: 22000000 INFO @ Fri, 10 Nov 2017 20:50:30: 21000000 INFO @ Fri, 10 Nov 2017 20:50:36: 23000000 INFO @ Fri, 10 Nov 2017 20:50:36: 23000000 INFO @ Fri, 10 Nov 2017 20:50:37: 22000000 INFO @ Fri, 10 Nov 2017 20:50:43: 24000000 INFO @ Fri, 10 Nov 2017 20:50:43: 24000000 INFO @ Fri, 10 Nov 2017 20:50:44: 23000000 INFO @ Fri, 10 Nov 2017 20:50:49: 25000000 INFO @ Fri, 10 Nov 2017 20:50:49: 25000000 INFO @ Fri, 10 Nov 2017 20:50:51: 24000000 INFO @ Fri, 10 Nov 2017 20:50:56: 26000000 INFO @ Fri, 10 Nov 2017 20:50:56: 26000000 INFO @ Fri, 10 Nov 2017 20:50:58: 25000000 INFO @ Fri, 10 Nov 2017 20:51:03: 27000000 INFO @ Fri, 10 Nov 2017 20:51:03: 27000000 INFO @ Fri, 10 Nov 2017 20:51:05: 26000000 INFO @ Fri, 10 Nov 2017 20:51:09: 28000000 INFO @ Fri, 10 Nov 2017 20:51:09: 28000000 INFO @ Fri, 10 Nov 2017 20:51:12: 27000000 INFO @ Fri, 10 Nov 2017 20:51:16: 29000000 INFO @ Fri, 10 Nov 2017 20:51:16: 29000000 INFO @ Fri, 10 Nov 2017 20:51:19: 28000000 INFO @ Fri, 10 Nov 2017 20:51:22: 30000000 INFO @ Fri, 10 Nov 2017 20:51:22: 30000000 INFO @ Fri, 10 Nov 2017 20:51:25: 29000000 INFO @ Fri, 10 Nov 2017 20:51:29: 31000000 INFO @ Fri, 10 Nov 2017 20:51:29: 31000000 INFO @ Fri, 10 Nov 2017 20:51:32: 30000000 INFO @ Fri, 10 Nov 2017 20:51:35: 32000000 INFO @ Fri, 10 Nov 2017 20:51:35: 32000000 INFO @ Fri, 10 Nov 2017 20:51:39: 31000000 INFO @ Fri, 10 Nov 2017 20:51:42: 33000000 INFO @ Fri, 10 Nov 2017 20:51:42: 33000000 INFO @ Fri, 10 Nov 2017 20:51:46: 32000000 INFO @ Fri, 10 Nov 2017 20:51:49: 34000000 INFO @ Fri, 10 Nov 2017 20:51:49: 34000000 INFO @ Fri, 10 Nov 2017 20:51:53: 33000000 INFO @ Fri, 10 Nov 2017 20:51:55: 35000000 INFO @ Fri, 10 Nov 2017 20:51:55: 35000000 INFO @ Fri, 10 Nov 2017 20:52:00: 34000000 INFO @ Fri, 10 Nov 2017 20:52:02: 36000000 INFO @ Fri, 10 Nov 2017 20:52:02: 36000000 INFO @ Fri, 10 Nov 2017 20:52:07: 35000000 INFO @ Fri, 10 Nov 2017 20:52:09: 37000000 INFO @ Fri, 10 Nov 2017 20:52:09: 37000000 INFO @ Fri, 10 Nov 2017 20:52:13: 36000000 INFO @ Fri, 10 Nov 2017 20:52:15: 38000000 INFO @ Fri, 10 Nov 2017 20:52:15: 38000000 INFO @ Fri, 10 Nov 2017 20:52:20: 37000000 INFO @ Fri, 10 Nov 2017 20:52:22: 39000000 INFO @ Fri, 10 Nov 2017 20:52:22: 39000000 INFO @ Fri, 10 Nov 2017 20:52:27: 38000000 INFO @ Fri, 10 Nov 2017 20:52:28: 40000000 INFO @ Fri, 10 Nov 2017 20:52:28: 40000000 INFO @ Fri, 10 Nov 2017 20:52:33: 39000000 INFO @ Fri, 10 Nov 2017 20:52:35: 41000000 INFO @ Fri, 10 Nov 2017 20:52:35: 41000000 INFO @ Fri, 10 Nov 2017 20:52:40: 40000000 INFO @ Fri, 10 Nov 2017 20:52:42: 42000000 INFO @ Fri, 10 Nov 2017 20:52:42: 42000000 INFO @ Fri, 10 Nov 2017 20:52:47: 41000000 INFO @ Fri, 10 Nov 2017 20:52:48: 43000000 INFO @ Fri, 10 Nov 2017 20:52:48: 43000000 INFO @ Fri, 10 Nov 2017 20:52:54: 42000000 INFO @ Fri, 10 Nov 2017 20:52:55: 44000000 INFO @ Fri, 10 Nov 2017 20:52:55: 44000000 INFO @ Fri, 10 Nov 2017 20:53:00: 43000000 INFO @ Fri, 10 Nov 2017 20:53:02: 45000000 INFO @ Fri, 10 Nov 2017 20:53:02: 45000000 INFO @ Fri, 10 Nov 2017 20:53:07: 44000000 INFO @ Fri, 10 Nov 2017 20:53:08: 46000000 INFO @ Fri, 10 Nov 2017 20:53:08: 46000000 INFO @ Fri, 10 Nov 2017 20:53:14: 45000000 INFO @ Fri, 10 Nov 2017 20:53:15: 47000000 INFO @ Fri, 10 Nov 2017 20:53:15: 47000000 INFO @ Fri, 10 Nov 2017 20:53:21: 46000000 INFO @ Fri, 10 Nov 2017 20:53:21: 48000000 INFO @ Fri, 10 Nov 2017 20:53:22: 48000000 INFO @ Fri, 10 Nov 2017 20:53:22: #1 tag size is determined as 51 bps INFO @ Fri, 10 Nov 2017 20:53:22: #1 tag size = 51 INFO @ Fri, 10 Nov 2017 20:53:22: #1 total tags in treatment: 48066885 INFO @ Fri, 10 Nov 2017 20:53:22: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 20:53:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 20:53:22: #1 tag size is determined as 51 bps INFO @ Fri, 10 Nov 2017 20:53:22: #1 tag size = 51 INFO @ Fri, 10 Nov 2017 20:53:22: #1 total tags in treatment: 48066885 INFO @ Fri, 10 Nov 2017 20:53:22: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 20:53:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 20:53:24: #1 tags after filtering in treatment: 48066841 INFO @ Fri, 10 Nov 2017 20:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 20:53:24: #1 finished! INFO @ Fri, 10 Nov 2017 20:53:24: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 20:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 20:53:24: #1 tags after filtering in treatment: 48066841 INFO @ Fri, 10 Nov 2017 20:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 20:53:24: #1 finished! INFO @ Fri, 10 Nov 2017 20:53:24: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 20:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 20:53:28: 47000000 INFO @ Fri, 10 Nov 2017 20:53:28: #2 number of paired peaks: 6353 INFO @ Fri, 10 Nov 2017 20:53:28: start model_add_line... INFO @ Fri, 10 Nov 2017 20:53:28: #2 number of paired peaks: 6353 INFO @ Fri, 10 Nov 2017 20:53:28: start model_add_line... INFO @ Fri, 10 Nov 2017 20:53:28: start X-correlation... INFO @ Fri, 10 Nov 2017 20:53:28: end of X-cor INFO @ Fri, 10 Nov 2017 20:53:28: #2 finished! INFO @ Fri, 10 Nov 2017 20:53:28: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Nov 2017 20:53:28: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Nov 2017 20:53:28: #2.2 Generate R script for model : SRX831355.10_model.r WARNING @ Fri, 10 Nov 2017 20:53:28: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 20:53:28: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Nov 2017 20:53:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 20:53:28: #3 Call peaks... INFO @ Fri, 10 Nov 2017 20:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 20:53:28: start X-correlation... INFO @ Fri, 10 Nov 2017 20:53:28: end of X-cor INFO @ Fri, 10 Nov 2017 20:53:28: #2 finished! INFO @ Fri, 10 Nov 2017 20:53:28: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Nov 2017 20:53:28: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Nov 2017 20:53:28: #2.2 Generate R script for model : SRX831355.20_model.r WARNING @ Fri, 10 Nov 2017 20:53:28: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 20:53:28: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Nov 2017 20:53:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 20:53:28: #3 Call peaks... INFO @ Fri, 10 Nov 2017 20:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 20:53:35: 48000000 INFO @ Fri, 10 Nov 2017 20:53:35: #1 tag size is determined as 51 bps INFO @ Fri, 10 Nov 2017 20:53:35: #1 tag size = 51 INFO @ Fri, 10 Nov 2017 20:53:35: #1 total tags in treatment: 48066885 INFO @ Fri, 10 Nov 2017 20:53:35: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 20:53:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 20:53:37: #1 tags after filtering in treatment: 48066841 INFO @ Fri, 10 Nov 2017 20:53:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 20:53:37: #1 finished! INFO @ Fri, 10 Nov 2017 20:53:37: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 20:53:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 20:53:41: #2 number of paired peaks: 6353 INFO @ Fri, 10 Nov 2017 20:53:41: start model_add_line... INFO @ Fri, 10 Nov 2017 20:53:42: start X-correlation... INFO @ Fri, 10 Nov 2017 20:53:42: end of X-cor INFO @ Fri, 10 Nov 2017 20:53:42: #2 finished! INFO @ Fri, 10 Nov 2017 20:53:42: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Nov 2017 20:53:42: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Nov 2017 20:53:42: #2.2 Generate R script for model : SRX831355.05_model.r WARNING @ Fri, 10 Nov 2017 20:53:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 20:53:42: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Nov 2017 20:53:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 20:53:42: #3 Call peaks... INFO @ Fri, 10 Nov 2017 20:53:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 20:55:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 20:55:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 20:55:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 20:56:21: #4 Write output xls file... SRX831355.10_peaks.xls INFO @ Fri, 10 Nov 2017 20:56:21: #4 Write peak in narrowPeak format file... SRX831355.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 20:56:21: #4 Write summits bed file... SRX831355.10_summits.bed INFO @ Fri, 10 Nov 2017 20:56:21: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1377 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 20:56:26: #4 Write output xls file... SRX831355.20_peaks.xls INFO @ Fri, 10 Nov 2017 20:56:26: #4 Write peak in narrowPeak format file... SRX831355.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 20:56:26: #4 Write summits bed file... SRX831355.20_summits.bed INFO @ Fri, 10 Nov 2017 20:56:26: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (628 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 20:56:52: #4 Write output xls file... SRX831355.05_peaks.xls INFO @ Fri, 10 Nov 2017 20:56:52: #4 Write peak in narrowPeak format file... SRX831355.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 20:56:52: #4 Write summits bed file... SRX831355.05_summits.bed INFO @ Fri, 10 Nov 2017 20:56:52: Done! pass1 - making usageList (61 chroms): 1 millis pass2 - checking and writing primary data (2868 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。