Job ID = 10194934 sra ファイルのダウンロード中... Completed: 659080K bytes transferred in 10 seconds (502712K 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 33883903 spots for /home/okishinya/chipatlas/results/rn6/SRX2512944/SRR5197457.sra Written 33883903 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:33:18 33883903 reads; of these: 33883903 (100.00%) were unpaired; of these: 950984 (2.81%) aligned 0 times 22593923 (66.68%) aligned exactly 1 time 10338996 (30.51%) aligned >1 times 97.19% overall alignment rate Time searching: 00:33:22 Overall time: 00:33:22 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 12 files... [bam_rmdupse_core] 1425071 / 32932919 = 0.0433 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 00:28:49: # Command line: callpeak -t SRX2512944.bam -f BAM -g 2.15e9 -n SRX2512944.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2512944.10 # format = BAM # ChIP-seq file = ['SRX2512944.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 00:28:49: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:28:49: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:28:49: # Command line: callpeak -t SRX2512944.bam -f BAM -g 2.15e9 -n SRX2512944.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2512944.20 # format = BAM # ChIP-seq file = ['SRX2512944.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 00:28:49: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:28:49: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:28:49: # Command line: callpeak -t SRX2512944.bam -f BAM -g 2.15e9 -n SRX2512944.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2512944.05 # format = BAM # ChIP-seq file = ['SRX2512944.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 00:28:49: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:28:49: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:28:57: 1000000 INFO @ Sat, 11 Nov 2017 00:29:01: 1000000 INFO @ Sat, 11 Nov 2017 00:29:03: 1000000 INFO @ Sat, 11 Nov 2017 00:29:07: 2000000 INFO @ Sat, 11 Nov 2017 00:29:14: 2000000 INFO @ Sat, 11 Nov 2017 00:29:17: 2000000 INFO @ Sat, 11 Nov 2017 00:29:18: 3000000 INFO @ Sat, 11 Nov 2017 00:29:27: 3000000 INFO @ Sat, 11 Nov 2017 00:29:28: 4000000 INFO @ Sat, 11 Nov 2017 00:29:32: 3000000 INFO @ Sat, 11 Nov 2017 00:29:39: 5000000 INFO @ Sat, 11 Nov 2017 00:29:40: 4000000 INFO @ Sat, 11 Nov 2017 00:29:47: 4000000 INFO @ Sat, 11 Nov 2017 00:29:50: 6000000 INFO @ Sat, 11 Nov 2017 00:29:54: 5000000 INFO @ Sat, 11 Nov 2017 00:30:00: 7000000 INFO @ Sat, 11 Nov 2017 00:30:01: 5000000 INFO @ Sat, 11 Nov 2017 00:30:07: 6000000 INFO @ Sat, 11 Nov 2017 00:30:10: 8000000 INFO @ Sat, 11 Nov 2017 00:30:16: 6000000 INFO @ Sat, 11 Nov 2017 00:30:20: 7000000 INFO @ Sat, 11 Nov 2017 00:30:21: 9000000 INFO @ Sat, 11 Nov 2017 00:30:31: 7000000 INFO @ Sat, 11 Nov 2017 00:30:32: 10000000 INFO @ Sat, 11 Nov 2017 00:30:34: 8000000 INFO @ Sat, 11 Nov 2017 00:30:42: 11000000 INFO @ Sat, 11 Nov 2017 00:30:46: 8000000 INFO @ Sat, 11 Nov 2017 00:30:47: 9000000 INFO @ Sat, 11 Nov 2017 00:30:53: 12000000 INFO @ Sat, 11 Nov 2017 00:31:00: 9000000 INFO @ Sat, 11 Nov 2017 00:31:00: 10000000 INFO @ Sat, 11 Nov 2017 00:31:03: 13000000 INFO @ Sat, 11 Nov 2017 00:31:13: 11000000 INFO @ Sat, 11 Nov 2017 00:31:14: 14000000 INFO @ Sat, 11 Nov 2017 00:31:15: 10000000 INFO @ Sat, 11 Nov 2017 00:31:24: 15000000 INFO @ Sat, 11 Nov 2017 00:31:26: 12000000 INFO @ Sat, 11 Nov 2017 00:31:30: 11000000 INFO @ Sat, 11 Nov 2017 00:31:34: 16000000 INFO @ Sat, 11 Nov 2017 00:31:39: 13000000 INFO @ Sat, 11 Nov 2017 00:31:45: 12000000 INFO @ Sat, 11 Nov 2017 00:31:45: 17000000 INFO @ Sat, 11 Nov 2017 00:31:52: 14000000 INFO @ Sat, 11 Nov 2017 00:31:55: 18000000 INFO @ Sat, 11 Nov 2017 00:31:59: 13000000 INFO @ Sat, 11 Nov 2017 00:32:05: 15000000 INFO @ Sat, 11 Nov 2017 00:32:06: 19000000 INFO @ Sat, 11 Nov 2017 00:32:14: 14000000 INFO @ Sat, 11 Nov 2017 00:32:17: 20000000 INFO @ Sat, 11 Nov 2017 00:32:17: 16000000 INFO @ Sat, 11 Nov 2017 00:32:29: 15000000 INFO @ Sat, 11 Nov 2017 00:32:29: 21000000 INFO @ Sat, 11 Nov 2017 00:32:30: 17000000 INFO @ Sat, 11 Nov 2017 00:32:41: 22000000 INFO @ Sat, 11 Nov 2017 00:32:43: 18000000 INFO @ Sat, 11 Nov 2017 00:32:43: 16000000 INFO @ Sat, 11 Nov 2017 00:32:53: 23000000 INFO @ Sat, 11 Nov 2017 00:32:56: 19000000 INFO @ Sat, 11 Nov 2017 00:32:58: 17000000 INFO @ Sat, 11 Nov 2017 00:33:05: 24000000 INFO @ Sat, 11 Nov 2017 00:33:11: 20000000 INFO @ Sat, 11 Nov 2017 00:33:13: 18000000 INFO @ Sat, 11 Nov 2017 00:33:18: 25000000 INFO @ Sat, 11 Nov 2017 00:33:25: 21000000 INFO @ Sat, 11 Nov 2017 00:33:28: 19000000 INFO @ Sat, 11 Nov 2017 00:33:30: 26000000 INFO @ Sat, 11 Nov 2017 00:33:38: 22000000 INFO @ Sat, 11 Nov 2017 00:33:42: 27000000 INFO @ Sat, 11 Nov 2017 00:33:43: 20000000 INFO @ Sat, 11 Nov 2017 00:33:51: 23000000 INFO @ Sat, 11 Nov 2017 00:33:54: 28000000 INFO @ Sat, 11 Nov 2017 00:33:57: 21000000 INFO @ Sat, 11 Nov 2017 00:34:07: 29000000 INFO @ Sat, 11 Nov 2017 00:34:07: 24000000 INFO @ Sat, 11 Nov 2017 00:34:11: 22000000 INFO @ Sat, 11 Nov 2017 00:34:19: 30000000 INFO @ Sat, 11 Nov 2017 00:34:20: 25000000 INFO @ Sat, 11 Nov 2017 00:34:25: 23000000 INFO @ Sat, 11 Nov 2017 00:34:31: 31000000 INFO @ Sat, 11 Nov 2017 00:34:33: 26000000 INFO @ Sat, 11 Nov 2017 00:34:38: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 00:34:38: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 00:34:38: #1 total tags in treatment: 31507848 INFO @ Sat, 11 Nov 2017 00:34:38: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:34:38: #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 00:34:39: #1 tags after filtering in treatment: 31507779 INFO @ Sat, 11 Nov 2017 00:34:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:34:39: #1 finished! INFO @ Sat, 11 Nov 2017 00:34:39: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:34:40: 24000000 INFO @ Sat, 11 Nov 2017 00:34:43: #2 number of paired peaks: 6746 INFO @ Sat, 11 Nov 2017 00:34:43: start model_add_line... INFO @ Sat, 11 Nov 2017 00:34:44: start X-correlation... INFO @ Sat, 11 Nov 2017 00:34:44: end of X-cor INFO @ Sat, 11 Nov 2017 00:34:44: #2 finished! INFO @ Sat, 11 Nov 2017 00:34:44: #2 predicted fragment length is 37 bps INFO @ Sat, 11 Nov 2017 00:34:44: #2 alternative fragment length(s) may be 37,591 bps INFO @ Sat, 11 Nov 2017 00:34:44: #2.2 Generate R script for model : SRX2512944.10_model.r WARNING @ Sat, 11 Nov 2017 00:34:44: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:34:44: #2 You may need to consider one of the other alternative d(s): 37,591 WARNING @ Sat, 11 Nov 2017 00:34:44: #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 00:34:44: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:34:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:34:47: 27000000 INFO @ Sat, 11 Nov 2017 00:34:55: 25000000 INFO @ Sat, 11 Nov 2017 00:35:00: 28000000 INFO @ Sat, 11 Nov 2017 00:35:10: 26000000 INFO @ Sat, 11 Nov 2017 00:35:14: 29000000 INFO @ Sat, 11 Nov 2017 00:35:25: 27000000 INFO @ Sat, 11 Nov 2017 00:35:27: 30000000 INFO @ Sat, 11 Nov 2017 00:35:40: 28000000 INFO @ Sat, 11 Nov 2017 00:35:40: 31000000 INFO @ Sat, 11 Nov 2017 00:35:47: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 00:35:47: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 00:35:47: #1 total tags in treatment: 31507848 INFO @ Sat, 11 Nov 2017 00:35:47: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:35:47: #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 00:35:48: #1 tags after filtering in treatment: 31507779 INFO @ Sat, 11 Nov 2017 00:35:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:35:48: #1 finished! INFO @ Sat, 11 Nov 2017 00:35:48: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:35:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:35:52: #2 number of paired peaks: 6746 INFO @ Sat, 11 Nov 2017 00:35:52: start model_add_line... INFO @ Sat, 11 Nov 2017 00:35:52: start X-correlation... INFO @ Sat, 11 Nov 2017 00:35:52: end of X-cor INFO @ Sat, 11 Nov 2017 00:35:52: #2 finished! INFO @ Sat, 11 Nov 2017 00:35:52: #2 predicted fragment length is 37 bps INFO @ Sat, 11 Nov 2017 00:35:52: #2 alternative fragment length(s) may be 37,591 bps INFO @ Sat, 11 Nov 2017 00:35:52: #2.2 Generate R script for model : SRX2512944.05_model.r WARNING @ Sat, 11 Nov 2017 00:35:52: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:35:52: #2 You may need to consider one of the other alternative d(s): 37,591 WARNING @ Sat, 11 Nov 2017 00:35:52: #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 00:35:52: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:35:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:35:54: 29000000 INFO @ Sat, 11 Nov 2017 00:36:09: 30000000 INFO @ Sat, 11 Nov 2017 00:36:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:36:24: 31000000 INFO @ Sat, 11 Nov 2017 00:36:32: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 00:36:32: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 00:36:32: #1 total tags in treatment: 31507848 INFO @ Sat, 11 Nov 2017 00:36:32: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:36:32: #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 00:36:33: #1 tags after filtering in treatment: 31507779 INFO @ Sat, 11 Nov 2017 00:36:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:36:33: #1 finished! INFO @ Sat, 11 Nov 2017 00:36:33: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:36:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:36:37: #2 number of paired peaks: 6746 INFO @ Sat, 11 Nov 2017 00:36:37: start model_add_line... INFO @ Sat, 11 Nov 2017 00:36:37: start X-correlation... INFO @ Sat, 11 Nov 2017 00:36:37: end of X-cor INFO @ Sat, 11 Nov 2017 00:36:37: #2 finished! INFO @ Sat, 11 Nov 2017 00:36:37: #2 predicted fragment length is 37 bps INFO @ Sat, 11 Nov 2017 00:36:37: #2 alternative fragment length(s) may be 37,591 bps INFO @ Sat, 11 Nov 2017 00:36:37: #2.2 Generate R script for model : SRX2512944.20_model.r WARNING @ Sat, 11 Nov 2017 00:36:37: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:36:37: #2 You may need to consider one of the other alternative d(s): 37,591 WARNING @ Sat, 11 Nov 2017 00:36:37: #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 00:36:37: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:36:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:37:14: #4 Write output xls file... SRX2512944.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:37:14: #4 Write peak in narrowPeak format file... SRX2512944.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:37:14: #4 Write summits bed file... SRX2512944.10_summits.bed INFO @ Sat, 11 Nov 2017 00:37:14: Done! pass1 - making usageList (44 chroms): 2 millis pass2 - checking and writing primary data (1432 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:37:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:38:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:38:18: #4 Write output xls file... SRX2512944.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:38:18: #4 Write peak in narrowPeak format file... SRX2512944.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:38:18: #4 Write summits bed file... SRX2512944.05_summits.bed INFO @ Sat, 11 Nov 2017 00:38:18: Done! pass1 - making usageList (56 chroms): 2 millis pass2 - checking and writing primary data (2819 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:39:05: #4 Write output xls file... SRX2512944.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:39:05: #4 Write peak in narrowPeak format file... SRX2512944.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:39:05: #4 Write summits bed file... SRX2512944.20_summits.bed INFO @ Sat, 11 Nov 2017 00:39:05: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (619 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。