Job ID = 10195007 sra ファイルのダウンロード中... Completed: 731208K bytes transferred in 9 seconds (607443K 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 36341204 spots for /home/okishinya/chipatlas/results/rn6/SRX831357/SRR1743293.sra Written 36341204 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: 00:12:30 36341204 reads; of these: 36341204 (100.00%) were unpaired; of these: 1303780 (3.59%) aligned 0 times 26090049 (71.79%) aligned exactly 1 time 8947375 (24.62%) aligned >1 times 96.41% overall alignment rate Time searching: 00:12:34 Overall time: 00:12:34 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] 787252 / 35037424 = 0.0225 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 19:28:44: # Command line: callpeak -t SRX831357.bam -f BAM -g 2.15e9 -n SRX831357.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX831357.10 # format = BAM # ChIP-seq file = ['SRX831357.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 19:28:44: # Command line: callpeak -t SRX831357.bam -f BAM -g 2.15e9 -n SRX831357.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX831357.20 # format = BAM # ChIP-seq file = ['SRX831357.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 19:28:44: # Command line: callpeak -t SRX831357.bam -f BAM -g 2.15e9 -n SRX831357.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX831357.05 # format = BAM # ChIP-seq file = ['SRX831357.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 19:28:44: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:28:44: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:28:44: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:28:44: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:28:44: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:28:44: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:28:50: 1000000 INFO @ Fri, 10 Nov 2017 19:28:51: 1000000 INFO @ Fri, 10 Nov 2017 19:28:51: 1000000 INFO @ Fri, 10 Nov 2017 19:28:56: 2000000 INFO @ Fri, 10 Nov 2017 19:28:58: 2000000 INFO @ Fri, 10 Nov 2017 19:28:58: 2000000 INFO @ Fri, 10 Nov 2017 19:29:02: 3000000 INFO @ Fri, 10 Nov 2017 19:29:05: 3000000 INFO @ Fri, 10 Nov 2017 19:29:05: 3000000 INFO @ Fri, 10 Nov 2017 19:29:08: 4000000 INFO @ Fri, 10 Nov 2017 19:29:12: 4000000 INFO @ Fri, 10 Nov 2017 19:29:12: 4000000 INFO @ Fri, 10 Nov 2017 19:29:15: 5000000 INFO @ Fri, 10 Nov 2017 19:29:18: 5000000 INFO @ Fri, 10 Nov 2017 19:29:19: 5000000 INFO @ Fri, 10 Nov 2017 19:29:21: 6000000 INFO @ Fri, 10 Nov 2017 19:29:25: 6000000 INFO @ Fri, 10 Nov 2017 19:29:26: 6000000 INFO @ Fri, 10 Nov 2017 19:29:27: 7000000 INFO @ Fri, 10 Nov 2017 19:29:33: 7000000 INFO @ Fri, 10 Nov 2017 19:29:33: 8000000 INFO @ Fri, 10 Nov 2017 19:29:34: 7000000 INFO @ Fri, 10 Nov 2017 19:29:39: 9000000 INFO @ Fri, 10 Nov 2017 19:29:40: 8000000 INFO @ Fri, 10 Nov 2017 19:29:41: 8000000 INFO @ Fri, 10 Nov 2017 19:29:45: 10000000 INFO @ Fri, 10 Nov 2017 19:29:47: 9000000 INFO @ Fri, 10 Nov 2017 19:29:49: 9000000 INFO @ Fri, 10 Nov 2017 19:29:51: 11000000 INFO @ Fri, 10 Nov 2017 19:29:54: 10000000 INFO @ Fri, 10 Nov 2017 19:29:56: 10000000 INFO @ Fri, 10 Nov 2017 19:29:58: 12000000 INFO @ Fri, 10 Nov 2017 19:30:01: 11000000 INFO @ Fri, 10 Nov 2017 19:30:03: 11000000 INFO @ Fri, 10 Nov 2017 19:30:04: 13000000 INFO @ Fri, 10 Nov 2017 19:30:08: 12000000 INFO @ Fri, 10 Nov 2017 19:30:10: 14000000 INFO @ Fri, 10 Nov 2017 19:30:11: 12000000 INFO @ Fri, 10 Nov 2017 19:30:16: 13000000 INFO @ Fri, 10 Nov 2017 19:30:16: 15000000 INFO @ Fri, 10 Nov 2017 19:30:18: 13000000 INFO @ Fri, 10 Nov 2017 19:30:22: 16000000 INFO @ Fri, 10 Nov 2017 19:30:23: 14000000 INFO @ Fri, 10 Nov 2017 19:30:26: 14000000 INFO @ Fri, 10 Nov 2017 19:30:28: 17000000 INFO @ Fri, 10 Nov 2017 19:30:30: 15000000 INFO @ Fri, 10 Nov 2017 19:30:33: 15000000 INFO @ Fri, 10 Nov 2017 19:30:34: 18000000 INFO @ Fri, 10 Nov 2017 19:30:37: 16000000 INFO @ Fri, 10 Nov 2017 19:30:41: 19000000 INFO @ Fri, 10 Nov 2017 19:30:41: 16000000 INFO @ Fri, 10 Nov 2017 19:30:44: 17000000 INFO @ Fri, 10 Nov 2017 19:30:47: 20000000 INFO @ Fri, 10 Nov 2017 19:30:48: 17000000 INFO @ Fri, 10 Nov 2017 19:30:51: 18000000 INFO @ Fri, 10 Nov 2017 19:30:53: 21000000 INFO @ Fri, 10 Nov 2017 19:30:55: 18000000 INFO @ Fri, 10 Nov 2017 19:30:58: 19000000 INFO @ Fri, 10 Nov 2017 19:31:00: 22000000 INFO @ Fri, 10 Nov 2017 19:31:02: 19000000 INFO @ Fri, 10 Nov 2017 19:31:05: 20000000 INFO @ Fri, 10 Nov 2017 19:31:06: 23000000 INFO @ Fri, 10 Nov 2017 19:31:09: 20000000 INFO @ Fri, 10 Nov 2017 19:31:12: 21000000 INFO @ Fri, 10 Nov 2017 19:31:13: 24000000 INFO @ Fri, 10 Nov 2017 19:31:15: 21000000 INFO @ Fri, 10 Nov 2017 19:31:19: 22000000 INFO @ Fri, 10 Nov 2017 19:31:19: 25000000 INFO @ Fri, 10 Nov 2017 19:31:22: 22000000 INFO @ Fri, 10 Nov 2017 19:31:26: 26000000 INFO @ Fri, 10 Nov 2017 19:31:26: 23000000 INFO @ Fri, 10 Nov 2017 19:31:29: 23000000 INFO @ Fri, 10 Nov 2017 19:31:33: 27000000 INFO @ Fri, 10 Nov 2017 19:31:33: 24000000 INFO @ Fri, 10 Nov 2017 19:31:36: 24000000 INFO @ Fri, 10 Nov 2017 19:31:40: 28000000 INFO @ Fri, 10 Nov 2017 19:31:40: 25000000 INFO @ Fri, 10 Nov 2017 19:31:44: 25000000 INFO @ Fri, 10 Nov 2017 19:31:47: 29000000 INFO @ Fri, 10 Nov 2017 19:31:48: 26000000 INFO @ Fri, 10 Nov 2017 19:31:52: 26000000 INFO @ Fri, 10 Nov 2017 19:31:55: 30000000 INFO @ Fri, 10 Nov 2017 19:31:56: 27000000 INFO @ Fri, 10 Nov 2017 19:32:01: 27000000 INFO @ Fri, 10 Nov 2017 19:32:02: 31000000 INFO @ Fri, 10 Nov 2017 19:32:05: 28000000 INFO @ Fri, 10 Nov 2017 19:32:09: 32000000 INFO @ Fri, 10 Nov 2017 19:32:10: 28000000 INFO @ Fri, 10 Nov 2017 19:32:13: 29000000 INFO @ Fri, 10 Nov 2017 19:32:17: 33000000 INFO @ Fri, 10 Nov 2017 19:32:19: 29000000 INFO @ Fri, 10 Nov 2017 19:32:22: 30000000 INFO @ Fri, 10 Nov 2017 19:32:24: 34000000 INFO @ Fri, 10 Nov 2017 19:32:26: #1 tag size is determined as 35 bps INFO @ Fri, 10 Nov 2017 19:32:26: #1 tag size = 35 INFO @ Fri, 10 Nov 2017 19:32:26: #1 total tags in treatment: 34250172 INFO @ Fri, 10 Nov 2017 19:32:26: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:32:26: #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 19:32:27: #1 tags after filtering in treatment: 34250100 INFO @ Fri, 10 Nov 2017 19:32:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:32:27: #1 finished! INFO @ Fri, 10 Nov 2017 19:32:27: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:32:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:32:27: 30000000 INFO @ Fri, 10 Nov 2017 19:32:29: 31000000 INFO @ Fri, 10 Nov 2017 19:32:30: #2 number of paired peaks: 4081 INFO @ Fri, 10 Nov 2017 19:32:30: start model_add_line... INFO @ Fri, 10 Nov 2017 19:32:30: start X-correlation... INFO @ Fri, 10 Nov 2017 19:32:30: end of X-cor INFO @ Fri, 10 Nov 2017 19:32:30: #2 finished! INFO @ Fri, 10 Nov 2017 19:32:30: #2 predicted fragment length is 35 bps INFO @ Fri, 10 Nov 2017 19:32:30: #2 alternative fragment length(s) may be 35,386,588 bps INFO @ Fri, 10 Nov 2017 19:32:30: #2.2 Generate R script for model : SRX831357.10_model.r WARNING @ Fri, 10 Nov 2017 19:32:30: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 19:32:30: #2 You may need to consider one of the other alternative d(s): 35,386,588 WARNING @ Fri, 10 Nov 2017 19:32:30: #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 19:32:30: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:32:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:32:34: 31000000 INFO @ Fri, 10 Nov 2017 19:32:35: 32000000 INFO @ Fri, 10 Nov 2017 19:32:41: 32000000 INFO @ Fri, 10 Nov 2017 19:32:42: 33000000 INFO @ Fri, 10 Nov 2017 19:32:48: 34000000 INFO @ Fri, 10 Nov 2017 19:32:48: 33000000 INFO @ Fri, 10 Nov 2017 19:32:50: #1 tag size is determined as 35 bps INFO @ Fri, 10 Nov 2017 19:32:50: #1 tag size = 35 INFO @ Fri, 10 Nov 2017 19:32:50: #1 total tags in treatment: 34250172 INFO @ Fri, 10 Nov 2017 19:32:50: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:32:50: #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 19:32:51: #1 tags after filtering in treatment: 34250100 INFO @ Fri, 10 Nov 2017 19:32:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:32:51: #1 finished! INFO @ Fri, 10 Nov 2017 19:32:51: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:32:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:32:54: #2 number of paired peaks: 4081 INFO @ Fri, 10 Nov 2017 19:32:54: start model_add_line... INFO @ Fri, 10 Nov 2017 19:32:54: start X-correlation... INFO @ Fri, 10 Nov 2017 19:32:54: end of X-cor INFO @ Fri, 10 Nov 2017 19:32:54: #2 finished! INFO @ Fri, 10 Nov 2017 19:32:54: #2 predicted fragment length is 35 bps INFO @ Fri, 10 Nov 2017 19:32:54: #2 alternative fragment length(s) may be 35,386,588 bps INFO @ Fri, 10 Nov 2017 19:32:54: #2.2 Generate R script for model : SRX831357.05_model.r WARNING @ Fri, 10 Nov 2017 19:32:54: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 19:32:54: #2 You may need to consider one of the other alternative d(s): 35,386,588 WARNING @ Fri, 10 Nov 2017 19:32:54: #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 19:32:54: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:32:56: 34000000 INFO @ Fri, 10 Nov 2017 19:32:58: #1 tag size is determined as 35 bps INFO @ Fri, 10 Nov 2017 19:32:58: #1 tag size = 35 INFO @ Fri, 10 Nov 2017 19:32:58: #1 total tags in treatment: 34250172 INFO @ Fri, 10 Nov 2017 19:32:58: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:32:58: #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 19:32:59: #1 tags after filtering in treatment: 34250100 INFO @ Fri, 10 Nov 2017 19:32:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:32:59: #1 finished! INFO @ Fri, 10 Nov 2017 19:32:59: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:33:02: #2 number of paired peaks: 4081 INFO @ Fri, 10 Nov 2017 19:33:02: start model_add_line... INFO @ Fri, 10 Nov 2017 19:33:02: start X-correlation... INFO @ Fri, 10 Nov 2017 19:33:02: end of X-cor INFO @ Fri, 10 Nov 2017 19:33:02: #2 finished! INFO @ Fri, 10 Nov 2017 19:33:02: #2 predicted fragment length is 35 bps INFO @ Fri, 10 Nov 2017 19:33:02: #2 alternative fragment length(s) may be 35,386,588 bps INFO @ Fri, 10 Nov 2017 19:33:02: #2.2 Generate R script for model : SRX831357.20_model.r WARNING @ Fri, 10 Nov 2017 19:33:02: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 19:33:02: #2 You may need to consider one of the other alternative d(s): 35,386,588 WARNING @ Fri, 10 Nov 2017 19:33:02: #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 19:33:02: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:33:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:34:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:34:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:34:38: #4 Write output xls file... SRX831357.10_peaks.xls INFO @ Fri, 10 Nov 2017 19:34:38: #4 Write peak in narrowPeak format file... SRX831357.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:34:38: #4 Write summits bed file... SRX831357.10_summits.bed INFO @ Fri, 10 Nov 2017 19:34:38: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (1077 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:35:05: #4 Write output xls file... SRX831357.05_peaks.xls INFO @ Fri, 10 Nov 2017 19:35:05: #4 Write peak in narrowPeak format file... SRX831357.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:35:05: #4 Write summits bed file... SRX831357.05_summits.bed INFO @ Fri, 10 Nov 2017 19:35:05: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (1912 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:35:16: #4 Write output xls file... SRX831357.20_peaks.xls INFO @ Fri, 10 Nov 2017 19:35:16: #4 Write peak in narrowPeak format file... SRX831357.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:35:16: #4 Write summits bed file... SRX831357.20_summits.bed INFO @ Fri, 10 Nov 2017 19:35:16: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (465 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。