Job ID = 10195041 sra ファイルのダウンロード中... Completed: 901949K bytes transferred in 11 seconds (655493K bits/sec), in 1 file. Completed: 561566K bytes transferred in 8 seconds (562605K 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 15508016 spots for /home/okishinya/chipatlas/results/rn6/SRX913510/SRR1870956.sra Written 15508016 spots total Written 28974953 spots for /home/okishinya/chipatlas/results/rn6/SRX913510/SRR1870957.sra Written 28974953 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 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:25:48 44482969 reads; of these: 44482969 (100.00%) were unpaired; of these: 7012552 (15.76%) aligned 0 times 26786322 (60.22%) aligned exactly 1 time 10684095 (24.02%) aligned >1 times 84.24% overall alignment rate Time searching: 00:25:50 Overall time: 00:25:50 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 16 files... [bam_rmdupse_core] 14691127 / 37470417 = 0.3921 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 07:50:15: # Command line: callpeak -t SRX913510.bam -f BAM -g 2.15e9 -n SRX913510.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX913510.20 # format = BAM # ChIP-seq file = ['SRX913510.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 07:50:15: # Command line: callpeak -t SRX913510.bam -f BAM -g 2.15e9 -n SRX913510.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX913510.05 # format = BAM # ChIP-seq file = ['SRX913510.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 07:50:15: # Command line: callpeak -t SRX913510.bam -f BAM -g 2.15e9 -n SRX913510.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX913510.10 # format = BAM # ChIP-seq file = ['SRX913510.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 07:50:15: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:50:15: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:50:15: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:50:15: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:50:15: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:50:15: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:50:21: 1000000 INFO @ Sat, 11 Nov 2017 07:50:21: 1000000 INFO @ Sat, 11 Nov 2017 07:50:21: 1000000 INFO @ Sat, 11 Nov 2017 07:50:28: 2000000 INFO @ Sat, 11 Nov 2017 07:50:28: 2000000 INFO @ Sat, 11 Nov 2017 07:50:28: 2000000 INFO @ Sat, 11 Nov 2017 07:50:34: 3000000 INFO @ Sat, 11 Nov 2017 07:50:34: 3000000 INFO @ Sat, 11 Nov 2017 07:50:34: 3000000 INFO @ Sat, 11 Nov 2017 07:50:40: 4000000 INFO @ Sat, 11 Nov 2017 07:50:41: 4000000 INFO @ Sat, 11 Nov 2017 07:50:41: 4000000 INFO @ Sat, 11 Nov 2017 07:50:47: 5000000 INFO @ Sat, 11 Nov 2017 07:50:47: 5000000 INFO @ Sat, 11 Nov 2017 07:50:48: 5000000 INFO @ Sat, 11 Nov 2017 07:50:54: 6000000 INFO @ Sat, 11 Nov 2017 07:50:54: 6000000 INFO @ Sat, 11 Nov 2017 07:50:55: 6000000 INFO @ Sat, 11 Nov 2017 07:51:01: 7000000 INFO @ Sat, 11 Nov 2017 07:51:02: 7000000 INFO @ Sat, 11 Nov 2017 07:51:02: 7000000 INFO @ Sat, 11 Nov 2017 07:51:08: 8000000 INFO @ Sat, 11 Nov 2017 07:51:09: 8000000 INFO @ Sat, 11 Nov 2017 07:51:10: 8000000 INFO @ Sat, 11 Nov 2017 07:51:15: 9000000 INFO @ Sat, 11 Nov 2017 07:51:16: 9000000 INFO @ Sat, 11 Nov 2017 07:51:18: 9000000 INFO @ Sat, 11 Nov 2017 07:51:22: 10000000 INFO @ Sat, 11 Nov 2017 07:51:23: 10000000 INFO @ Sat, 11 Nov 2017 07:51:26: 10000000 INFO @ Sat, 11 Nov 2017 07:51:30: 11000000 INFO @ Sat, 11 Nov 2017 07:51:31: 11000000 INFO @ Sat, 11 Nov 2017 07:51:34: 11000000 INFO @ Sat, 11 Nov 2017 07:51:37: 12000000 INFO @ Sat, 11 Nov 2017 07:51:38: 12000000 INFO @ Sat, 11 Nov 2017 07:51:42: 12000000 INFO @ Sat, 11 Nov 2017 07:51:44: 13000000 INFO @ Sat, 11 Nov 2017 07:51:45: 13000000 INFO @ Sat, 11 Nov 2017 07:51:49: 13000000 INFO @ Sat, 11 Nov 2017 07:51:51: 14000000 INFO @ Sat, 11 Nov 2017 07:51:53: 14000000 INFO @ Sat, 11 Nov 2017 07:51:57: 14000000 INFO @ Sat, 11 Nov 2017 07:51:58: 15000000 INFO @ Sat, 11 Nov 2017 07:52:00: 15000000 INFO @ Sat, 11 Nov 2017 07:52:05: 15000000 INFO @ Sat, 11 Nov 2017 07:52:06: 16000000 INFO @ Sat, 11 Nov 2017 07:52:07: 16000000 INFO @ Sat, 11 Nov 2017 07:52:13: 17000000 INFO @ Sat, 11 Nov 2017 07:52:13: 16000000 INFO @ Sat, 11 Nov 2017 07:52:14: 17000000 INFO @ Sat, 11 Nov 2017 07:52:20: 18000000 INFO @ Sat, 11 Nov 2017 07:52:21: 17000000 INFO @ Sat, 11 Nov 2017 07:52:22: 18000000 INFO @ Sat, 11 Nov 2017 07:52:27: 19000000 INFO @ Sat, 11 Nov 2017 07:52:29: 18000000 INFO @ Sat, 11 Nov 2017 07:52:29: 19000000 INFO @ Sat, 11 Nov 2017 07:52:34: 20000000 INFO @ Sat, 11 Nov 2017 07:52:36: 20000000 INFO @ Sat, 11 Nov 2017 07:52:36: 19000000 INFO @ Sat, 11 Nov 2017 07:52:41: 21000000 INFO @ Sat, 11 Nov 2017 07:52:44: 21000000 INFO @ Sat, 11 Nov 2017 07:52:44: 20000000 INFO @ Sat, 11 Nov 2017 07:52:49: 22000000 INFO @ Sat, 11 Nov 2017 07:52:51: 22000000 INFO @ Sat, 11 Nov 2017 07:52:52: 21000000 INFO @ Sat, 11 Nov 2017 07:52:55: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 07:52:55: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 07:52:55: #1 total tags in treatment: 22779290 INFO @ Sat, 11 Nov 2017 07:52:55: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 07:52:55: #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 07:52:55: #1 tags after filtering in treatment: 22779209 INFO @ Sat, 11 Nov 2017 07:52:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 07:52:55: #1 finished! INFO @ Sat, 11 Nov 2017 07:52:55: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 07:52:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 07:52:57: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 07:52:57: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 07:52:57: #1 total tags in treatment: 22779290 INFO @ Sat, 11 Nov 2017 07:52:57: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 07:52:57: #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 07:52:57: #2 number of paired peaks: 7443 INFO @ Sat, 11 Nov 2017 07:52:57: start model_add_line... INFO @ Sat, 11 Nov 2017 07:52:58: #1 tags after filtering in treatment: 22779209 INFO @ Sat, 11 Nov 2017 07:52:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 07:52:58: #1 finished! INFO @ Sat, 11 Nov 2017 07:52:58: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 07:52:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 07:52:58: start X-correlation... INFO @ Sat, 11 Nov 2017 07:52:58: end of X-cor INFO @ Sat, 11 Nov 2017 07:52:58: #2 finished! INFO @ Sat, 11 Nov 2017 07:52:58: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Nov 2017 07:52:58: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Nov 2017 07:52:58: #2.2 Generate R script for model : SRX913510.05_model.r WARNING @ Sat, 11 Nov 2017 07:52:58: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 07:52:58: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Nov 2017 07:52:58: #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 07:52:58: #3 Call peaks... INFO @ Sat, 11 Nov 2017 07:52:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 07:52:59: 22000000 INFO @ Sat, 11 Nov 2017 07:53:00: #2 number of paired peaks: 7443 INFO @ Sat, 11 Nov 2017 07:53:00: start model_add_line... INFO @ Sat, 11 Nov 2017 07:53:00: start X-correlation... INFO @ Sat, 11 Nov 2017 07:53:00: end of X-cor INFO @ Sat, 11 Nov 2017 07:53:00: #2 finished! INFO @ Sat, 11 Nov 2017 07:53:00: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Nov 2017 07:53:00: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Nov 2017 07:53:00: #2.2 Generate R script for model : SRX913510.20_model.r WARNING @ Sat, 11 Nov 2017 07:53:00: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 07:53:00: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Nov 2017 07:53:00: #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 07:53:00: #3 Call peaks... INFO @ Sat, 11 Nov 2017 07:53:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 07:53:04: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 07:53:04: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 07:53:04: #1 total tags in treatment: 22779290 INFO @ Sat, 11 Nov 2017 07:53:04: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 07:53:04: #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 07:53:05: #1 tags after filtering in treatment: 22779209 INFO @ Sat, 11 Nov 2017 07:53:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 07:53:05: #1 finished! INFO @ Sat, 11 Nov 2017 07:53:05: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 07:53:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 07:53:07: #2 number of paired peaks: 7443 INFO @ Sat, 11 Nov 2017 07:53:07: start model_add_line... INFO @ Sat, 11 Nov 2017 07:53:08: start X-correlation... INFO @ Sat, 11 Nov 2017 07:53:08: end of X-cor INFO @ Sat, 11 Nov 2017 07:53:08: #2 finished! INFO @ Sat, 11 Nov 2017 07:53:08: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Nov 2017 07:53:08: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Nov 2017 07:53:08: #2.2 Generate R script for model : SRX913510.10_model.r WARNING @ Sat, 11 Nov 2017 07:53:08: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 07:53:08: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Nov 2017 07:53:08: #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 07:53:08: #3 Call peaks... INFO @ Sat, 11 Nov 2017 07:53:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 07:53:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 07:54:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 07:54:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 07:54:23: #4 Write output xls file... SRX913510.05_peaks.xls INFO @ Sat, 11 Nov 2017 07:54:23: #4 Write peak in narrowPeak format file... SRX913510.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 07:54:23: #4 Write summits bed file... SRX913510.05_summits.bed INFO @ Sat, 11 Nov 2017 07:54:23: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (1341 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 07:54:31: #4 Write output xls file... SRX913510.20_peaks.xls INFO @ Sat, 11 Nov 2017 07:54:31: #4 Write peak in narrowPeak format file... SRX913510.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 07:54:31: #4 Write summits bed file... SRX913510.20_summits.bed INFO @ Sat, 11 Nov 2017 07:54:31: Done! pass1 - making usageList (41 chroms): 0 millis pass2 - checking and writing primary data (238 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 07:54:35: #4 Write output xls file... SRX913510.10_peaks.xls INFO @ Sat, 11 Nov 2017 07:54:35: #4 Write peak in narrowPeak format file... SRX913510.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 07:54:35: #4 Write summits bed file... SRX913510.10_summits.bed INFO @ Sat, 11 Nov 2017 07:54:35: Done! pass1 - making usageList (57 chroms): 1 millis pass2 - checking and writing primary data (654 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。