Job ID = 10194764 sra ファイルのダウンロード中... Completed: 1256429K bytes transferred in 12 seconds (838562K 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 27598999 spots for /home/okishinya/chipatlas/results/rn6/SRX1184183/SRR2243268.sra Written 27598999 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:32:45 27598999 reads; of these: 27598999 (100.00%) were unpaired; of these: 3904720 (14.15%) aligned 0 times 18357915 (66.52%) aligned exactly 1 time 5336364 (19.34%) aligned >1 times 85.85% overall alignment rate Time searching: 00:32:48 Overall time: 00:32:49 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] 3562886 / 23694279 = 0.1504 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 17:04:47: # Command line: callpeak -t SRX1184183.bam -f BAM -g 2.15e9 -n SRX1184183.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1184183.10 # format = BAM # ChIP-seq file = ['SRX1184183.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 17:04:47: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:04:47: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:04:47: # Command line: callpeak -t SRX1184183.bam -f BAM -g 2.15e9 -n SRX1184183.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1184183.05 # format = BAM # ChIP-seq file = ['SRX1184183.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 17:04:47: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:04:47: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:04:47: # Command line: callpeak -t SRX1184183.bam -f BAM -g 2.15e9 -n SRX1184183.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1184183.20 # format = BAM # ChIP-seq file = ['SRX1184183.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 17:04:47: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:04:47: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:04:54: 1000000 INFO @ Fri, 10 Nov 2017 17:04:55: 1000000 INFO @ Fri, 10 Nov 2017 17:04:55: 1000000 INFO @ Fri, 10 Nov 2017 17:05:02: 2000000 INFO @ Fri, 10 Nov 2017 17:05:03: 2000000 INFO @ Fri, 10 Nov 2017 17:05:03: 2000000 INFO @ Fri, 10 Nov 2017 17:05:09: 3000000 INFO @ Fri, 10 Nov 2017 17:05:10: 3000000 INFO @ Fri, 10 Nov 2017 17:05:10: 3000000 INFO @ Fri, 10 Nov 2017 17:05:17: 4000000 INFO @ Fri, 10 Nov 2017 17:05:18: 4000000 INFO @ Fri, 10 Nov 2017 17:05:18: 4000000 INFO @ Fri, 10 Nov 2017 17:05:24: 5000000 INFO @ Fri, 10 Nov 2017 17:05:26: 5000000 INFO @ Fri, 10 Nov 2017 17:05:26: 5000000 INFO @ Fri, 10 Nov 2017 17:05:31: 6000000 INFO @ Fri, 10 Nov 2017 17:05:34: 6000000 INFO @ Fri, 10 Nov 2017 17:05:34: 6000000 INFO @ Fri, 10 Nov 2017 17:05:39: 7000000 INFO @ Fri, 10 Nov 2017 17:05:41: 7000000 INFO @ Fri, 10 Nov 2017 17:05:41: 7000000 INFO @ Fri, 10 Nov 2017 17:05:46: 8000000 INFO @ Fri, 10 Nov 2017 17:05:49: 8000000 INFO @ Fri, 10 Nov 2017 17:05:49: 8000000 INFO @ Fri, 10 Nov 2017 17:05:53: 9000000 INFO @ Fri, 10 Nov 2017 17:05:57: 9000000 INFO @ Fri, 10 Nov 2017 17:05:57: 9000000 INFO @ Fri, 10 Nov 2017 17:06:01: 10000000 INFO @ Fri, 10 Nov 2017 17:06:05: 10000000 INFO @ Fri, 10 Nov 2017 17:06:05: 10000000 INFO @ Fri, 10 Nov 2017 17:06:08: 11000000 INFO @ Fri, 10 Nov 2017 17:06:13: 11000000 INFO @ Fri, 10 Nov 2017 17:06:13: 11000000 INFO @ Fri, 10 Nov 2017 17:06:16: 12000000 INFO @ Fri, 10 Nov 2017 17:06:20: 12000000 INFO @ Fri, 10 Nov 2017 17:06:20: 12000000 INFO @ Fri, 10 Nov 2017 17:06:23: 13000000 INFO @ Fri, 10 Nov 2017 17:06:28: 13000000 INFO @ Fri, 10 Nov 2017 17:06:28: 13000000 INFO @ Fri, 10 Nov 2017 17:06:30: 14000000 INFO @ Fri, 10 Nov 2017 17:06:36: 14000000 INFO @ Fri, 10 Nov 2017 17:06:36: 14000000 INFO @ Fri, 10 Nov 2017 17:06:38: 15000000 INFO @ Fri, 10 Nov 2017 17:06:44: 15000000 INFO @ Fri, 10 Nov 2017 17:06:44: 15000000 INFO @ Fri, 10 Nov 2017 17:06:45: 16000000 INFO @ Fri, 10 Nov 2017 17:06:52: 16000000 INFO @ Fri, 10 Nov 2017 17:06:52: 16000000 INFO @ Fri, 10 Nov 2017 17:06:52: 17000000 INFO @ Fri, 10 Nov 2017 17:06:59: 17000000 INFO @ Fri, 10 Nov 2017 17:06:59: 17000000 INFO @ Fri, 10 Nov 2017 17:07:00: 18000000 INFO @ Fri, 10 Nov 2017 17:07:08: 18000000 INFO @ Fri, 10 Nov 2017 17:07:08: 18000000 INFO @ Fri, 10 Nov 2017 17:07:08: 19000000 INFO @ Fri, 10 Nov 2017 17:07:16: 19000000 INFO @ Fri, 10 Nov 2017 17:07:16: 19000000 INFO @ Fri, 10 Nov 2017 17:07:18: 20000000 INFO @ Fri, 10 Nov 2017 17:07:19: #1 tag size is determined as 75 bps INFO @ Fri, 10 Nov 2017 17:07:19: #1 tag size = 75 INFO @ Fri, 10 Nov 2017 17:07:19: #1 total tags in treatment: 20131393 INFO @ Fri, 10 Nov 2017 17:07:19: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:07:19: #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 17:07:20: #1 tags after filtering in treatment: 20131261 INFO @ Fri, 10 Nov 2017 17:07:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:07:20: #1 finished! INFO @ Fri, 10 Nov 2017 17:07:20: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:07:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:07:23: #2 number of paired peaks: 27681 INFO @ Fri, 10 Nov 2017 17:07:23: start model_add_line... INFO @ Fri, 10 Nov 2017 17:07:23: 20000000 INFO @ Fri, 10 Nov 2017 17:07:23: start X-correlation... INFO @ Fri, 10 Nov 2017 17:07:23: end of X-cor INFO @ Fri, 10 Nov 2017 17:07:23: #2 finished! INFO @ Fri, 10 Nov 2017 17:07:23: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Nov 2017 17:07:23: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Nov 2017 17:07:23: #2.2 Generate R script for model : SRX1184183.05_model.r WARNING @ Fri, 10 Nov 2017 17:07:23: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 17:07:23: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Fri, 10 Nov 2017 17:07:23: #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 17:07:23: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:07:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:07:24: 20000000 INFO @ Fri, 10 Nov 2017 17:07:24: #1 tag size is determined as 75 bps INFO @ Fri, 10 Nov 2017 17:07:24: #1 tag size = 75 INFO @ Fri, 10 Nov 2017 17:07:24: #1 total tags in treatment: 20131393 INFO @ Fri, 10 Nov 2017 17:07:24: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:07:24: #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 17:07:25: #1 tags after filtering in treatment: 20131261 INFO @ Fri, 10 Nov 2017 17:07:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:07:25: #1 finished! INFO @ Fri, 10 Nov 2017 17:07:25: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:07:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:07:25: #1 tag size is determined as 75 bps INFO @ Fri, 10 Nov 2017 17:07:25: #1 tag size = 75 INFO @ Fri, 10 Nov 2017 17:07:25: #1 total tags in treatment: 20131393 INFO @ Fri, 10 Nov 2017 17:07:25: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:07:25: #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 17:07:26: #1 tags after filtering in treatment: 20131261 INFO @ Fri, 10 Nov 2017 17:07:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:07:26: #1 finished! INFO @ Fri, 10 Nov 2017 17:07:26: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:07:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:07:28: #2 number of paired peaks: 27681 INFO @ Fri, 10 Nov 2017 17:07:28: start model_add_line... INFO @ Fri, 10 Nov 2017 17:07:28: start X-correlation... INFO @ Fri, 10 Nov 2017 17:07:28: end of X-cor INFO @ Fri, 10 Nov 2017 17:07:28: #2 finished! INFO @ Fri, 10 Nov 2017 17:07:28: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Nov 2017 17:07:28: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Nov 2017 17:07:28: #2.2 Generate R script for model : SRX1184183.20_model.r WARNING @ Fri, 10 Nov 2017 17:07:28: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 17:07:28: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Fri, 10 Nov 2017 17:07:28: #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 17:07:28: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:07:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:07:28: #2 number of paired peaks: 27681 INFO @ Fri, 10 Nov 2017 17:07:28: start model_add_line... INFO @ Fri, 10 Nov 2017 17:07:29: start X-correlation... INFO @ Fri, 10 Nov 2017 17:07:29: end of X-cor INFO @ Fri, 10 Nov 2017 17:07:29: #2 finished! INFO @ Fri, 10 Nov 2017 17:07:29: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Nov 2017 17:07:29: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Nov 2017 17:07:29: #2.2 Generate R script for model : SRX1184183.10_model.r WARNING @ Fri, 10 Nov 2017 17:07:29: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 17:07:29: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Fri, 10 Nov 2017 17:07:29: #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 17:07:29: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:07:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:08:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:08:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:08:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:08:44: #4 Write output xls file... SRX1184183.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:08:44: #4 Write peak in narrowPeak format file... SRX1184183.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:08:44: #4 Write summits bed file... SRX1184183.05_summits.bed INFO @ Fri, 10 Nov 2017 17:08:44: Done! pass1 - making usageList (94 chroms): 5 millis pass2 - checking and writing primary data (21808 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:08:47: #4 Write output xls file... SRX1184183.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:08:47: #4 Write peak in narrowPeak format file... SRX1184183.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:08:47: #4 Write summits bed file... SRX1184183.20_summits.bed INFO @ Fri, 10 Nov 2017 17:08:47: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (5271 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:08:50: #4 Write output xls file... SRX1184183.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:08:50: #4 Write peak in narrowPeak format file... SRX1184183.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:08:50: #4 Write summits bed file... SRX1184183.10_summits.bed INFO @ Fri, 10 Nov 2017 17:08:50: Done! pass1 - making usageList (64 chroms): 3 millis pass2 - checking and writing primary data (12100 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。