Job ID = 10194986 sra ファイルのダウンロード中... Completed: 850408K bytes transferred in 9 seconds (715246K bits/sec), in 1 file. Completed: 80302K bytes transferred in 3 seconds (176058K 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 6266091 spots for /home/okishinya/chipatlas/results/rn6/SRX695943/SRR1569504.sra Written 6266091 spots total Written 45912634 spots for /home/okishinya/chipatlas/results/rn6/SRX695943/SRR1569503.sra Written 45912634 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:18:28 52178725 reads; of these: 52178725 (100.00%) were unpaired; of these: 20054873 (38.43%) aligned 0 times 23464480 (44.97%) aligned exactly 1 time 8659372 (16.60%) aligned >1 times 61.57% overall alignment rate Time searching: 00:18:31 Overall time: 00:18:31 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] 20837095 / 32123852 = 0.6486 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 19:03:19: # Command line: callpeak -t SRX695943.bam -f BAM -g 2.15e9 -n SRX695943.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX695943.20 # format = BAM # ChIP-seq file = ['SRX695943.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 19:03:19: # Command line: callpeak -t SRX695943.bam -f BAM -g 2.15e9 -n SRX695943.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX695943.10 # format = BAM # ChIP-seq file = ['SRX695943.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 19:03:19: # Command line: callpeak -t SRX695943.bam -f BAM -g 2.15e9 -n SRX695943.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX695943.05 # format = BAM # ChIP-seq file = ['SRX695943.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 19:03:19: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:03:19: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:03:19: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:03:19: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:03:19: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:03:19: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:03:25: 1000000 INFO @ Fri, 10 Nov 2017 19:03:25: 1000000 INFO @ Fri, 10 Nov 2017 19:03:25: 1000000 INFO @ Fri, 10 Nov 2017 19:03:31: 2000000 INFO @ Fri, 10 Nov 2017 19:03:31: 2000000 INFO @ Fri, 10 Nov 2017 19:03:31: 2000000 INFO @ Fri, 10 Nov 2017 19:03:37: 3000000 INFO @ Fri, 10 Nov 2017 19:03:37: 3000000 INFO @ Fri, 10 Nov 2017 19:03:37: 3000000 INFO @ Fri, 10 Nov 2017 19:03:43: 4000000 INFO @ Fri, 10 Nov 2017 19:03:43: 4000000 INFO @ Fri, 10 Nov 2017 19:03:43: 4000000 INFO @ Fri, 10 Nov 2017 19:03:49: 5000000 INFO @ Fri, 10 Nov 2017 19:03:49: 5000000 INFO @ Fri, 10 Nov 2017 19:03:50: 5000000 INFO @ Fri, 10 Nov 2017 19:03:54: 6000000 INFO @ Fri, 10 Nov 2017 19:03:55: 6000000 INFO @ Fri, 10 Nov 2017 19:03:56: 6000000 INFO @ Fri, 10 Nov 2017 19:04:00: 7000000 INFO @ Fri, 10 Nov 2017 19:04:02: 7000000 INFO @ Fri, 10 Nov 2017 19:04:02: 7000000 INFO @ Fri, 10 Nov 2017 19:04:06: 8000000 INFO @ Fri, 10 Nov 2017 19:04:08: 8000000 INFO @ Fri, 10 Nov 2017 19:04:08: 8000000 INFO @ Fri, 10 Nov 2017 19:04:12: 9000000 INFO @ Fri, 10 Nov 2017 19:04:14: 9000000 INFO @ Fri, 10 Nov 2017 19:04:15: 9000000 INFO @ Fri, 10 Nov 2017 19:04:17: 10000000 INFO @ Fri, 10 Nov 2017 19:04:21: 10000000 INFO @ Fri, 10 Nov 2017 19:04:21: 10000000 INFO @ Fri, 10 Nov 2017 19:04:24: 11000000 INFO @ Fri, 10 Nov 2017 19:04:26: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 19:04:26: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 19:04:26: #1 total tags in treatment: 11286757 INFO @ Fri, 10 Nov 2017 19:04:26: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:04:26: #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 19:04:26: #1 tags after filtering in treatment: 11286608 INFO @ Fri, 10 Nov 2017 19:04:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:04:26: #1 finished! INFO @ Fri, 10 Nov 2017 19:04:26: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:04:27: 11000000 INFO @ Fri, 10 Nov 2017 19:04:28: 11000000 INFO @ Fri, 10 Nov 2017 19:04:28: #2 number of paired peaks: 14499 INFO @ Fri, 10 Nov 2017 19:04:28: start model_add_line... INFO @ Fri, 10 Nov 2017 19:04:29: start X-correlation... INFO @ Fri, 10 Nov 2017 19:04:29: end of X-cor INFO @ Fri, 10 Nov 2017 19:04:29: #2 finished! INFO @ Fri, 10 Nov 2017 19:04:29: #2 predicted fragment length is 39 bps INFO @ Fri, 10 Nov 2017 19:04:29: #2 alternative fragment length(s) may be 39,173,223,378,394,490,538,589 bps INFO @ Fri, 10 Nov 2017 19:04:29: #2.2 Generate R script for model : SRX695943.05_model.r WARNING @ Fri, 10 Nov 2017 19:04:29: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 19:04:29: #2 You may need to consider one of the other alternative d(s): 39,173,223,378,394,490,538,589 WARNING @ Fri, 10 Nov 2017 19:04:29: #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 19:04:29: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:04:29: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 19:04:29: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 19:04:29: #1 total tags in treatment: 11286757 INFO @ Fri, 10 Nov 2017 19:04:29: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:04:29: #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 19:04:29: #1 tags after filtering in treatment: 11286608 INFO @ Fri, 10 Nov 2017 19:04:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:04:29: #1 finished! INFO @ Fri, 10 Nov 2017 19:04:29: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:04:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:04:30: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 19:04:30: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 19:04:30: #1 total tags in treatment: 11286757 INFO @ Fri, 10 Nov 2017 19:04:30: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:04:30: #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 19:04:30: #1 tags after filtering in treatment: 11286608 INFO @ Fri, 10 Nov 2017 19:04:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:04:30: #1 finished! INFO @ Fri, 10 Nov 2017 19:04:30: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:04:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:04:31: #2 number of paired peaks: 14499 INFO @ Fri, 10 Nov 2017 19:04:31: start model_add_line... INFO @ Fri, 10 Nov 2017 19:04:31: start X-correlation... INFO @ Fri, 10 Nov 2017 19:04:31: end of X-cor INFO @ Fri, 10 Nov 2017 19:04:31: #2 finished! INFO @ Fri, 10 Nov 2017 19:04:31: #2 predicted fragment length is 39 bps INFO @ Fri, 10 Nov 2017 19:04:31: #2 alternative fragment length(s) may be 39,173,223,378,394,490,538,589 bps INFO @ Fri, 10 Nov 2017 19:04:31: #2.2 Generate R script for model : SRX695943.10_model.r WARNING @ Fri, 10 Nov 2017 19:04:31: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 19:04:31: #2 You may need to consider one of the other alternative d(s): 39,173,223,378,394,490,538,589 WARNING @ Fri, 10 Nov 2017 19:04:31: #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 19:04:31: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:04:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:04:32: #2 number of paired peaks: 14499 INFO @ Fri, 10 Nov 2017 19:04:32: start model_add_line... INFO @ Fri, 10 Nov 2017 19:04:33: start X-correlation... INFO @ Fri, 10 Nov 2017 19:04:33: end of X-cor INFO @ Fri, 10 Nov 2017 19:04:33: #2 finished! INFO @ Fri, 10 Nov 2017 19:04:33: #2 predicted fragment length is 39 bps INFO @ Fri, 10 Nov 2017 19:04:33: #2 alternative fragment length(s) may be 39,173,223,378,394,490,538,589 bps INFO @ Fri, 10 Nov 2017 19:04:33: #2.2 Generate R script for model : SRX695943.20_model.r WARNING @ Fri, 10 Nov 2017 19:04:33: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 19:04:33: #2 You may need to consider one of the other alternative d(s): 39,173,223,378,394,490,538,589 WARNING @ Fri, 10 Nov 2017 19:04:33: #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 19:04:33: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:04:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:04:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:04:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:04:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:05:12: #4 Write output xls file... SRX695943.05_peaks.xls INFO @ Fri, 10 Nov 2017 19:05:12: #4 Write peak in narrowPeak format file... SRX695943.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:05:12: #4 Write summits bed file... SRX695943.05_summits.bed INFO @ Fri, 10 Nov 2017 19:05:12: Done! pass1 - making usageList (71 chroms): 1 millis pass2 - checking and writing primary data (3654 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:05:16: #4 Write output xls file... SRX695943.20_peaks.xls INFO @ Fri, 10 Nov 2017 19:05:16: #4 Write peak in narrowPeak format file... SRX695943.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:05:16: #4 Write summits bed file... SRX695943.20_summits.bed INFO @ Fri, 10 Nov 2017 19:05:16: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (605 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:05:17: #4 Write output xls file... SRX695943.10_peaks.xls INFO @ Fri, 10 Nov 2017 19:05:17: #4 Write peak in narrowPeak format file... SRX695943.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:05:17: #4 Write summits bed file... SRX695943.10_summits.bed INFO @ Fri, 10 Nov 2017 19:05:17: Done! pass1 - making usageList (61 chroms): 1 millis pass2 - checking and writing primary data (1803 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。