Job ID = 9158344 sra ファイルのダウンロード中... Completed: 1169425K bytes transferred in 12 seconds (752074K bits/sec), in 2 files, 3 directories. 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 17988834 spots for /home/okishinya/chipatlas/results/dm3/SRX113313/SRR392922.sra Written 17988834 spots total Written 21633808 spots for /home/okishinya/chipatlas/results/dm3/SRX113313/SRR392923.sra Written 21633808 spots total 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:53 39622642 reads; of these: 39622642 (100.00%) were unpaired; of these: 8908255 (22.48%) aligned 0 times 27337678 (69.00%) aligned exactly 1 time 3376709 (8.52%) aligned >1 times 77.52% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 10525523 / 30714387 = 0.3427 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 @ Tue, 27 Jun 2017 16:30:09: # Command line: callpeak -t SRX113313.bam -f BAM -g dm -n SRX113313.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX113313.20 # format = BAM # ChIP-seq file = ['SRX113313.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 27 Jun 2017 16:30:09: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:30:09: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:30:09: # Command line: callpeak -t SRX113313.bam -f BAM -g dm -n SRX113313.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX113313.05 # format = BAM # ChIP-seq file = ['SRX113313.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 27 Jun 2017 16:30:09: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:30:09: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:30:09: # Command line: callpeak -t SRX113313.bam -f BAM -g dm -n SRX113313.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX113313.10 # format = BAM # ChIP-seq file = ['SRX113313.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 27 Jun 2017 16:30:09: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:30:09: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:30:15: 1000000 INFO @ Tue, 27 Jun 2017 16:30:15: 1000000 INFO @ Tue, 27 Jun 2017 16:30:15: 1000000 INFO @ Tue, 27 Jun 2017 16:30:21: 2000000 INFO @ Tue, 27 Jun 2017 16:30:21: 2000000 INFO @ Tue, 27 Jun 2017 16:30:21: 2000000 INFO @ Tue, 27 Jun 2017 16:30:27: 3000000 INFO @ Tue, 27 Jun 2017 16:30:27: 3000000 INFO @ Tue, 27 Jun 2017 16:30:27: 3000000 INFO @ Tue, 27 Jun 2017 16:30:32: 4000000 INFO @ Tue, 27 Jun 2017 16:30:33: 4000000 INFO @ Tue, 27 Jun 2017 16:30:33: 4000000 INFO @ Tue, 27 Jun 2017 16:30:38: 5000000 INFO @ Tue, 27 Jun 2017 16:30:39: 5000000 INFO @ Tue, 27 Jun 2017 16:30:39: 5000000 INFO @ Tue, 27 Jun 2017 16:30:44: 6000000 INFO @ Tue, 27 Jun 2017 16:30:45: 6000000 INFO @ Tue, 27 Jun 2017 16:30:45: 6000000 INFO @ Tue, 27 Jun 2017 16:30:50: 7000000 INFO @ Tue, 27 Jun 2017 16:30:51: 7000000 INFO @ Tue, 27 Jun 2017 16:30:52: 7000000 INFO @ Tue, 27 Jun 2017 16:30:55: 8000000 INFO @ Tue, 27 Jun 2017 16:30:57: 8000000 INFO @ Tue, 27 Jun 2017 16:30:58: 8000000 INFO @ Tue, 27 Jun 2017 16:31:01: 9000000 INFO @ Tue, 27 Jun 2017 16:31:04: 9000000 INFO @ Tue, 27 Jun 2017 16:31:05: 9000000 INFO @ Tue, 27 Jun 2017 16:31:07: 10000000 INFO @ Tue, 27 Jun 2017 16:31:10: 10000000 INFO @ Tue, 27 Jun 2017 16:31:11: 10000000 INFO @ Tue, 27 Jun 2017 16:31:13: 11000000 INFO @ Tue, 27 Jun 2017 16:31:16: 11000000 INFO @ Tue, 27 Jun 2017 16:31:17: 11000000 INFO @ Tue, 27 Jun 2017 16:31:18: 12000000 INFO @ Tue, 27 Jun 2017 16:31:22: 12000000 INFO @ Tue, 27 Jun 2017 16:31:24: 12000000 INFO @ Tue, 27 Jun 2017 16:31:24: 13000000 INFO @ Tue, 27 Jun 2017 16:31:29: 13000000 INFO @ Tue, 27 Jun 2017 16:31:30: 14000000 INFO @ Tue, 27 Jun 2017 16:31:30: 13000000 INFO @ Tue, 27 Jun 2017 16:31:36: 14000000 INFO @ Tue, 27 Jun 2017 16:31:36: 15000000 INFO @ Tue, 27 Jun 2017 16:31:37: 14000000 INFO @ Tue, 27 Jun 2017 16:31:42: 15000000 INFO @ Tue, 27 Jun 2017 16:31:42: 16000000 INFO @ Tue, 27 Jun 2017 16:31:43: 15000000 INFO @ Tue, 27 Jun 2017 16:31:48: 17000000 INFO @ Tue, 27 Jun 2017 16:31:48: 16000000 INFO @ Tue, 27 Jun 2017 16:31:50: 16000000 INFO @ Tue, 27 Jun 2017 16:31:54: 18000000 INFO @ Tue, 27 Jun 2017 16:31:55: 17000000 INFO @ Tue, 27 Jun 2017 16:31:57: 17000000 INFO @ Tue, 27 Jun 2017 16:32:00: 19000000 INFO @ Tue, 27 Jun 2017 16:32:01: 18000000 INFO @ Tue, 27 Jun 2017 16:32:03: 18000000 INFO @ Tue, 27 Jun 2017 16:32:06: 20000000 INFO @ Tue, 27 Jun 2017 16:32:07: #1 tag size is determined as 44 bps INFO @ Tue, 27 Jun 2017 16:32:07: #1 tag size = 44 INFO @ Tue, 27 Jun 2017 16:32:07: #1 total tags in treatment: 20188864 INFO @ Tue, 27 Jun 2017 16:32:07: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:32:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 16:32:08: 19000000 INFO @ Tue, 27 Jun 2017 16:32:08: #1 tags after filtering in treatment: 20188864 INFO @ Tue, 27 Jun 2017 16:32:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 16:32:08: #1 finished! INFO @ Tue, 27 Jun 2017 16:32:08: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:32:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:32:09: #2 number of paired peaks: 457 WARNING @ Tue, 27 Jun 2017 16:32:09: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Tue, 27 Jun 2017 16:32:09: start model_add_line... INFO @ Tue, 27 Jun 2017 16:32:09: start X-correlation... INFO @ Tue, 27 Jun 2017 16:32:09: end of X-cor INFO @ Tue, 27 Jun 2017 16:32:09: #2 finished! INFO @ Tue, 27 Jun 2017 16:32:09: #2 predicted fragment length is 3 bps INFO @ Tue, 27 Jun 2017 16:32:09: #2 alternative fragment length(s) may be 3 bps INFO @ Tue, 27 Jun 2017 16:32:09: #2.2 Generate R script for model : SRX113313.10_model.r WARNING @ Tue, 27 Jun 2017 16:32:09: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:32:09: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Tue, 27 Jun 2017 16:32:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 16:32:09: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:32:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:32:09: 19000000 INFO @ Tue, 27 Jun 2017 16:32:14: 20000000 INFO @ Tue, 27 Jun 2017 16:32:15: #1 tag size is determined as 44 bps INFO @ Tue, 27 Jun 2017 16:32:15: #1 tag size = 44 INFO @ Tue, 27 Jun 2017 16:32:15: #1 total tags in treatment: 20188864 INFO @ Tue, 27 Jun 2017 16:32:15: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:32:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 16:32:15: #1 tags after filtering in treatment: 20188864 INFO @ Tue, 27 Jun 2017 16:32:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 16:32:15: #1 finished! INFO @ Tue, 27 Jun 2017 16:32:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:32:16: 20000000 INFO @ Tue, 27 Jun 2017 16:32:17: #1 tag size is determined as 44 bps INFO @ Tue, 27 Jun 2017 16:32:17: #1 tag size = 44 INFO @ Tue, 27 Jun 2017 16:32:17: #1 total tags in treatment: 20188864 INFO @ Tue, 27 Jun 2017 16:32:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:32:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 16:32:17: #2 number of paired peaks: 457 WARNING @ Tue, 27 Jun 2017 16:32:17: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Tue, 27 Jun 2017 16:32:17: start model_add_line... INFO @ Tue, 27 Jun 2017 16:32:17: start X-correlation... INFO @ Tue, 27 Jun 2017 16:32:17: end of X-cor INFO @ Tue, 27 Jun 2017 16:32:17: #2 finished! INFO @ Tue, 27 Jun 2017 16:32:17: #2 predicted fragment length is 3 bps INFO @ Tue, 27 Jun 2017 16:32:17: #2 alternative fragment length(s) may be 3 bps INFO @ Tue, 27 Jun 2017 16:32:17: #2.2 Generate R script for model : SRX113313.20_model.r WARNING @ Tue, 27 Jun 2017 16:32:17: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:32:17: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Tue, 27 Jun 2017 16:32:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 16:32:17: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:32:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:32:17: #1 tags after filtering in treatment: 20188864 INFO @ Tue, 27 Jun 2017 16:32:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 16:32:17: #1 finished! INFO @ Tue, 27 Jun 2017 16:32:17: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:32:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:32:19: #2 number of paired peaks: 457 WARNING @ Tue, 27 Jun 2017 16:32:19: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Tue, 27 Jun 2017 16:32:19: start model_add_line... INFO @ Tue, 27 Jun 2017 16:32:19: start X-correlation... INFO @ Tue, 27 Jun 2017 16:32:19: end of X-cor INFO @ Tue, 27 Jun 2017 16:32:19: #2 finished! INFO @ Tue, 27 Jun 2017 16:32:19: #2 predicted fragment length is 3 bps INFO @ Tue, 27 Jun 2017 16:32:19: #2 alternative fragment length(s) may be 3 bps INFO @ Tue, 27 Jun 2017 16:32:19: #2.2 Generate R script for model : SRX113313.05_model.r WARNING @ Tue, 27 Jun 2017 16:32:19: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:32:19: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Tue, 27 Jun 2017 16:32:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 16:32:19: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:32:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:32:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:32:54: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:32:58: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:33:13: #4 Write output xls file... SRX113313.10_peaks.xls INFO @ Tue, 27 Jun 2017 16:33:13: #4 Write peak in narrowPeak format file... SRX113313.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:33:13: #4 Write summits bed file... SRX113313.10_summits.bed INFO @ Tue, 27 Jun 2017 16:33:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 16:33:16: #4 Write output xls file... SRX113313.20_peaks.xls INFO @ Tue, 27 Jun 2017 16:33:16: #4 Write peak in narrowPeak format file... SRX113313.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:33:16: #4 Write summits bed file... SRX113313.20_summits.bed INFO @ Tue, 27 Jun 2017 16:33:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 16:33:17: #4 Write output xls file... SRX113313.05_peaks.xls INFO @ Tue, 27 Jun 2017 16:33:17: #4 Write peak in narrowPeak format file... SRX113313.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:33:17: #4 Write summits bed file... SRX113313.05_summits.bed INFO @ Tue, 27 Jun 2017 16:33:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。