Job ID = 2590481 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,704,488 reads read : 15,408,976 reads written : 7,704,488 reads 0-length : 7,704,488 spots read : 7,694,255 reads read : 15,388,510 reads written : 7,694,255 reads 0-length : 7,694,255 spots read : 7,728,309 reads read : 15,456,618 reads written : 7,728,309 reads 0-length : 7,728,309 spots read : 7,763,872 reads read : 15,527,744 reads written : 7,763,872 reads 0-length : 7,763,872 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: 00:10:15 30890924 reads; of these: 30890924 (100.00%) were unpaired; of these: 1137975 (3.68%) aligned 0 times 22596010 (73.15%) aligned exactly 1 time 7156939 (23.17%) aligned >1 times 96.32% overall alignment rate Time searching: 00:10:15 Overall time: 00:10:15 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 16 files... [bam_rmdupse_core] 4289131 / 29752949 = 0.1442 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 @ Mon, 12 Aug 2019 22:21:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.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 @ Mon, 12 Aug 2019 22:21:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:21:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:21:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.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 @ Mon, 12 Aug 2019 22:21:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:21:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:21:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.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 @ Mon, 12 Aug 2019 22:21:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:21:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:21:08: 1000000 INFO @ Mon, 12 Aug 2019 22:21:11: 1000000 INFO @ Mon, 12 Aug 2019 22:21:11: 1000000 INFO @ Mon, 12 Aug 2019 22:21:16: 2000000 INFO @ Mon, 12 Aug 2019 22:21:20: 2000000 INFO @ Mon, 12 Aug 2019 22:21:20: 2000000 INFO @ Mon, 12 Aug 2019 22:21:23: 3000000 INFO @ Mon, 12 Aug 2019 22:21:28: 3000000 INFO @ Mon, 12 Aug 2019 22:21:29: 3000000 INFO @ Mon, 12 Aug 2019 22:21:31: 4000000 INFO @ Mon, 12 Aug 2019 22:21:36: 4000000 INFO @ Mon, 12 Aug 2019 22:21:38: 4000000 INFO @ Mon, 12 Aug 2019 22:21:38: 5000000 INFO @ Mon, 12 Aug 2019 22:21:45: 5000000 INFO @ Mon, 12 Aug 2019 22:21:46: 6000000 INFO @ Mon, 12 Aug 2019 22:21:47: 5000000 INFO @ Mon, 12 Aug 2019 22:21:53: 6000000 INFO @ Mon, 12 Aug 2019 22:21:53: 7000000 INFO @ Mon, 12 Aug 2019 22:21:56: 6000000 INFO @ Mon, 12 Aug 2019 22:22:01: 8000000 INFO @ Mon, 12 Aug 2019 22:22:02: 7000000 INFO @ Mon, 12 Aug 2019 22:22:04: 7000000 INFO @ Mon, 12 Aug 2019 22:22:08: 9000000 INFO @ Mon, 12 Aug 2019 22:22:10: 8000000 INFO @ Mon, 12 Aug 2019 22:22:13: 8000000 INFO @ Mon, 12 Aug 2019 22:22:16: 10000000 INFO @ Mon, 12 Aug 2019 22:22:18: 9000000 INFO @ Mon, 12 Aug 2019 22:22:22: 9000000 INFO @ Mon, 12 Aug 2019 22:22:23: 11000000 INFO @ Mon, 12 Aug 2019 22:22:27: 10000000 INFO @ Mon, 12 Aug 2019 22:22:31: 10000000 INFO @ Mon, 12 Aug 2019 22:22:31: 12000000 INFO @ Mon, 12 Aug 2019 22:22:35: 11000000 INFO @ Mon, 12 Aug 2019 22:22:39: 13000000 INFO @ Mon, 12 Aug 2019 22:22:40: 11000000 INFO @ Mon, 12 Aug 2019 22:22:43: 12000000 INFO @ Mon, 12 Aug 2019 22:22:47: 14000000 INFO @ Mon, 12 Aug 2019 22:22:49: 12000000 INFO @ Mon, 12 Aug 2019 22:22:52: 13000000 INFO @ Mon, 12 Aug 2019 22:22:55: 15000000 INFO @ Mon, 12 Aug 2019 22:22:58: 13000000 INFO @ Mon, 12 Aug 2019 22:23:01: 14000000 INFO @ Mon, 12 Aug 2019 22:23:03: 16000000 INFO @ Mon, 12 Aug 2019 22:23:08: 14000000 INFO @ Mon, 12 Aug 2019 22:23:10: 15000000 INFO @ Mon, 12 Aug 2019 22:23:11: 17000000 INFO @ Mon, 12 Aug 2019 22:23:17: 15000000 INFO @ Mon, 12 Aug 2019 22:23:18: 18000000 INFO @ Mon, 12 Aug 2019 22:23:18: 16000000 INFO @ Mon, 12 Aug 2019 22:23:26: 19000000 INFO @ Mon, 12 Aug 2019 22:23:27: 17000000 INFO @ Mon, 12 Aug 2019 22:23:28: 16000000 INFO @ Mon, 12 Aug 2019 22:23:33: 20000000 INFO @ Mon, 12 Aug 2019 22:23:36: 18000000 INFO @ Mon, 12 Aug 2019 22:23:37: 17000000 INFO @ Mon, 12 Aug 2019 22:23:41: 21000000 INFO @ Mon, 12 Aug 2019 22:23:44: 19000000 INFO @ Mon, 12 Aug 2019 22:23:47: 18000000 INFO @ Mon, 12 Aug 2019 22:23:48: 22000000 INFO @ Mon, 12 Aug 2019 22:23:52: 20000000 INFO @ Mon, 12 Aug 2019 22:23:56: 23000000 INFO @ Mon, 12 Aug 2019 22:23:56: 19000000 INFO @ Mon, 12 Aug 2019 22:24:00: 21000000 INFO @ Mon, 12 Aug 2019 22:24:03: 24000000 INFO @ Mon, 12 Aug 2019 22:24:05: 20000000 INFO @ Mon, 12 Aug 2019 22:24:08: 22000000 INFO @ Mon, 12 Aug 2019 22:24:11: 25000000 INFO @ Mon, 12 Aug 2019 22:24:14: 21000000 INFO @ Mon, 12 Aug 2019 22:24:14: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:24:14: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:24:14: #1 total tags in treatment: 25463818 INFO @ Mon, 12 Aug 2019 22:24:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:24:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:24:15: #1 tags after filtering in treatment: 25463818 INFO @ Mon, 12 Aug 2019 22:24:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:24:15: #1 finished! INFO @ Mon, 12 Aug 2019 22:24:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:24:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:24:16: 23000000 INFO @ Mon, 12 Aug 2019 22:24:17: #2 number of paired peaks: 291 WARNING @ Mon, 12 Aug 2019 22:24:17: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Mon, 12 Aug 2019 22:24:17: start model_add_line... INFO @ Mon, 12 Aug 2019 22:24:17: start X-correlation... INFO @ Mon, 12 Aug 2019 22:24:17: end of X-cor INFO @ Mon, 12 Aug 2019 22:24:17: #2 finished! INFO @ Mon, 12 Aug 2019 22:24:17: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 22:24:17: #2 alternative fragment length(s) may be 2,49 bps INFO @ Mon, 12 Aug 2019 22:24:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.05_model.r WARNING @ Mon, 12 Aug 2019 22:24:17: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:24:17: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Mon, 12 Aug 2019 22:24:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:24:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:24:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:24:23: 22000000 INFO @ Mon, 12 Aug 2019 22:24:24: 24000000 INFO @ Mon, 12 Aug 2019 22:24:32: 25000000 INFO @ Mon, 12 Aug 2019 22:24:32: 23000000 INFO @ Mon, 12 Aug 2019 22:24:36: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:24:36: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:24:36: #1 total tags in treatment: 25463818 INFO @ Mon, 12 Aug 2019 22:24:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:24:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:24:36: #1 tags after filtering in treatment: 25463818 INFO @ Mon, 12 Aug 2019 22:24:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:24:36: #1 finished! INFO @ Mon, 12 Aug 2019 22:24:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:24:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:24:38: #2 number of paired peaks: 291 WARNING @ Mon, 12 Aug 2019 22:24:38: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Mon, 12 Aug 2019 22:24:38: start model_add_line... INFO @ Mon, 12 Aug 2019 22:24:38: start X-correlation... INFO @ Mon, 12 Aug 2019 22:24:38: end of X-cor INFO @ Mon, 12 Aug 2019 22:24:38: #2 finished! INFO @ Mon, 12 Aug 2019 22:24:38: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 22:24:38: #2 alternative fragment length(s) may be 2,49 bps INFO @ Mon, 12 Aug 2019 22:24:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.20_model.r WARNING @ Mon, 12 Aug 2019 22:24:38: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:24:38: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Mon, 12 Aug 2019 22:24:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:24:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:24:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:24:41: 24000000 INFO @ Mon, 12 Aug 2019 22:24:49: 25000000 INFO @ Mon, 12 Aug 2019 22:24:53: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:24:53: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:24:53: #1 total tags in treatment: 25463818 INFO @ Mon, 12 Aug 2019 22:24:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:24:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:24:54: #1 tags after filtering in treatment: 25463818 INFO @ Mon, 12 Aug 2019 22:24:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:24:54: #1 finished! INFO @ Mon, 12 Aug 2019 22:24:54: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:24:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:24:56: #2 number of paired peaks: 291 WARNING @ Mon, 12 Aug 2019 22:24:56: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Mon, 12 Aug 2019 22:24:56: start model_add_line... INFO @ Mon, 12 Aug 2019 22:24:56: start X-correlation... INFO @ Mon, 12 Aug 2019 22:24:56: end of X-cor INFO @ Mon, 12 Aug 2019 22:24:56: #2 finished! INFO @ Mon, 12 Aug 2019 22:24:56: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 22:24:56: #2 alternative fragment length(s) may be 2,49 bps INFO @ Mon, 12 Aug 2019 22:24:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.10_model.r WARNING @ Mon, 12 Aug 2019 22:24:56: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:24:56: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Mon, 12 Aug 2019 22:24:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:24:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:24:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:25:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:25:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:25:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:25:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:25:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.05_summits.bed INFO @ Mon, 12 Aug 2019 22:25:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3793 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:25:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:26:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:26:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:26:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.20_summits.bed INFO @ Mon, 12 Aug 2019 22:26:12: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (552 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:26:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:26:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:26:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981711/SRX3981711.10_summits.bed INFO @ Mon, 12 Aug 2019 22:26:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1688 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。