Job ID = 2590477 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,102,119 reads read : 14,204,238 reads written : 7,102,119 reads 0-length : 7,102,119 spots read : 7,099,332 reads read : 14,198,664 reads written : 7,099,332 reads 0-length : 7,099,332 spots read : 7,127,665 reads read : 14,255,330 reads written : 7,127,665 reads 0-length : 7,127,665 spots read : 7,158,814 reads read : 14,317,628 reads written : 7,158,814 reads 0-length : 7,158,814 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: 00:10:23 28487930 reads; of these: 28487930 (100.00%) were unpaired; of these: 992500 (3.48%) aligned 0 times 20745230 (72.82%) aligned exactly 1 time 6750200 (23.69%) aligned >1 times 96.52% overall alignment rate Time searching: 00:10:23 Overall time: 00:10:23 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] 4091610 / 27495430 = 0.1488 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 22:18:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.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 22:18:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:18:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:18:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.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 22:18:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:18:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:18:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.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 22:18:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:18:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:18:54: 1000000 INFO @ Mon, 12 Aug 2019 22:18:58: 1000000 INFO @ Mon, 12 Aug 2019 22:18:59: 1000000 INFO @ Mon, 12 Aug 2019 22:19:01: 2000000 INFO @ Mon, 12 Aug 2019 22:19:07: 2000000 INFO @ Mon, 12 Aug 2019 22:19:07: 2000000 INFO @ Mon, 12 Aug 2019 22:19:08: 3000000 INFO @ Mon, 12 Aug 2019 22:19:15: 4000000 INFO @ Mon, 12 Aug 2019 22:19:15: 3000000 INFO @ Mon, 12 Aug 2019 22:19:16: 3000000 INFO @ Mon, 12 Aug 2019 22:19:21: 5000000 INFO @ Mon, 12 Aug 2019 22:19:24: 4000000 INFO @ Mon, 12 Aug 2019 22:19:26: 4000000 INFO @ Mon, 12 Aug 2019 22:19:28: 6000000 INFO @ Mon, 12 Aug 2019 22:19:33: 5000000 INFO @ Mon, 12 Aug 2019 22:19:35: 7000000 INFO @ Mon, 12 Aug 2019 22:19:35: 5000000 INFO @ Mon, 12 Aug 2019 22:19:41: 8000000 INFO @ Mon, 12 Aug 2019 22:19:42: 6000000 INFO @ Mon, 12 Aug 2019 22:19:44: 6000000 INFO @ Mon, 12 Aug 2019 22:19:48: 9000000 INFO @ Mon, 12 Aug 2019 22:19:50: 7000000 INFO @ Mon, 12 Aug 2019 22:19:54: 7000000 INFO @ Mon, 12 Aug 2019 22:19:55: 10000000 INFO @ Mon, 12 Aug 2019 22:19:59: 8000000 INFO @ Mon, 12 Aug 2019 22:20:01: 11000000 INFO @ Mon, 12 Aug 2019 22:20:03: 8000000 INFO @ Mon, 12 Aug 2019 22:20:07: 9000000 INFO @ Mon, 12 Aug 2019 22:20:08: 12000000 INFO @ Mon, 12 Aug 2019 22:20:12: 9000000 INFO @ Mon, 12 Aug 2019 22:20:15: 13000000 INFO @ Mon, 12 Aug 2019 22:20:15: 10000000 INFO @ Mon, 12 Aug 2019 22:20:21: 10000000 INFO @ Mon, 12 Aug 2019 22:20:21: 14000000 INFO @ Mon, 12 Aug 2019 22:20:24: 11000000 INFO @ Mon, 12 Aug 2019 22:20:28: 15000000 INFO @ Mon, 12 Aug 2019 22:20:30: 11000000 INFO @ Mon, 12 Aug 2019 22:20:32: 12000000 INFO @ Mon, 12 Aug 2019 22:20:34: 16000000 INFO @ Mon, 12 Aug 2019 22:20:39: 12000000 INFO @ Mon, 12 Aug 2019 22:20:40: 13000000 INFO @ Mon, 12 Aug 2019 22:20:41: 17000000 INFO @ Mon, 12 Aug 2019 22:20:48: 18000000 INFO @ Mon, 12 Aug 2019 22:20:48: 13000000 INFO @ Mon, 12 Aug 2019 22:20:48: 14000000 INFO @ Mon, 12 Aug 2019 22:20:54: 19000000 INFO @ Mon, 12 Aug 2019 22:20:56: 15000000 INFO @ Mon, 12 Aug 2019 22:20:57: 14000000 INFO @ Mon, 12 Aug 2019 22:21:01: 20000000 INFO @ Mon, 12 Aug 2019 22:21:04: 16000000 INFO @ Mon, 12 Aug 2019 22:21:06: 15000000 INFO @ Mon, 12 Aug 2019 22:21:08: 21000000 INFO @ Mon, 12 Aug 2019 22:21:13: 17000000 INFO @ Mon, 12 Aug 2019 22:21:14: 22000000 INFO @ Mon, 12 Aug 2019 22:21:15: 16000000 INFO @ Mon, 12 Aug 2019 22:21:21: 18000000 INFO @ Mon, 12 Aug 2019 22:21:21: 23000000 INFO @ Mon, 12 Aug 2019 22:21:24: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:21:24: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:21:24: #1 total tags in treatment: 23403820 INFO @ Mon, 12 Aug 2019 22:21:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:21:24: #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 22:21:24: 17000000 INFO @ Mon, 12 Aug 2019 22:21:25: #1 tags after filtering in treatment: 23403820 INFO @ Mon, 12 Aug 2019 22:21:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:21:25: #1 finished! INFO @ Mon, 12 Aug 2019 22:21:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:21:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:21:26: #2 number of paired peaks: 213 WARNING @ Mon, 12 Aug 2019 22:21:26: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 12 Aug 2019 22:21:26: start model_add_line... INFO @ Mon, 12 Aug 2019 22:21:27: start X-correlation... INFO @ Mon, 12 Aug 2019 22:21:27: end of X-cor INFO @ Mon, 12 Aug 2019 22:21:27: #2 finished! INFO @ Mon, 12 Aug 2019 22:21:27: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 22:21:27: #2 alternative fragment length(s) may be 2,49,588 bps INFO @ Mon, 12 Aug 2019 22:21:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.05_model.r WARNING @ Mon, 12 Aug 2019 22:21:27: #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 22:21:27: #2 You may need to consider one of the other alternative d(s): 2,49,588 WARNING @ Mon, 12 Aug 2019 22:21:27: #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 22:21:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:21:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:21:29: 19000000 INFO @ Mon, 12 Aug 2019 22:21:34: 18000000 INFO @ Mon, 12 Aug 2019 22:21:37: 20000000 INFO @ Mon, 12 Aug 2019 22:21:43: 19000000 INFO @ Mon, 12 Aug 2019 22:21:45: 21000000 INFO @ Mon, 12 Aug 2019 22:21:53: 20000000 INFO @ Mon, 12 Aug 2019 22:21:53: 22000000 INFO @ Mon, 12 Aug 2019 22:22:02: 23000000 INFO @ Mon, 12 Aug 2019 22:22:03: 21000000 INFO @ Mon, 12 Aug 2019 22:22:05: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:22:05: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:22:05: #1 total tags in treatment: 23403820 INFO @ Mon, 12 Aug 2019 22:22:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:22:05: #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 22:22:06: #1 tags after filtering in treatment: 23403820 INFO @ Mon, 12 Aug 2019 22:22:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:22:06: #1 finished! INFO @ Mon, 12 Aug 2019 22:22:06: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:22:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:22:08: #2 number of paired peaks: 213 WARNING @ Mon, 12 Aug 2019 22:22:08: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 12 Aug 2019 22:22:08: start model_add_line... INFO @ Mon, 12 Aug 2019 22:22:08: start X-correlation... INFO @ Mon, 12 Aug 2019 22:22:08: end of X-cor INFO @ Mon, 12 Aug 2019 22:22:08: #2 finished! INFO @ Mon, 12 Aug 2019 22:22:08: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 22:22:08: #2 alternative fragment length(s) may be 2,49,588 bps INFO @ Mon, 12 Aug 2019 22:22:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.10_model.r WARNING @ Mon, 12 Aug 2019 22:22:08: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:22:08: #2 You may need to consider one of the other alternative d(s): 2,49,588 WARNING @ Mon, 12 Aug 2019 22:22:08: #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 22:22:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:22:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:22:12: 22000000 INFO @ Mon, 12 Aug 2019 22:22:21: 23000000 INFO @ Mon, 12 Aug 2019 22:22:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:22:25: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:22:25: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:22:25: #1 total tags in treatment: 23403820 INFO @ Mon, 12 Aug 2019 22:22:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:22:25: #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 22:22:26: #1 tags after filtering in treatment: 23403820 INFO @ Mon, 12 Aug 2019 22:22:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:22:26: #1 finished! INFO @ Mon, 12 Aug 2019 22:22:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:22:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:22:28: #2 number of paired peaks: 213 WARNING @ Mon, 12 Aug 2019 22:22:28: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 12 Aug 2019 22:22:28: start model_add_line... INFO @ Mon, 12 Aug 2019 22:22:28: start X-correlation... INFO @ Mon, 12 Aug 2019 22:22:28: end of X-cor INFO @ Mon, 12 Aug 2019 22:22:28: #2 finished! INFO @ Mon, 12 Aug 2019 22:22:28: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 22:22:28: #2 alternative fragment length(s) may be 2,49,588 bps INFO @ Mon, 12 Aug 2019 22:22:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.20_model.r WARNING @ Mon, 12 Aug 2019 22:22:28: #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 22:22:28: #2 You may need to consider one of the other alternative d(s): 2,49,588 WARNING @ Mon, 12 Aug 2019 22:22:28: #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 22:22:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:22:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:22:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:22:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:22:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.05_summits.bed INFO @ Mon, 12 Aug 2019 22:22:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2915 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:23:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:23:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:23:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:23:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:23:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.10_summits.bed INFO @ Mon, 12 Aug 2019 22:23:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1407 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:23:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:23:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:23:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981707/SRX3981707.20_summits.bed INFO @ Mon, 12 Aug 2019 22:23:55: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (465 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。