Job ID = 2590483 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,788,980 reads read : 17,577,960 reads written : 8,788,980 reads 0-length : 8,788,980 spots read : 8,781,857 reads read : 17,563,714 reads written : 8,781,857 reads 0-length : 8,781,857 spots read : 8,817,725 reads read : 17,635,450 reads written : 8,817,725 reads 0-length : 8,817,725 spots read : 8,846,952 reads read : 17,693,904 reads written : 8,846,952 reads 0-length : 8,846,952 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: 00:12:46 35235514 reads; of these: 35235514 (100.00%) were unpaired; of these: 1224748 (3.48%) aligned 0 times 24921905 (70.73%) aligned exactly 1 time 9088861 (25.79%) aligned >1 times 96.52% overall alignment rate Time searching: 00:12:46 Overall time: 00:12:46 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] 4783190 / 34010766 = 0.1406 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 22:25:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.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 22:25:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:25:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:25:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.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 22:25:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:25:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:25:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.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 22:25:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:25:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:26:02: 1000000 INFO @ Mon, 12 Aug 2019 22:26:04: 1000000 INFO @ Mon, 12 Aug 2019 22:26:04: 1000000 INFO @ Mon, 12 Aug 2019 22:26:11: 2000000 INFO @ Mon, 12 Aug 2019 22:26:12: 2000000 INFO @ Mon, 12 Aug 2019 22:26:12: 2000000 INFO @ Mon, 12 Aug 2019 22:26:20: 3000000 INFO @ Mon, 12 Aug 2019 22:26:20: 3000000 INFO @ Mon, 12 Aug 2019 22:26:21: 3000000 INFO @ Mon, 12 Aug 2019 22:26:28: 4000000 INFO @ Mon, 12 Aug 2019 22:26:28: 4000000 INFO @ Mon, 12 Aug 2019 22:26:30: 4000000 INFO @ Mon, 12 Aug 2019 22:26:36: 5000000 INFO @ Mon, 12 Aug 2019 22:26:37: 5000000 INFO @ Mon, 12 Aug 2019 22:26:38: 5000000 INFO @ Mon, 12 Aug 2019 22:26:44: 6000000 INFO @ Mon, 12 Aug 2019 22:26:46: 6000000 INFO @ Mon, 12 Aug 2019 22:26:47: 6000000 INFO @ Mon, 12 Aug 2019 22:26:52: 7000000 INFO @ Mon, 12 Aug 2019 22:26:55: 7000000 INFO @ Mon, 12 Aug 2019 22:26:56: 7000000 INFO @ Mon, 12 Aug 2019 22:27:00: 8000000 INFO @ Mon, 12 Aug 2019 22:27:04: 8000000 INFO @ Mon, 12 Aug 2019 22:27:05: 8000000 INFO @ Mon, 12 Aug 2019 22:27:08: 9000000 INFO @ Mon, 12 Aug 2019 22:27:12: 9000000 INFO @ Mon, 12 Aug 2019 22:27:14: 9000000 INFO @ Mon, 12 Aug 2019 22:27:16: 10000000 INFO @ Mon, 12 Aug 2019 22:27:21: 10000000 INFO @ Mon, 12 Aug 2019 22:27:23: 10000000 INFO @ Mon, 12 Aug 2019 22:27:24: 11000000 INFO @ Mon, 12 Aug 2019 22:27:30: 11000000 INFO @ Mon, 12 Aug 2019 22:27:32: 11000000 INFO @ Mon, 12 Aug 2019 22:27:32: 12000000 INFO @ Mon, 12 Aug 2019 22:27:39: 12000000 INFO @ Mon, 12 Aug 2019 22:27:40: 13000000 INFO @ Mon, 12 Aug 2019 22:27:40: 12000000 INFO @ Mon, 12 Aug 2019 22:27:48: 13000000 INFO @ Mon, 12 Aug 2019 22:27:48: 14000000 INFO @ Mon, 12 Aug 2019 22:27:49: 13000000 INFO @ Mon, 12 Aug 2019 22:27:55: 15000000 INFO @ Mon, 12 Aug 2019 22:27:56: 14000000 INFO @ Mon, 12 Aug 2019 22:27:58: 14000000 INFO @ Mon, 12 Aug 2019 22:28:04: 16000000 INFO @ Mon, 12 Aug 2019 22:28:04: 15000000 INFO @ Mon, 12 Aug 2019 22:28:06: 15000000 INFO @ Mon, 12 Aug 2019 22:28:13: 16000000 INFO @ Mon, 12 Aug 2019 22:28:13: 17000000 INFO @ Mon, 12 Aug 2019 22:28:15: 16000000 INFO @ Mon, 12 Aug 2019 22:28:20: 18000000 INFO @ Mon, 12 Aug 2019 22:28:21: 17000000 INFO @ Mon, 12 Aug 2019 22:28:22: 17000000 INFO @ Mon, 12 Aug 2019 22:28:27: 19000000 INFO @ Mon, 12 Aug 2019 22:28:28: 18000000 INFO @ Mon, 12 Aug 2019 22:28:30: 18000000 INFO @ Mon, 12 Aug 2019 22:28:34: 20000000 INFO @ Mon, 12 Aug 2019 22:28:36: 19000000 INFO @ Mon, 12 Aug 2019 22:28:38: 19000000 INFO @ Mon, 12 Aug 2019 22:28:41: 21000000 INFO @ Mon, 12 Aug 2019 22:28:44: 20000000 INFO @ Mon, 12 Aug 2019 22:28:46: 20000000 INFO @ Mon, 12 Aug 2019 22:28:48: 22000000 INFO @ Mon, 12 Aug 2019 22:28:52: 21000000 INFO @ Mon, 12 Aug 2019 22:28:54: 21000000 INFO @ Mon, 12 Aug 2019 22:28:55: 23000000 INFO @ Mon, 12 Aug 2019 22:29:00: 22000000 INFO @ Mon, 12 Aug 2019 22:29:02: 22000000 INFO @ Mon, 12 Aug 2019 22:29:02: 24000000 INFO @ Mon, 12 Aug 2019 22:29:07: 23000000 INFO @ Mon, 12 Aug 2019 22:29:09: 25000000 INFO @ Mon, 12 Aug 2019 22:29:09: 23000000 INFO @ Mon, 12 Aug 2019 22:29:15: 24000000 INFO @ Mon, 12 Aug 2019 22:29:15: 26000000 INFO @ Mon, 12 Aug 2019 22:29:17: 24000000 INFO @ Mon, 12 Aug 2019 22:29:22: 27000000 INFO @ Mon, 12 Aug 2019 22:29:22: 25000000 INFO @ Mon, 12 Aug 2019 22:29:24: 25000000 INFO @ Mon, 12 Aug 2019 22:29:29: 28000000 INFO @ Mon, 12 Aug 2019 22:29:30: 26000000 INFO @ Mon, 12 Aug 2019 22:29:32: 26000000 INFO @ Mon, 12 Aug 2019 22:29:35: 29000000 INFO @ Mon, 12 Aug 2019 22:29:37: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:29:37: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:29:37: #1 total tags in treatment: 29227576 INFO @ Mon, 12 Aug 2019 22:29:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:29:37: #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 22:29:38: 27000000 INFO @ Mon, 12 Aug 2019 22:29:38: #1 tags after filtering in treatment: 29227576 INFO @ Mon, 12 Aug 2019 22:29:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:29:38: #1 finished! INFO @ Mon, 12 Aug 2019 22:29:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:29:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:29:40: 27000000 INFO @ Mon, 12 Aug 2019 22:29:40: #2 number of paired peaks: 197 WARNING @ Mon, 12 Aug 2019 22:29:40: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Mon, 12 Aug 2019 22:29:40: start model_add_line... INFO @ Mon, 12 Aug 2019 22:29:41: start X-correlation... INFO @ Mon, 12 Aug 2019 22:29:41: end of X-cor INFO @ Mon, 12 Aug 2019 22:29:41: #2 finished! INFO @ Mon, 12 Aug 2019 22:29:41: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 22:29:41: #2 alternative fragment length(s) may be 2,52,590 bps INFO @ Mon, 12 Aug 2019 22:29:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.20_model.r WARNING @ Mon, 12 Aug 2019 22:29:41: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:29:41: #2 You may need to consider one of the other alternative d(s): 2,52,590 WARNING @ Mon, 12 Aug 2019 22:29:41: #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 22:29:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:29:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:29:45: 28000000 INFO @ Mon, 12 Aug 2019 22:29:47: 28000000 INFO @ Mon, 12 Aug 2019 22:29:53: 29000000 INFO @ Mon, 12 Aug 2019 22:29:55: 29000000 INFO @ Mon, 12 Aug 2019 22:29:55: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:29:55: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:29:55: #1 total tags in treatment: 29227576 INFO @ Mon, 12 Aug 2019 22:29:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:29:55: #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 22:29:55: #1 tags after filtering in treatment: 29227576 INFO @ Mon, 12 Aug 2019 22:29:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:29:55: #1 finished! INFO @ Mon, 12 Aug 2019 22:29:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:29:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:29:57: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:29:57: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:29:57: #1 total tags in treatment: 29227576 INFO @ Mon, 12 Aug 2019 22:29:57: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:29:57: #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 22:29:57: #1 tags after filtering in treatment: 29227576 INFO @ Mon, 12 Aug 2019 22:29:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:29:57: #1 finished! INFO @ Mon, 12 Aug 2019 22:29:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:29:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:29:58: #2 number of paired peaks: 197 WARNING @ Mon, 12 Aug 2019 22:29:58: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Mon, 12 Aug 2019 22:29:58: start model_add_line... INFO @ Mon, 12 Aug 2019 22:29:58: start X-correlation... INFO @ Mon, 12 Aug 2019 22:29:58: end of X-cor INFO @ Mon, 12 Aug 2019 22:29:58: #2 finished! INFO @ Mon, 12 Aug 2019 22:29:58: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 22:29:58: #2 alternative fragment length(s) may be 2,52,590 bps INFO @ Mon, 12 Aug 2019 22:29:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.05_model.r WARNING @ Mon, 12 Aug 2019 22:29:58: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:29:58: #2 You may need to consider one of the other alternative d(s): 2,52,590 WARNING @ Mon, 12 Aug 2019 22:29:58: #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 22:29:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:29:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:30:00: #2 number of paired peaks: 197 WARNING @ Mon, 12 Aug 2019 22:30:00: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Mon, 12 Aug 2019 22:30:00: start model_add_line... INFO @ Mon, 12 Aug 2019 22:30:00: start X-correlation... INFO @ Mon, 12 Aug 2019 22:30:00: end of X-cor INFO @ Mon, 12 Aug 2019 22:30:00: #2 finished! INFO @ Mon, 12 Aug 2019 22:30:00: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 22:30:00: #2 alternative fragment length(s) may be 2,52,590 bps INFO @ Mon, 12 Aug 2019 22:30:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.10_model.r WARNING @ Mon, 12 Aug 2019 22:30:00: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:30:00: #2 You may need to consider one of the other alternative d(s): 2,52,590 WARNING @ Mon, 12 Aug 2019 22:30:00: #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 22:30:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:30:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:30:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:31:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:31:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:31:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:31:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:31:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.20_summits.bed INFO @ Mon, 12 Aug 2019 22:31:22: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (595 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:31:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:31:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:31:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.05_summits.bed INFO @ Mon, 12 Aug 2019 22:31:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3629 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:31:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:31:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:31:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981712/SRX3981712.10_summits.bed INFO @ Mon, 12 Aug 2019 22:31:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1780 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。