Job ID = 2591015 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,444,454 reads read : 17,444,454 reads written : 17,444,454 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:05:34 17444454 reads; of these: 17444454 (100.00%) were unpaired; of these: 5141656 (29.47%) aligned 0 times 9163290 (52.53%) aligned exactly 1 time 3139508 (18.00%) aligned >1 times 70.53% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 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 8 files... [bam_rmdupse_core] 1341412 / 12302798 = 0.1090 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, 13 Aug 2019 00:43:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.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, 13 Aug 2019 00:43:18: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:43:18: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:43:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.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, 13 Aug 2019 00:43:19: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:43:19: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:43:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.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, 13 Aug 2019 00:43:20: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:43:20: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:43:26: 1000000 INFO @ Tue, 13 Aug 2019 00:43:27: 1000000 INFO @ Tue, 13 Aug 2019 00:43:27: 1000000 INFO @ Tue, 13 Aug 2019 00:43:34: 2000000 INFO @ Tue, 13 Aug 2019 00:43:35: 2000000 INFO @ Tue, 13 Aug 2019 00:43:35: 2000000 INFO @ Tue, 13 Aug 2019 00:43:41: 3000000 INFO @ Tue, 13 Aug 2019 00:43:42: 3000000 INFO @ Tue, 13 Aug 2019 00:43:44: 3000000 INFO @ Tue, 13 Aug 2019 00:43:48: 4000000 INFO @ Tue, 13 Aug 2019 00:43:50: 4000000 INFO @ Tue, 13 Aug 2019 00:43:52: 4000000 INFO @ Tue, 13 Aug 2019 00:43:55: 5000000 INFO @ Tue, 13 Aug 2019 00:43:57: 5000000 INFO @ Tue, 13 Aug 2019 00:44:01: 5000000 INFO @ Tue, 13 Aug 2019 00:44:02: 6000000 INFO @ Tue, 13 Aug 2019 00:44:05: 6000000 INFO @ Tue, 13 Aug 2019 00:44:09: 7000000 INFO @ Tue, 13 Aug 2019 00:44:09: 6000000 INFO @ Tue, 13 Aug 2019 00:44:12: 7000000 INFO @ Tue, 13 Aug 2019 00:44:16: 8000000 INFO @ Tue, 13 Aug 2019 00:44:17: 7000000 INFO @ Tue, 13 Aug 2019 00:44:19: 8000000 INFO @ Tue, 13 Aug 2019 00:44:22: 9000000 INFO @ Tue, 13 Aug 2019 00:44:26: 8000000 INFO @ Tue, 13 Aug 2019 00:44:27: 9000000 INFO @ Tue, 13 Aug 2019 00:44:29: 10000000 INFO @ Tue, 13 Aug 2019 00:44:34: 10000000 INFO @ Tue, 13 Aug 2019 00:44:34: 9000000 INFO @ Tue, 13 Aug 2019 00:44:36: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:44:36: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:44:36: #1 total tags in treatment: 10961386 INFO @ Tue, 13 Aug 2019 00:44:36: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:44:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:44:36: #1 tags after filtering in treatment: 10961386 INFO @ Tue, 13 Aug 2019 00:44:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:44:36: #1 finished! INFO @ Tue, 13 Aug 2019 00:44:36: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:44:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:44:37: #2 number of paired peaks: 246 WARNING @ Tue, 13 Aug 2019 00:44:37: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Tue, 13 Aug 2019 00:44:37: start model_add_line... INFO @ Tue, 13 Aug 2019 00:44:37: start X-correlation... INFO @ Tue, 13 Aug 2019 00:44:37: end of X-cor INFO @ Tue, 13 Aug 2019 00:44:37: #2 finished! INFO @ Tue, 13 Aug 2019 00:44:37: #2 predicted fragment length is 113 bps INFO @ Tue, 13 Aug 2019 00:44:37: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 13 Aug 2019 00:44:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.20_model.r INFO @ Tue, 13 Aug 2019 00:44:37: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:44:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:44:41: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:44:41: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:44:41: #1 total tags in treatment: 10961386 INFO @ Tue, 13 Aug 2019 00:44:41: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:44:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:44:41: #1 tags after filtering in treatment: 10961386 INFO @ Tue, 13 Aug 2019 00:44:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:44:41: #1 finished! INFO @ Tue, 13 Aug 2019 00:44:41: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:44:42: #2 number of paired peaks: 246 WARNING @ Tue, 13 Aug 2019 00:44:42: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Tue, 13 Aug 2019 00:44:42: start model_add_line... INFO @ Tue, 13 Aug 2019 00:44:43: 10000000 INFO @ Tue, 13 Aug 2019 00:44:43: start X-correlation... INFO @ Tue, 13 Aug 2019 00:44:43: end of X-cor INFO @ Tue, 13 Aug 2019 00:44:43: #2 finished! INFO @ Tue, 13 Aug 2019 00:44:43: #2 predicted fragment length is 113 bps INFO @ Tue, 13 Aug 2019 00:44:43: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 13 Aug 2019 00:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.10_model.r INFO @ Tue, 13 Aug 2019 00:44:43: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:44:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:44:51: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:44:51: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:44:51: #1 total tags in treatment: 10961386 INFO @ Tue, 13 Aug 2019 00:44:51: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:44:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:44:51: #1 tags after filtering in treatment: 10961386 INFO @ Tue, 13 Aug 2019 00:44:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:44:51: #1 finished! INFO @ Tue, 13 Aug 2019 00:44:51: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:44:52: #2 number of paired peaks: 246 WARNING @ Tue, 13 Aug 2019 00:44:52: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Tue, 13 Aug 2019 00:44:52: start model_add_line... INFO @ Tue, 13 Aug 2019 00:44:52: start X-correlation... INFO @ Tue, 13 Aug 2019 00:44:52: end of X-cor INFO @ Tue, 13 Aug 2019 00:44:52: #2 finished! INFO @ Tue, 13 Aug 2019 00:44:52: #2 predicted fragment length is 113 bps INFO @ Tue, 13 Aug 2019 00:44:52: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 13 Aug 2019 00:44:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.05_model.r INFO @ Tue, 13 Aug 2019 00:44:52: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:45:08: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:45:13: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:45:23: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:45:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.20_summits.bed INFO @ Tue, 13 Aug 2019 00:45:23: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1087 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:45:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:45:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:45:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.10_summits.bed INFO @ Tue, 13 Aug 2019 00:45:29: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1918 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:45:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:45:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:45:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661065/SRX661065.05_summits.bed INFO @ Tue, 13 Aug 2019 00:45:38: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3002 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。