Job ID = 1293639 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,324,819 reads read : 18,324,819 reads written : 18,324,819 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:07:42 18324819 reads; of these: 18324819 (100.00%) were unpaired; of these: 510990 (2.79%) aligned 0 times 13118741 (71.59%) aligned exactly 1 time 4695088 (25.62%) aligned >1 times 97.21% overall alignment rate Time searching: 00:07:42 Overall time: 00:07:42 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] 3758507 / 17813829 = 0.2110 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, 03 Jun 2019 01:26:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.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, 03 Jun 2019 01:26:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:26:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:26:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.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, 03 Jun 2019 01:26:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:26:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:26:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.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, 03 Jun 2019 01:26:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:26:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:26:15: 1000000 INFO @ Mon, 03 Jun 2019 01:26:17: 1000000 INFO @ Mon, 03 Jun 2019 01:26:17: 1000000 INFO @ Mon, 03 Jun 2019 01:26:21: 2000000 INFO @ Mon, 03 Jun 2019 01:26:26: 2000000 INFO @ Mon, 03 Jun 2019 01:26:26: 2000000 INFO @ Mon, 03 Jun 2019 01:26:27: 3000000 INFO @ Mon, 03 Jun 2019 01:26:34: 4000000 INFO @ Mon, 03 Jun 2019 01:26:34: 3000000 INFO @ Mon, 03 Jun 2019 01:26:34: 3000000 INFO @ Mon, 03 Jun 2019 01:26:40: 5000000 INFO @ Mon, 03 Jun 2019 01:26:42: 4000000 INFO @ Mon, 03 Jun 2019 01:26:42: 4000000 INFO @ Mon, 03 Jun 2019 01:26:46: 6000000 INFO @ Mon, 03 Jun 2019 01:26:50: 5000000 INFO @ Mon, 03 Jun 2019 01:26:51: 5000000 INFO @ Mon, 03 Jun 2019 01:26:53: 7000000 INFO @ Mon, 03 Jun 2019 01:26:59: 6000000 INFO @ Mon, 03 Jun 2019 01:26:59: 6000000 INFO @ Mon, 03 Jun 2019 01:26:59: 8000000 INFO @ Mon, 03 Jun 2019 01:27:06: 9000000 INFO @ Mon, 03 Jun 2019 01:27:07: 7000000 INFO @ Mon, 03 Jun 2019 01:27:07: 7000000 INFO @ Mon, 03 Jun 2019 01:27:12: 10000000 INFO @ Mon, 03 Jun 2019 01:27:15: 8000000 INFO @ Mon, 03 Jun 2019 01:27:15: 8000000 INFO @ Mon, 03 Jun 2019 01:27:18: 11000000 INFO @ Mon, 03 Jun 2019 01:27:24: 9000000 INFO @ Mon, 03 Jun 2019 01:27:24: 9000000 INFO @ Mon, 03 Jun 2019 01:27:25: 12000000 INFO @ Mon, 03 Jun 2019 01:27:31: 13000000 INFO @ Mon, 03 Jun 2019 01:27:32: 10000000 INFO @ Mon, 03 Jun 2019 01:27:32: 10000000 INFO @ Mon, 03 Jun 2019 01:27:37: 14000000 INFO @ Mon, 03 Jun 2019 01:27:38: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:27:38: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:27:38: #1 total tags in treatment: 14055322 INFO @ Mon, 03 Jun 2019 01:27:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:27:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:27:38: #1 tags after filtering in treatment: 14055322 INFO @ Mon, 03 Jun 2019 01:27:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:27:38: #1 finished! INFO @ Mon, 03 Jun 2019 01:27:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:27:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:27:39: #2 number of paired peaks: 360 WARNING @ Mon, 03 Jun 2019 01:27:39: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Mon, 03 Jun 2019 01:27:39: start model_add_line... INFO @ Mon, 03 Jun 2019 01:27:40: start X-correlation... INFO @ Mon, 03 Jun 2019 01:27:40: end of X-cor INFO @ Mon, 03 Jun 2019 01:27:40: #2 finished! INFO @ Mon, 03 Jun 2019 01:27:40: #2 predicted fragment length is 124 bps INFO @ Mon, 03 Jun 2019 01:27:40: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 03 Jun 2019 01:27:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.10_model.r INFO @ Mon, 03 Jun 2019 01:27:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:27:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:27:41: 11000000 INFO @ Mon, 03 Jun 2019 01:27:41: 11000000 INFO @ Mon, 03 Jun 2019 01:27:49: 12000000 INFO @ Mon, 03 Jun 2019 01:27:49: 12000000 INFO @ Mon, 03 Jun 2019 01:27:57: 13000000 INFO @ Mon, 03 Jun 2019 01:27:57: 13000000 INFO @ Mon, 03 Jun 2019 01:28:06: 14000000 INFO @ Mon, 03 Jun 2019 01:28:06: 14000000 INFO @ Mon, 03 Jun 2019 01:28:06: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:28:06: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:28:06: #1 total tags in treatment: 14055322 INFO @ Mon, 03 Jun 2019 01:28:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:28:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:28:06: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:28:06: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:28:06: #1 total tags in treatment: 14055322 INFO @ Mon, 03 Jun 2019 01:28:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:28:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:28:07: #1 tags after filtering in treatment: 14055322 INFO @ Mon, 03 Jun 2019 01:28:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:28:07: #1 finished! INFO @ Mon, 03 Jun 2019 01:28:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:28:07: #1 tags after filtering in treatment: 14055322 INFO @ Mon, 03 Jun 2019 01:28:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:28:07: #1 finished! INFO @ Mon, 03 Jun 2019 01:28:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:28:08: #2 number of paired peaks: 360 WARNING @ Mon, 03 Jun 2019 01:28:08: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Mon, 03 Jun 2019 01:28:08: start model_add_line... INFO @ Mon, 03 Jun 2019 01:28:08: #2 number of paired peaks: 360 WARNING @ Mon, 03 Jun 2019 01:28:08: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Mon, 03 Jun 2019 01:28:08: start model_add_line... INFO @ Mon, 03 Jun 2019 01:28:08: start X-correlation... INFO @ Mon, 03 Jun 2019 01:28:08: end of X-cor INFO @ Mon, 03 Jun 2019 01:28:08: #2 finished! INFO @ Mon, 03 Jun 2019 01:28:08: #2 predicted fragment length is 124 bps INFO @ Mon, 03 Jun 2019 01:28:08: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 03 Jun 2019 01:28:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.20_model.r INFO @ Mon, 03 Jun 2019 01:28:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:28:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:28:08: start X-correlation... INFO @ Mon, 03 Jun 2019 01:28:08: end of X-cor INFO @ Mon, 03 Jun 2019 01:28:08: #2 finished! INFO @ Mon, 03 Jun 2019 01:28:08: #2 predicted fragment length is 124 bps INFO @ Mon, 03 Jun 2019 01:28:08: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 03 Jun 2019 01:28:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.05_model.r INFO @ Mon, 03 Jun 2019 01:28:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:28:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:28:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:28:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:28:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:28:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.10_summits.bed INFO @ Mon, 03 Jun 2019 01:28:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2147 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:28:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:28:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:29:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:29:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:29:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.05_summits.bed INFO @ Mon, 03 Jun 2019 01:29:06: Done! INFO @ Mon, 03 Jun 2019 01:29:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:29:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:29:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032413/SRX1032413.20_summits.bed INFO @ Mon, 03 Jun 2019 01:29:06: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3853 records, 4 fields): 10 millis pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1348 records, 4 fields): 7 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。