Job ID = 1293905 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,471,875 reads read : 31,471,875 reads written : 31,471,875 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: 00:10:01 31471875 reads; of these: 31471875 (100.00%) were unpaired; of these: 2811182 (8.93%) aligned 0 times 21633816 (68.74%) aligned exactly 1 time 7026877 (22.33%) aligned >1 times 91.07% overall alignment rate Time searching: 00:10:01 Overall time: 00:10:01 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] 8266296 / 28660693 = 0.2884 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 03:22:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.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 03:22:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.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 03:22:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:22:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:22:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:22:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:22:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.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 03:22:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:22:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:22:33: 1000000 INFO @ Mon, 03 Jun 2019 03:22:33: 1000000 INFO @ Mon, 03 Jun 2019 03:22:35: 1000000 INFO @ Mon, 03 Jun 2019 03:22:41: 2000000 INFO @ Mon, 03 Jun 2019 03:22:41: 2000000 INFO @ Mon, 03 Jun 2019 03:22:45: 2000000 INFO @ Mon, 03 Jun 2019 03:22:49: 3000000 INFO @ Mon, 03 Jun 2019 03:22:49: 3000000 INFO @ Mon, 03 Jun 2019 03:22:55: 3000000 INFO @ Mon, 03 Jun 2019 03:22:57: 4000000 INFO @ Mon, 03 Jun 2019 03:22:57: 4000000 INFO @ Mon, 03 Jun 2019 03:23:04: 5000000 INFO @ Mon, 03 Jun 2019 03:23:04: 5000000 INFO @ Mon, 03 Jun 2019 03:23:05: 4000000 INFO @ Mon, 03 Jun 2019 03:23:12: 6000000 INFO @ Mon, 03 Jun 2019 03:23:12: 6000000 INFO @ Mon, 03 Jun 2019 03:23:14: 5000000 INFO @ Mon, 03 Jun 2019 03:23:20: 7000000 INFO @ Mon, 03 Jun 2019 03:23:20: 7000000 INFO @ Mon, 03 Jun 2019 03:23:23: 6000000 INFO @ Mon, 03 Jun 2019 03:23:28: 8000000 INFO @ Mon, 03 Jun 2019 03:23:28: 8000000 INFO @ Mon, 03 Jun 2019 03:23:33: 7000000 INFO @ Mon, 03 Jun 2019 03:23:36: 9000000 INFO @ Mon, 03 Jun 2019 03:23:36: 9000000 INFO @ Mon, 03 Jun 2019 03:23:44: 8000000 INFO @ Mon, 03 Jun 2019 03:23:45: 10000000 INFO @ Mon, 03 Jun 2019 03:23:45: 10000000 INFO @ Mon, 03 Jun 2019 03:23:53: 11000000 INFO @ Mon, 03 Jun 2019 03:23:53: 11000000 INFO @ Mon, 03 Jun 2019 03:23:54: 9000000 INFO @ Mon, 03 Jun 2019 03:24:01: 12000000 INFO @ Mon, 03 Jun 2019 03:24:01: 12000000 INFO @ Mon, 03 Jun 2019 03:24:04: 10000000 INFO @ Mon, 03 Jun 2019 03:24:09: 13000000 INFO @ Mon, 03 Jun 2019 03:24:09: 13000000 INFO @ Mon, 03 Jun 2019 03:24:15: 11000000 INFO @ Mon, 03 Jun 2019 03:24:17: 14000000 INFO @ Mon, 03 Jun 2019 03:24:17: 14000000 INFO @ Mon, 03 Jun 2019 03:24:25: 15000000 INFO @ Mon, 03 Jun 2019 03:24:25: 15000000 INFO @ Mon, 03 Jun 2019 03:24:25: 12000000 INFO @ Mon, 03 Jun 2019 03:24:33: 16000000 INFO @ Mon, 03 Jun 2019 03:24:33: 16000000 INFO @ Mon, 03 Jun 2019 03:24:35: 13000000 INFO @ Mon, 03 Jun 2019 03:24:40: 17000000 INFO @ Mon, 03 Jun 2019 03:24:40: 17000000 INFO @ Mon, 03 Jun 2019 03:24:45: 14000000 INFO @ Mon, 03 Jun 2019 03:24:48: 18000000 INFO @ Mon, 03 Jun 2019 03:24:48: 18000000 INFO @ Mon, 03 Jun 2019 03:24:55: 15000000 INFO @ Mon, 03 Jun 2019 03:24:56: 19000000 INFO @ Mon, 03 Jun 2019 03:24:56: 19000000 INFO @ Mon, 03 Jun 2019 03:25:04: 20000000 INFO @ Mon, 03 Jun 2019 03:25:04: 20000000 INFO @ Mon, 03 Jun 2019 03:25:05: 16000000 INFO @ Mon, 03 Jun 2019 03:25:07: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 03:25:07: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 03:25:07: #1 total tags in treatment: 20394397 INFO @ Mon, 03 Jun 2019 03:25:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:25:07: #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 03:25:07: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 03:25:07: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 03:25:07: #1 total tags in treatment: 20394397 INFO @ Mon, 03 Jun 2019 03:25:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:25:07: #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 03:25:07: #1 tags after filtering in treatment: 20394397 INFO @ Mon, 03 Jun 2019 03:25:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:25:07: #1 finished! INFO @ Mon, 03 Jun 2019 03:25:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:25:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:25:08: #1 tags after filtering in treatment: 20394397 INFO @ Mon, 03 Jun 2019 03:25:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:25:08: #1 finished! INFO @ Mon, 03 Jun 2019 03:25:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:25:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:25:09: #2 number of paired peaks: 577 WARNING @ Mon, 03 Jun 2019 03:25:09: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Mon, 03 Jun 2019 03:25:09: start model_add_line... INFO @ Mon, 03 Jun 2019 03:25:09: start X-correlation... INFO @ Mon, 03 Jun 2019 03:25:09: end of X-cor INFO @ Mon, 03 Jun 2019 03:25:09: #2 finished! INFO @ Mon, 03 Jun 2019 03:25:09: #2 predicted fragment length is 92 bps INFO @ Mon, 03 Jun 2019 03:25:09: #2 alternative fragment length(s) may be 4,92 bps INFO @ Mon, 03 Jun 2019 03:25:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.20_model.r INFO @ Mon, 03 Jun 2019 03:25:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:25:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:25:09: #2 number of paired peaks: 577 WARNING @ Mon, 03 Jun 2019 03:25:09: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Mon, 03 Jun 2019 03:25:09: start model_add_line... INFO @ Mon, 03 Jun 2019 03:25:10: start X-correlation... INFO @ Mon, 03 Jun 2019 03:25:10: end of X-cor INFO @ Mon, 03 Jun 2019 03:25:10: #2 finished! INFO @ Mon, 03 Jun 2019 03:25:10: #2 predicted fragment length is 92 bps INFO @ Mon, 03 Jun 2019 03:25:10: #2 alternative fragment length(s) may be 4,92 bps INFO @ Mon, 03 Jun 2019 03:25:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.10_model.r INFO @ Mon, 03 Jun 2019 03:25:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:25:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:25:15: 17000000 INFO @ Mon, 03 Jun 2019 03:25:24: 18000000 INFO @ Mon, 03 Jun 2019 03:25:34: 19000000 INFO @ Mon, 03 Jun 2019 03:25:44: 20000000 INFO @ Mon, 03 Jun 2019 03:25:47: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 03:25:47: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 03:25:47: #1 total tags in treatment: 20394397 INFO @ Mon, 03 Jun 2019 03:25:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:25:47: #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 03:25:48: #1 tags after filtering in treatment: 20394397 INFO @ Mon, 03 Jun 2019 03:25:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:25:48: #1 finished! INFO @ Mon, 03 Jun 2019 03:25:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:25:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:25:49: #2 number of paired peaks: 577 WARNING @ Mon, 03 Jun 2019 03:25:49: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Mon, 03 Jun 2019 03:25:49: start model_add_line... INFO @ Mon, 03 Jun 2019 03:25:50: start X-correlation... INFO @ Mon, 03 Jun 2019 03:25:50: end of X-cor INFO @ Mon, 03 Jun 2019 03:25:50: #2 finished! INFO @ Mon, 03 Jun 2019 03:25:50: #2 predicted fragment length is 92 bps INFO @ Mon, 03 Jun 2019 03:25:50: #2 alternative fragment length(s) may be 4,92 bps INFO @ Mon, 03 Jun 2019 03:25:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.05_model.r INFO @ Mon, 03 Jun 2019 03:25:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:25:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:26:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:26:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:26:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:26:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:26:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.20_summits.bed INFO @ Mon, 03 Jun 2019 03:26:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1625 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:26:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:26:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:26:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.10_summits.bed INFO @ Mon, 03 Jun 2019 03:26:29: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5134 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:26:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:27:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:27:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:27:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX147000/SRX147000.05_summits.bed INFO @ Mon, 03 Jun 2019 03:27:11: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (16348 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。