Job ID = 2590797 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 38,041,560 reads read : 76,083,120 reads written : 38,041,560 reads 0-length : 38,041,560 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: 00:13:11 38041560 reads; of these: 38041560 (100.00%) were unpaired; of these: 3241028 (8.52%) aligned 0 times 26421016 (69.45%) aligned exactly 1 time 8379516 (22.03%) aligned >1 times 91.48% overall alignment rate Time searching: 00:13:11 Overall time: 00:13:11 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] 14907497 / 34800532 = 0.4284 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 23:42:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.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 23:42:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:42:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:42:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.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 23:42:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:42:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:42:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.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 23:42:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:42:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:42:45: 1000000 INFO @ Mon, 12 Aug 2019 23:42:48: 1000000 INFO @ Mon, 12 Aug 2019 23:42:49: 1000000 INFO @ Mon, 12 Aug 2019 23:42:53: 2000000 INFO @ Mon, 12 Aug 2019 23:42:57: 2000000 INFO @ Mon, 12 Aug 2019 23:42:59: 2000000 INFO @ Mon, 12 Aug 2019 23:43:00: 3000000 INFO @ Mon, 12 Aug 2019 23:43:06: 3000000 INFO @ Mon, 12 Aug 2019 23:43:08: 4000000 INFO @ Mon, 12 Aug 2019 23:43:08: 3000000 INFO @ Mon, 12 Aug 2019 23:43:15: 4000000 INFO @ Mon, 12 Aug 2019 23:43:15: 5000000 INFO @ Mon, 12 Aug 2019 23:43:17: 4000000 INFO @ Mon, 12 Aug 2019 23:43:22: 6000000 INFO @ Mon, 12 Aug 2019 23:43:24: 5000000 INFO @ Mon, 12 Aug 2019 23:43:27: 5000000 INFO @ Mon, 12 Aug 2019 23:43:30: 7000000 INFO @ Mon, 12 Aug 2019 23:43:33: 6000000 INFO @ Mon, 12 Aug 2019 23:43:36: 6000000 INFO @ Mon, 12 Aug 2019 23:43:37: 8000000 INFO @ Mon, 12 Aug 2019 23:43:42: 7000000 INFO @ Mon, 12 Aug 2019 23:43:45: 9000000 INFO @ Mon, 12 Aug 2019 23:43:45: 7000000 INFO @ Mon, 12 Aug 2019 23:43:51: 8000000 INFO @ Mon, 12 Aug 2019 23:43:52: 10000000 INFO @ Mon, 12 Aug 2019 23:43:55: 8000000 INFO @ Mon, 12 Aug 2019 23:44:00: 11000000 INFO @ Mon, 12 Aug 2019 23:44:00: 9000000 INFO @ Mon, 12 Aug 2019 23:44:05: 9000000 INFO @ Mon, 12 Aug 2019 23:44:07: 12000000 INFO @ Mon, 12 Aug 2019 23:44:09: 10000000 INFO @ Mon, 12 Aug 2019 23:44:15: 13000000 INFO @ Mon, 12 Aug 2019 23:44:17: 10000000 INFO @ Mon, 12 Aug 2019 23:44:18: 11000000 INFO @ Mon, 12 Aug 2019 23:44:24: 14000000 INFO @ Mon, 12 Aug 2019 23:44:27: 12000000 INFO @ Mon, 12 Aug 2019 23:44:28: 11000000 INFO @ Mon, 12 Aug 2019 23:44:32: 15000000 INFO @ Mon, 12 Aug 2019 23:44:36: 13000000 INFO @ Mon, 12 Aug 2019 23:44:39: 12000000 INFO @ Mon, 12 Aug 2019 23:44:41: 16000000 INFO @ Mon, 12 Aug 2019 23:44:44: 14000000 INFO @ Mon, 12 Aug 2019 23:44:49: 17000000 INFO @ Mon, 12 Aug 2019 23:44:51: 13000000 INFO @ Mon, 12 Aug 2019 23:44:53: 15000000 INFO @ Mon, 12 Aug 2019 23:44:56: 18000000 INFO @ Mon, 12 Aug 2019 23:45:02: 14000000 INFO @ Mon, 12 Aug 2019 23:45:02: 16000000 INFO @ Mon, 12 Aug 2019 23:45:03: 19000000 INFO @ Mon, 12 Aug 2019 23:45:10: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:45:10: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:45:10: #1 total tags in treatment: 19893035 INFO @ Mon, 12 Aug 2019 23:45:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:45:10: #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 23:45:10: #1 tags after filtering in treatment: 19893035 INFO @ Mon, 12 Aug 2019 23:45:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:45:10: #1 finished! INFO @ Mon, 12 Aug 2019 23:45:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:45:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:45:11: 17000000 INFO @ Mon, 12 Aug 2019 23:45:12: #2 number of paired peaks: 866 WARNING @ Mon, 12 Aug 2019 23:45:12: Fewer paired peaks (866) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 866 pairs to build model! INFO @ Mon, 12 Aug 2019 23:45:12: start model_add_line... INFO @ Mon, 12 Aug 2019 23:45:12: start X-correlation... INFO @ Mon, 12 Aug 2019 23:45:12: end of X-cor INFO @ Mon, 12 Aug 2019 23:45:12: #2 finished! INFO @ Mon, 12 Aug 2019 23:45:12: #2 predicted fragment length is 235 bps INFO @ Mon, 12 Aug 2019 23:45:12: #2 alternative fragment length(s) may be 235 bps INFO @ Mon, 12 Aug 2019 23:45:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.05_model.r INFO @ Mon, 12 Aug 2019 23:45:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:45:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:45:13: 15000000 INFO @ Mon, 12 Aug 2019 23:45:20: 18000000 INFO @ Mon, 12 Aug 2019 23:45:24: 16000000 INFO @ Mon, 12 Aug 2019 23:45:28: 19000000 INFO @ Mon, 12 Aug 2019 23:45:36: 17000000 INFO @ Mon, 12 Aug 2019 23:45:36: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:45:36: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:45:36: #1 total tags in treatment: 19893035 INFO @ Mon, 12 Aug 2019 23:45:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:45:36: #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 23:45:37: #1 tags after filtering in treatment: 19893035 INFO @ Mon, 12 Aug 2019 23:45:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:45:37: #1 finished! INFO @ Mon, 12 Aug 2019 23:45:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:45:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:45:39: #2 number of paired peaks: 866 WARNING @ Mon, 12 Aug 2019 23:45:39: Fewer paired peaks (866) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 866 pairs to build model! INFO @ Mon, 12 Aug 2019 23:45:39: start model_add_line... INFO @ Mon, 12 Aug 2019 23:45:39: start X-correlation... INFO @ Mon, 12 Aug 2019 23:45:39: end of X-cor INFO @ Mon, 12 Aug 2019 23:45:39: #2 finished! INFO @ Mon, 12 Aug 2019 23:45:39: #2 predicted fragment length is 235 bps INFO @ Mon, 12 Aug 2019 23:45:39: #2 alternative fragment length(s) may be 235 bps INFO @ Mon, 12 Aug 2019 23:45:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.10_model.r INFO @ Mon, 12 Aug 2019 23:45:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:45:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:45:45: 18000000 INFO @ Mon, 12 Aug 2019 23:45:55: 19000000 INFO @ Mon, 12 Aug 2019 23:46:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:46:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:46:03: #1 total tags in treatment: 19893035 INFO @ Mon, 12 Aug 2019 23:46:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:46:03: #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 23:46:04: #1 tags after filtering in treatment: 19893035 INFO @ Mon, 12 Aug 2019 23:46:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:46:04: #1 finished! INFO @ Mon, 12 Aug 2019 23:46:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:46:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:46:06: #2 number of paired peaks: 866 WARNING @ Mon, 12 Aug 2019 23:46:06: Fewer paired peaks (866) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 866 pairs to build model! INFO @ Mon, 12 Aug 2019 23:46:06: start model_add_line... INFO @ Mon, 12 Aug 2019 23:46:06: start X-correlation... INFO @ Mon, 12 Aug 2019 23:46:06: end of X-cor INFO @ Mon, 12 Aug 2019 23:46:06: #2 finished! INFO @ Mon, 12 Aug 2019 23:46:06: #2 predicted fragment length is 235 bps INFO @ Mon, 12 Aug 2019 23:46:06: #2 alternative fragment length(s) may be 235 bps INFO @ Mon, 12 Aug 2019 23:46:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.20_model.r INFO @ Mon, 12 Aug 2019 23:46:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:46:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:46:11: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:46:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:46:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:46:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:46:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.05_summits.bed INFO @ Mon, 12 Aug 2019 23:46:38: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (11361 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:47:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:47:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:47:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.10_summits.bed INFO @ Mon, 12 Aug 2019 23:47:06: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8143 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:47:06: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:47:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:47:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:47:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011039/SRX5011039.20_summits.bed INFO @ Mon, 12 Aug 2019 23:47:33: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (5201 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。