Job ID = 2591010 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,849,105 reads read : 23,849,105 reads written : 23,849,105 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: 00:07:33 23849105 reads; of these: 23849105 (100.00%) were unpaired; of these: 3105713 (13.02%) aligned 0 times 17654926 (74.03%) aligned exactly 1 time 3088466 (12.95%) aligned >1 times 86.98% overall alignment rate Time searching: 00:07:33 Overall time: 00:07:33 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 12 files... [bam_rmdupse_core] 3577314 / 20743392 = 0.1725 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 00:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.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 00:50:21: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:50:21: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.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 00:50:21: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:50:21: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:50:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.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 00:50:22: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:50:22: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:50:29: 1000000 INFO @ Tue, 13 Aug 2019 00:50:30: 1000000 INFO @ Tue, 13 Aug 2019 00:50:31: 1000000 INFO @ Tue, 13 Aug 2019 00:50:36: 2000000 INFO @ Tue, 13 Aug 2019 00:50:39: 2000000 INFO @ Tue, 13 Aug 2019 00:50:40: 2000000 INFO @ Tue, 13 Aug 2019 00:50:43: 3000000 INFO @ Tue, 13 Aug 2019 00:50:48: 3000000 INFO @ Tue, 13 Aug 2019 00:50:49: 3000000 INFO @ Tue, 13 Aug 2019 00:50:49: 4000000 INFO @ Tue, 13 Aug 2019 00:50:56: 5000000 INFO @ Tue, 13 Aug 2019 00:50:57: 4000000 INFO @ Tue, 13 Aug 2019 00:50:58: 4000000 INFO @ Tue, 13 Aug 2019 00:51:02: 6000000 INFO @ Tue, 13 Aug 2019 00:51:06: 5000000 INFO @ Tue, 13 Aug 2019 00:51:08: 5000000 INFO @ Tue, 13 Aug 2019 00:51:09: 7000000 INFO @ Tue, 13 Aug 2019 00:51:15: 8000000 INFO @ Tue, 13 Aug 2019 00:51:16: 6000000 INFO @ Tue, 13 Aug 2019 00:51:17: 6000000 INFO @ Tue, 13 Aug 2019 00:51:22: 9000000 INFO @ Tue, 13 Aug 2019 00:51:25: 7000000 INFO @ Tue, 13 Aug 2019 00:51:26: 7000000 INFO @ Tue, 13 Aug 2019 00:51:28: 10000000 INFO @ Tue, 13 Aug 2019 00:51:34: 8000000 INFO @ Tue, 13 Aug 2019 00:51:35: 11000000 INFO @ Tue, 13 Aug 2019 00:51:35: 8000000 INFO @ Tue, 13 Aug 2019 00:51:41: 12000000 INFO @ Tue, 13 Aug 2019 00:51:43: 9000000 INFO @ Tue, 13 Aug 2019 00:51:44: 9000000 INFO @ Tue, 13 Aug 2019 00:51:48: 13000000 INFO @ Tue, 13 Aug 2019 00:51:52: 10000000 INFO @ Tue, 13 Aug 2019 00:51:54: 10000000 INFO @ Tue, 13 Aug 2019 00:51:58: 14000000 INFO @ Tue, 13 Aug 2019 00:52:03: 11000000 INFO @ Tue, 13 Aug 2019 00:52:04: 11000000 INFO @ Tue, 13 Aug 2019 00:52:06: 15000000 INFO @ Tue, 13 Aug 2019 00:52:12: 12000000 INFO @ Tue, 13 Aug 2019 00:52:12: 16000000 INFO @ Tue, 13 Aug 2019 00:52:13: 12000000 INFO @ Tue, 13 Aug 2019 00:52:19: 17000000 INFO @ Tue, 13 Aug 2019 00:52:20: #1 tag size is determined as 51 bps INFO @ Tue, 13 Aug 2019 00:52:20: #1 tag size = 51 INFO @ Tue, 13 Aug 2019 00:52:20: #1 total tags in treatment: 17166078 INFO @ Tue, 13 Aug 2019 00:52:20: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:52:20: #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 00:52:20: #1 tags after filtering in treatment: 17166078 INFO @ Tue, 13 Aug 2019 00:52:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:52:20: #1 finished! INFO @ Tue, 13 Aug 2019 00:52:20: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:52:21: 13000000 INFO @ Tue, 13 Aug 2019 00:52:22: #2 number of paired peaks: 158 WARNING @ Tue, 13 Aug 2019 00:52:22: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 13 Aug 2019 00:52:22: start model_add_line... INFO @ Tue, 13 Aug 2019 00:52:22: start X-correlation... INFO @ Tue, 13 Aug 2019 00:52:22: end of X-cor INFO @ Tue, 13 Aug 2019 00:52:22: #2 finished! INFO @ Tue, 13 Aug 2019 00:52:22: #2 predicted fragment length is 154 bps INFO @ Tue, 13 Aug 2019 00:52:22: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 13 Aug 2019 00:52:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.20_model.r INFO @ Tue, 13 Aug 2019 00:52:22: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:52:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:52:22: 13000000 INFO @ Tue, 13 Aug 2019 00:52:29: 14000000 INFO @ Tue, 13 Aug 2019 00:52:31: 14000000 INFO @ Tue, 13 Aug 2019 00:52:38: 15000000 INFO @ Tue, 13 Aug 2019 00:52:40: 15000000 INFO @ Tue, 13 Aug 2019 00:52:47: 16000000 INFO @ Tue, 13 Aug 2019 00:52:49: 16000000 INFO @ Tue, 13 Aug 2019 00:52:56: 17000000 INFO @ Tue, 13 Aug 2019 00:52:58: #1 tag size is determined as 51 bps INFO @ Tue, 13 Aug 2019 00:52:58: #1 tag size = 51 INFO @ Tue, 13 Aug 2019 00:52:58: #1 total tags in treatment: 17166078 INFO @ Tue, 13 Aug 2019 00:52:58: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:52:58: #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 00:52:58: 17000000 INFO @ Tue, 13 Aug 2019 00:52:58: #1 tags after filtering in treatment: 17166078 INFO @ Tue, 13 Aug 2019 00:52:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:52:58: #1 finished! INFO @ Tue, 13 Aug 2019 00:52:58: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:52:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:52:59: #1 tag size is determined as 51 bps INFO @ Tue, 13 Aug 2019 00:52:59: #1 tag size = 51 INFO @ Tue, 13 Aug 2019 00:52:59: #1 total tags in treatment: 17166078 INFO @ Tue, 13 Aug 2019 00:52:59: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:52:59: #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 00:52:59: #1 tags after filtering in treatment: 17166078 INFO @ Tue, 13 Aug 2019 00:52:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:52:59: #1 finished! INFO @ Tue, 13 Aug 2019 00:52:59: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:52:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:52:59: #2 number of paired peaks: 158 WARNING @ Tue, 13 Aug 2019 00:52:59: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 13 Aug 2019 00:52:59: start model_add_line... INFO @ Tue, 13 Aug 2019 00:53:00: start X-correlation... INFO @ Tue, 13 Aug 2019 00:53:00: end of X-cor INFO @ Tue, 13 Aug 2019 00:53:00: #2 finished! INFO @ Tue, 13 Aug 2019 00:53:00: #2 predicted fragment length is 154 bps INFO @ Tue, 13 Aug 2019 00:53:00: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 13 Aug 2019 00:53:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.05_model.r INFO @ Tue, 13 Aug 2019 00:53:00: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:53:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:53:01: #2 number of paired peaks: 158 WARNING @ Tue, 13 Aug 2019 00:53:01: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 13 Aug 2019 00:53:01: start model_add_line... INFO @ Tue, 13 Aug 2019 00:53:01: start X-correlation... INFO @ Tue, 13 Aug 2019 00:53:01: end of X-cor INFO @ Tue, 13 Aug 2019 00:53:01: #2 finished! INFO @ Tue, 13 Aug 2019 00:53:01: #2 predicted fragment length is 154 bps INFO @ Tue, 13 Aug 2019 00:53:01: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 13 Aug 2019 00:53:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.10_model.r INFO @ Tue, 13 Aug 2019 00:53:01: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:53:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:53:13: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:53:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:53:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:53:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.20_summits.bed INFO @ Tue, 13 Aug 2019 00:53:39: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1619 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:53:47: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:53:49: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:54:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:54:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:54:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.05_summits.bed INFO @ Tue, 13 Aug 2019 00:54:12: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (11338 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:54:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:54:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:54:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645428/SRX645428.10_summits.bed INFO @ Tue, 13 Aug 2019 00:54:14: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (5162 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。