Job ID = 2590351 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,869,402 reads read : 25,738,804 reads written : 12,869,402 reads 0-length : 12,869,402 spots read : 12,530,390 reads read : 25,060,780 reads written : 12,530,390 reads 0-length : 12,530,390 spots read : 12,853,850 reads read : 25,707,700 reads written : 12,853,850 reads 0-length : 12,853,850 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: 00:10:58 38253642 reads; of these: 38253642 (100.00%) were unpaired; of these: 1167807 (3.05%) aligned 0 times 29404634 (76.87%) aligned exactly 1 time 7681201 (20.08%) aligned >1 times 96.95% overall alignment rate Time searching: 00:10:58 Overall time: 00:10:58 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] 5787038 / 37085835 = 0.1560 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 21:27:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.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 21:27:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:27:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:27:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.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 21:27:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:27:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:27:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.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 21:27:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:27:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:27:28: 1000000 INFO @ Mon, 12 Aug 2019 21:27:29: 1000000 INFO @ Mon, 12 Aug 2019 21:27:29: 1000000 INFO @ Mon, 12 Aug 2019 21:27:36: 2000000 INFO @ Mon, 12 Aug 2019 21:27:36: 2000000 INFO @ Mon, 12 Aug 2019 21:27:37: 2000000 INFO @ Mon, 12 Aug 2019 21:27:43: 3000000 INFO @ Mon, 12 Aug 2019 21:27:43: 3000000 INFO @ Mon, 12 Aug 2019 21:27:44: 3000000 INFO @ Mon, 12 Aug 2019 21:27:50: 4000000 INFO @ Mon, 12 Aug 2019 21:27:51: 4000000 INFO @ Mon, 12 Aug 2019 21:27:51: 4000000 INFO @ Mon, 12 Aug 2019 21:27:57: 5000000 INFO @ Mon, 12 Aug 2019 21:27:58: 5000000 INFO @ Mon, 12 Aug 2019 21:27:58: 5000000 INFO @ Mon, 12 Aug 2019 21:28:05: 6000000 INFO @ Mon, 12 Aug 2019 21:28:05: 6000000 INFO @ Mon, 12 Aug 2019 21:28:05: 6000000 INFO @ Mon, 12 Aug 2019 21:28:12: 7000000 INFO @ Mon, 12 Aug 2019 21:28:12: 7000000 INFO @ Mon, 12 Aug 2019 21:28:12: 7000000 INFO @ Mon, 12 Aug 2019 21:28:19: 8000000 INFO @ Mon, 12 Aug 2019 21:28:19: 8000000 INFO @ Mon, 12 Aug 2019 21:28:20: 8000000 INFO @ Mon, 12 Aug 2019 21:28:26: 9000000 INFO @ Mon, 12 Aug 2019 21:28:26: 9000000 INFO @ Mon, 12 Aug 2019 21:28:27: 9000000 INFO @ Mon, 12 Aug 2019 21:28:33: 10000000 INFO @ Mon, 12 Aug 2019 21:28:33: 10000000 INFO @ Mon, 12 Aug 2019 21:28:34: 10000000 INFO @ Mon, 12 Aug 2019 21:28:40: 11000000 INFO @ Mon, 12 Aug 2019 21:28:40: 11000000 INFO @ Mon, 12 Aug 2019 21:28:43: 11000000 INFO @ Mon, 12 Aug 2019 21:28:47: 12000000 INFO @ Mon, 12 Aug 2019 21:28:48: 12000000 INFO @ Mon, 12 Aug 2019 21:28:51: 12000000 INFO @ Mon, 12 Aug 2019 21:28:54: 13000000 INFO @ Mon, 12 Aug 2019 21:28:55: 13000000 INFO @ Mon, 12 Aug 2019 21:28:59: 13000000 INFO @ Mon, 12 Aug 2019 21:29:01: 14000000 INFO @ Mon, 12 Aug 2019 21:29:02: 14000000 INFO @ Mon, 12 Aug 2019 21:29:07: 14000000 INFO @ Mon, 12 Aug 2019 21:29:09: 15000000 INFO @ Mon, 12 Aug 2019 21:29:09: 15000000 INFO @ Mon, 12 Aug 2019 21:29:16: 16000000 INFO @ Mon, 12 Aug 2019 21:29:16: 15000000 INFO @ Mon, 12 Aug 2019 21:29:16: 16000000 INFO @ Mon, 12 Aug 2019 21:29:23: 17000000 INFO @ Mon, 12 Aug 2019 21:29:23: 17000000 INFO @ Mon, 12 Aug 2019 21:29:24: 16000000 INFO @ Mon, 12 Aug 2019 21:29:30: 18000000 INFO @ Mon, 12 Aug 2019 21:29:30: 18000000 INFO @ Mon, 12 Aug 2019 21:29:33: 17000000 INFO @ Mon, 12 Aug 2019 21:29:37: 19000000 INFO @ Mon, 12 Aug 2019 21:29:38: 19000000 INFO @ Mon, 12 Aug 2019 21:29:41: 18000000 INFO @ Mon, 12 Aug 2019 21:29:44: 20000000 INFO @ Mon, 12 Aug 2019 21:29:45: 20000000 INFO @ Mon, 12 Aug 2019 21:29:50: 19000000 INFO @ Mon, 12 Aug 2019 21:29:51: 21000000 INFO @ Mon, 12 Aug 2019 21:29:52: 21000000 INFO @ Mon, 12 Aug 2019 21:29:58: 20000000 INFO @ Mon, 12 Aug 2019 21:29:58: 22000000 INFO @ Mon, 12 Aug 2019 21:29:59: 22000000 INFO @ Mon, 12 Aug 2019 21:30:05: 23000000 INFO @ Mon, 12 Aug 2019 21:30:06: 23000000 INFO @ Mon, 12 Aug 2019 21:30:06: 21000000 INFO @ Mon, 12 Aug 2019 21:30:13: 24000000 INFO @ Mon, 12 Aug 2019 21:30:13: 24000000 INFO @ Mon, 12 Aug 2019 21:30:15: 22000000 INFO @ Mon, 12 Aug 2019 21:30:20: 25000000 INFO @ Mon, 12 Aug 2019 21:30:20: 25000000 INFO @ Mon, 12 Aug 2019 21:30:23: 23000000 INFO @ Mon, 12 Aug 2019 21:30:27: 26000000 INFO @ Mon, 12 Aug 2019 21:30:27: 26000000 INFO @ Mon, 12 Aug 2019 21:30:31: 24000000 INFO @ Mon, 12 Aug 2019 21:30:34: 27000000 INFO @ Mon, 12 Aug 2019 21:30:35: 27000000 INFO @ Mon, 12 Aug 2019 21:30:40: 25000000 INFO @ Mon, 12 Aug 2019 21:30:41: 28000000 INFO @ Mon, 12 Aug 2019 21:30:42: 28000000 INFO @ Mon, 12 Aug 2019 21:30:48: 26000000 INFO @ Mon, 12 Aug 2019 21:30:48: 29000000 INFO @ Mon, 12 Aug 2019 21:30:49: 29000000 INFO @ Mon, 12 Aug 2019 21:30:55: 30000000 INFO @ Mon, 12 Aug 2019 21:30:56: 30000000 INFO @ Mon, 12 Aug 2019 21:30:56: 27000000 INFO @ Mon, 12 Aug 2019 21:31:02: 31000000 INFO @ Mon, 12 Aug 2019 21:31:03: 31000000 INFO @ Mon, 12 Aug 2019 21:31:05: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:31:05: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:31:05: #1 total tags in treatment: 31298797 INFO @ Mon, 12 Aug 2019 21:31:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:31:05: #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 21:31:05: 28000000 INFO @ Mon, 12 Aug 2019 21:31:05: #1 tags after filtering in treatment: 31298797 INFO @ Mon, 12 Aug 2019 21:31:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:31:05: #1 finished! INFO @ Mon, 12 Aug 2019 21:31:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:31:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:31:06: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:31:06: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:31:06: #1 total tags in treatment: 31298797 INFO @ Mon, 12 Aug 2019 21:31:06: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:31:06: #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 21:31:06: #1 tags after filtering in treatment: 31298797 INFO @ Mon, 12 Aug 2019 21:31:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:31:06: #1 finished! INFO @ Mon, 12 Aug 2019 21:31:06: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:31:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:31:08: #2 number of paired peaks: 242 WARNING @ Mon, 12 Aug 2019 21:31:08: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Mon, 12 Aug 2019 21:31:08: start model_add_line... INFO @ Mon, 12 Aug 2019 21:31:08: start X-correlation... INFO @ Mon, 12 Aug 2019 21:31:08: end of X-cor INFO @ Mon, 12 Aug 2019 21:31:08: #2 finished! INFO @ Mon, 12 Aug 2019 21:31:08: #2 predicted fragment length is 115 bps INFO @ Mon, 12 Aug 2019 21:31:08: #2 alternative fragment length(s) may be 3,99,115 bps INFO @ Mon, 12 Aug 2019 21:31:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.05_model.r INFO @ Mon, 12 Aug 2019 21:31:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:31:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:31:09: #2 number of paired peaks: 242 WARNING @ Mon, 12 Aug 2019 21:31:09: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Mon, 12 Aug 2019 21:31:09: start model_add_line... INFO @ Mon, 12 Aug 2019 21:31:09: start X-correlation... INFO @ Mon, 12 Aug 2019 21:31:09: end of X-cor INFO @ Mon, 12 Aug 2019 21:31:09: #2 finished! INFO @ Mon, 12 Aug 2019 21:31:09: #2 predicted fragment length is 115 bps INFO @ Mon, 12 Aug 2019 21:31:09: #2 alternative fragment length(s) may be 3,99,115 bps INFO @ Mon, 12 Aug 2019 21:31:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.10_model.r INFO @ Mon, 12 Aug 2019 21:31:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:31:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:31:13: 29000000 INFO @ Mon, 12 Aug 2019 21:31:22: 30000000 INFO @ Mon, 12 Aug 2019 21:31:30: 31000000 INFO @ Mon, 12 Aug 2019 21:31:33: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:31:33: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:31:33: #1 total tags in treatment: 31298797 INFO @ Mon, 12 Aug 2019 21:31:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:31:33: #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 21:31:33: #1 tags after filtering in treatment: 31298797 INFO @ Mon, 12 Aug 2019 21:31:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:31:33: #1 finished! INFO @ Mon, 12 Aug 2019 21:31:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:31:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:31:36: #2 number of paired peaks: 242 WARNING @ Mon, 12 Aug 2019 21:31:36: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Mon, 12 Aug 2019 21:31:36: start model_add_line... INFO @ Mon, 12 Aug 2019 21:31:36: start X-correlation... INFO @ Mon, 12 Aug 2019 21:31:36: end of X-cor INFO @ Mon, 12 Aug 2019 21:31:36: #2 finished! INFO @ Mon, 12 Aug 2019 21:31:36: #2 predicted fragment length is 115 bps INFO @ Mon, 12 Aug 2019 21:31:36: #2 alternative fragment length(s) may be 3,99,115 bps INFO @ Mon, 12 Aug 2019 21:31:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.20_model.r INFO @ Mon, 12 Aug 2019 21:31:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:31:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:32:24: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:32:24: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:32:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:33:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:33:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:33:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.05_summits.bed INFO @ Mon, 12 Aug 2019 21:33:01: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (9916 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:33:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:33:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:33:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.10_summits.bed INFO @ Mon, 12 Aug 2019 21:33:01: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5321 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:33:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:33:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:33:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981625/SRX3981625.20_summits.bed INFO @ Mon, 12 Aug 2019 21:33:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1624 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。