Job ID = 2590344 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,645,597 reads read : 27,291,194 reads written : 13,645,597 reads 0-length : 13,645,597 spots read : 13,463,557 reads read : 26,927,114 reads written : 13,463,557 reads 0-length : 13,463,557 spots read : 13,630,879 reads read : 27,261,758 reads written : 13,630,879 reads 0-length : 13,630,879 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: 00:00:01 Multiseed full-index search: 00:11:39 40740033 reads; of these: 40740033 (100.00%) were unpaired; of these: 1425936 (3.50%) aligned 0 times 31461624 (77.23%) aligned exactly 1 time 7852473 (19.27%) aligned >1 times 96.50% overall alignment rate Time searching: 00:11:40 Overall time: 00:11:40 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 20 files... [bam_rmdupse_core] 7053306 / 39314097 = 0.1794 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 21:26:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.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 21:26:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:26:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:26:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.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 21:26:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:26:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:26:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.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 21:26:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:26:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:26:53: 1000000 INFO @ Mon, 12 Aug 2019 21:26:53: 1000000 INFO @ Mon, 12 Aug 2019 21:26:53: 1000000 INFO @ Mon, 12 Aug 2019 21:27:00: 2000000 INFO @ Mon, 12 Aug 2019 21:27:01: 2000000 INFO @ Mon, 12 Aug 2019 21:27:01: 2000000 INFO @ Mon, 12 Aug 2019 21:27:07: 3000000 INFO @ Mon, 12 Aug 2019 21:27:08: 3000000 INFO @ Mon, 12 Aug 2019 21:27:09: 3000000 INFO @ Mon, 12 Aug 2019 21:27:14: 4000000 INFO @ Mon, 12 Aug 2019 21:27:16: 4000000 INFO @ Mon, 12 Aug 2019 21:27:16: 4000000 INFO @ Mon, 12 Aug 2019 21:27:21: 5000000 INFO @ Mon, 12 Aug 2019 21:27:24: 5000000 INFO @ Mon, 12 Aug 2019 21:27:24: 5000000 INFO @ Mon, 12 Aug 2019 21:27:28: 6000000 INFO @ Mon, 12 Aug 2019 21:27:31: 6000000 INFO @ Mon, 12 Aug 2019 21:27:32: 6000000 INFO @ Mon, 12 Aug 2019 21:27:35: 7000000 INFO @ Mon, 12 Aug 2019 21:27:39: 7000000 INFO @ Mon, 12 Aug 2019 21:27:39: 7000000 INFO @ Mon, 12 Aug 2019 21:27:42: 8000000 INFO @ Mon, 12 Aug 2019 21:27:46: 8000000 INFO @ Mon, 12 Aug 2019 21:27:47: 8000000 INFO @ Mon, 12 Aug 2019 21:27:49: 9000000 INFO @ Mon, 12 Aug 2019 21:27:54: 9000000 INFO @ Mon, 12 Aug 2019 21:27:55: 9000000 INFO @ Mon, 12 Aug 2019 21:27:56: 10000000 INFO @ Mon, 12 Aug 2019 21:28:01: 10000000 INFO @ Mon, 12 Aug 2019 21:28:02: 10000000 INFO @ Mon, 12 Aug 2019 21:28:03: 11000000 INFO @ Mon, 12 Aug 2019 21:28:09: 11000000 INFO @ Mon, 12 Aug 2019 21:28:10: 11000000 INFO @ Mon, 12 Aug 2019 21:28:10: 12000000 INFO @ Mon, 12 Aug 2019 21:28:16: 12000000 INFO @ Mon, 12 Aug 2019 21:28:17: 13000000 INFO @ Mon, 12 Aug 2019 21:28:17: 12000000 INFO @ Mon, 12 Aug 2019 21:28:24: 14000000 INFO @ Mon, 12 Aug 2019 21:28:24: 13000000 INFO @ Mon, 12 Aug 2019 21:28:25: 13000000 INFO @ Mon, 12 Aug 2019 21:28:31: 15000000 INFO @ Mon, 12 Aug 2019 21:28:31: 14000000 INFO @ Mon, 12 Aug 2019 21:28:32: 14000000 INFO @ Mon, 12 Aug 2019 21:28:38: 16000000 INFO @ Mon, 12 Aug 2019 21:28:39: 15000000 INFO @ Mon, 12 Aug 2019 21:28:40: 15000000 INFO @ Mon, 12 Aug 2019 21:28:44: 17000000 INFO @ Mon, 12 Aug 2019 21:28:46: 16000000 INFO @ Mon, 12 Aug 2019 21:28:47: 16000000 INFO @ Mon, 12 Aug 2019 21:28:51: 18000000 INFO @ Mon, 12 Aug 2019 21:28:54: 17000000 INFO @ Mon, 12 Aug 2019 21:28:55: 17000000 INFO @ Mon, 12 Aug 2019 21:28:58: 19000000 INFO @ Mon, 12 Aug 2019 21:29:01: 18000000 INFO @ Mon, 12 Aug 2019 21:29:02: 18000000 INFO @ Mon, 12 Aug 2019 21:29:05: 20000000 INFO @ Mon, 12 Aug 2019 21:29:08: 19000000 INFO @ Mon, 12 Aug 2019 21:29:10: 19000000 INFO @ Mon, 12 Aug 2019 21:29:12: 21000000 INFO @ Mon, 12 Aug 2019 21:29:16: 20000000 INFO @ Mon, 12 Aug 2019 21:29:17: 20000000 INFO @ Mon, 12 Aug 2019 21:29:19: 22000000 INFO @ Mon, 12 Aug 2019 21:29:23: 21000000 INFO @ Mon, 12 Aug 2019 21:29:25: 21000000 INFO @ Mon, 12 Aug 2019 21:29:26: 23000000 INFO @ Mon, 12 Aug 2019 21:29:31: 22000000 INFO @ Mon, 12 Aug 2019 21:29:32: 22000000 INFO @ Mon, 12 Aug 2019 21:29:33: 24000000 INFO @ Mon, 12 Aug 2019 21:29:38: 23000000 INFO @ Mon, 12 Aug 2019 21:29:40: 25000000 INFO @ Mon, 12 Aug 2019 21:29:40: 23000000 INFO @ Mon, 12 Aug 2019 21:29:46: 24000000 INFO @ Mon, 12 Aug 2019 21:29:46: 26000000 INFO @ Mon, 12 Aug 2019 21:29:47: 24000000 INFO @ Mon, 12 Aug 2019 21:29:53: 25000000 INFO @ Mon, 12 Aug 2019 21:29:53: 27000000 INFO @ Mon, 12 Aug 2019 21:29:55: 25000000 INFO @ Mon, 12 Aug 2019 21:30:00: 28000000 INFO @ Mon, 12 Aug 2019 21:30:01: 26000000 INFO @ Mon, 12 Aug 2019 21:30:03: 26000000 INFO @ Mon, 12 Aug 2019 21:30:07: 29000000 INFO @ Mon, 12 Aug 2019 21:30:08: 27000000 INFO @ Mon, 12 Aug 2019 21:30:10: 27000000 INFO @ Mon, 12 Aug 2019 21:30:14: 30000000 INFO @ Mon, 12 Aug 2019 21:30:15: 28000000 INFO @ Mon, 12 Aug 2019 21:30:17: 28000000 INFO @ Mon, 12 Aug 2019 21:30:21: 31000000 INFO @ Mon, 12 Aug 2019 21:30:23: 29000000 INFO @ Mon, 12 Aug 2019 21:30:25: 29000000 INFO @ Mon, 12 Aug 2019 21:30:27: 32000000 INFO @ Mon, 12 Aug 2019 21:30:29: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:30:29: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:30:29: #1 total tags in treatment: 32260791 INFO @ Mon, 12 Aug 2019 21:30:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:30:29: #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 21:30:30: 30000000 INFO @ Mon, 12 Aug 2019 21:30:30: #1 tags after filtering in treatment: 32260791 INFO @ Mon, 12 Aug 2019 21:30:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:30:30: #1 finished! INFO @ Mon, 12 Aug 2019 21:30:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:30:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:30:32: 30000000 INFO @ Mon, 12 Aug 2019 21:30:33: #2 number of paired peaks: 475 WARNING @ Mon, 12 Aug 2019 21:30:33: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Mon, 12 Aug 2019 21:30:33: start model_add_line... INFO @ Mon, 12 Aug 2019 21:30:33: start X-correlation... INFO @ Mon, 12 Aug 2019 21:30:33: end of X-cor INFO @ Mon, 12 Aug 2019 21:30:33: #2 finished! INFO @ Mon, 12 Aug 2019 21:30:33: #2 predicted fragment length is 136 bps INFO @ Mon, 12 Aug 2019 21:30:33: #2 alternative fragment length(s) may be 3,136 bps INFO @ Mon, 12 Aug 2019 21:30:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.20_model.r INFO @ Mon, 12 Aug 2019 21:30:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:30:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:30:37: 31000000 INFO @ Mon, 12 Aug 2019 21:30:39: 31000000 INFO @ Mon, 12 Aug 2019 21:30:44: 32000000 INFO @ Mon, 12 Aug 2019 21:30:46: 32000000 INFO @ Mon, 12 Aug 2019 21:30:46: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:30:46: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:30:46: #1 total tags in treatment: 32260791 INFO @ Mon, 12 Aug 2019 21:30:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:30:46: #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 21:30:47: #1 tags after filtering in treatment: 32260791 INFO @ Mon, 12 Aug 2019 21:30:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:30:47: #1 finished! INFO @ Mon, 12 Aug 2019 21:30:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:30:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:30:48: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:30:48: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:30:48: #1 total tags in treatment: 32260791 INFO @ Mon, 12 Aug 2019 21:30:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:30:48: #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 21:30:49: #1 tags after filtering in treatment: 32260791 INFO @ Mon, 12 Aug 2019 21:30:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:30:49: #1 finished! INFO @ Mon, 12 Aug 2019 21:30:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:30:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:30:50: #2 number of paired peaks: 475 WARNING @ Mon, 12 Aug 2019 21:30:50: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Mon, 12 Aug 2019 21:30:50: start model_add_line... INFO @ Mon, 12 Aug 2019 21:30:50: start X-correlation... INFO @ Mon, 12 Aug 2019 21:30:50: end of X-cor INFO @ Mon, 12 Aug 2019 21:30:50: #2 finished! INFO @ Mon, 12 Aug 2019 21:30:50: #2 predicted fragment length is 136 bps INFO @ Mon, 12 Aug 2019 21:30:50: #2 alternative fragment length(s) may be 3,136 bps INFO @ Mon, 12 Aug 2019 21:30:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.05_model.r INFO @ Mon, 12 Aug 2019 21:30:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:30:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:30:52: #2 number of paired peaks: 475 WARNING @ Mon, 12 Aug 2019 21:30:52: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Mon, 12 Aug 2019 21:30:52: start model_add_line... INFO @ Mon, 12 Aug 2019 21:30:52: start X-correlation... INFO @ Mon, 12 Aug 2019 21:30:52: end of X-cor INFO @ Mon, 12 Aug 2019 21:30:52: #2 finished! INFO @ Mon, 12 Aug 2019 21:30:52: #2 predicted fragment length is 136 bps INFO @ Mon, 12 Aug 2019 21:30:52: #2 alternative fragment length(s) may be 3,136 bps INFO @ Mon, 12 Aug 2019 21:30:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.10_model.r INFO @ Mon, 12 Aug 2019 21:30:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:30:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:31:54: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:32:11: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:32:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:32:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:32:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:32:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.20_summits.bed INFO @ Mon, 12 Aug 2019 21:32:29: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2951 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:32:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:32:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:32:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.05_summits.bed INFO @ Mon, 12 Aug 2019 21:32:47: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (11063 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:32:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:32:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:32:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981619/SRX3981619.10_summits.bed INFO @ Mon, 12 Aug 2019 21:32:49: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (7035 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。