Job ID = 2161388 sra ファイルのダウンロード中... Completed: 916484K bytes transferred in 9 seconds (822661K bits/sec), in 2 files, 3 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 44514 0 44514 0 0 48260 0 --:--:-- --:--:-- --:--:-- 60811 100 44514 0 44514 0 0 48219 0 --:--:-- --:--:-- --:--:-- 60811 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 28662814 spots for /home/okishinya/chipatlas/results/dm3/SRX025476/SRR063874.sra Written 28662814 spots total Written 29264366 spots for /home/okishinya/chipatlas/results/dm3/SRX025476/SRR063875.sra Written 29264366 spots total 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: 00:13:04 57927180 reads; of these: 57927180 (100.00%) were unpaired; of these: 8998690 (15.53%) aligned 0 times 41910584 (72.35%) aligned exactly 1 time 7017906 (12.12%) aligned >1 times 84.47% overall alignment rate Time searching: 00:13:04 Overall time: 00:13:04 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] 29161687 / 48928490 = 0.5960 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, 21 Apr 2015 12:53:44: # Command line: callpeak -t SRX025476.bam -f BAM -g dm -n SRX025476.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX025476.20 # format = BAM # ChIP-seq file = ['SRX025476.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 INFO @ Tue, 21 Apr 2015 12:53:44: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:53:44: # Command line: callpeak -t SRX025476.bam -f BAM -g dm -n SRX025476.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX025476.10 # format = BAM # ChIP-seq file = ['SRX025476.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 INFO @ Tue, 21 Apr 2015 12:53:44: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:53:44: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:53:44: # Command line: callpeak -t SRX025476.bam -f BAM -g dm -n SRX025476.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX025476.05 # format = BAM # ChIP-seq file = ['SRX025476.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 INFO @ Tue, 21 Apr 2015 12:53:44: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:53:44: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:53:44: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:53:50: 1000000 INFO @ Tue, 21 Apr 2015 12:53:50: 1000000 INFO @ Tue, 21 Apr 2015 12:53:50: 1000000 INFO @ Tue, 21 Apr 2015 12:53:56: 2000000 INFO @ Tue, 21 Apr 2015 12:53:56: 2000000 INFO @ Tue, 21 Apr 2015 12:53:56: 2000000 INFO @ Tue, 21 Apr 2015 12:54:01: 3000000 INFO @ Tue, 21 Apr 2015 12:54:02: 3000000 INFO @ Tue, 21 Apr 2015 12:54:02: 3000000 INFO @ Tue, 21 Apr 2015 12:54:07: 4000000 INFO @ Tue, 21 Apr 2015 12:54:07: 4000000 INFO @ Tue, 21 Apr 2015 12:54:07: 4000000 INFO @ Tue, 21 Apr 2015 12:54:13: 5000000 INFO @ Tue, 21 Apr 2015 12:54:13: 5000000 INFO @ Tue, 21 Apr 2015 12:54:13: 5000000 INFO @ Tue, 21 Apr 2015 12:54:19: 6000000 INFO @ Tue, 21 Apr 2015 12:54:19: 6000000 INFO @ Tue, 21 Apr 2015 12:54:19: 6000000 INFO @ Tue, 21 Apr 2015 12:54:24: 7000000 INFO @ Tue, 21 Apr 2015 12:54:24: 7000000 INFO @ Tue, 21 Apr 2015 12:54:24: 7000000 INFO @ Tue, 21 Apr 2015 12:54:30: 8000000 INFO @ Tue, 21 Apr 2015 12:54:30: 8000000 INFO @ Tue, 21 Apr 2015 12:54:30: 8000000 INFO @ Tue, 21 Apr 2015 12:54:35: 9000000 INFO @ Tue, 21 Apr 2015 12:54:35: 9000000 INFO @ Tue, 21 Apr 2015 12:54:35: 9000000 INFO @ Tue, 21 Apr 2015 12:54:40: 10000000 INFO @ Tue, 21 Apr 2015 12:54:40: 10000000 INFO @ Tue, 21 Apr 2015 12:54:40: 10000000 INFO @ Tue, 21 Apr 2015 12:54:46: 11000000 INFO @ Tue, 21 Apr 2015 12:54:46: 11000000 INFO @ Tue, 21 Apr 2015 12:54:46: 11000000 INFO @ Tue, 21 Apr 2015 12:54:51: 12000000 INFO @ Tue, 21 Apr 2015 12:54:51: 12000000 INFO @ Tue, 21 Apr 2015 12:54:51: 12000000 INFO @ Tue, 21 Apr 2015 12:54:57: 13000000 INFO @ Tue, 21 Apr 2015 12:54:57: 13000000 INFO @ Tue, 21 Apr 2015 12:54:57: 13000000 INFO @ Tue, 21 Apr 2015 12:55:02: 14000000 INFO @ Tue, 21 Apr 2015 12:55:02: 14000000 INFO @ Tue, 21 Apr 2015 12:55:03: 14000000 INFO @ Tue, 21 Apr 2015 12:55:08: 15000000 INFO @ Tue, 21 Apr 2015 12:55:08: 15000000 INFO @ Tue, 21 Apr 2015 12:55:09: 15000000 INFO @ Tue, 21 Apr 2015 12:55:14: 16000000 INFO @ Tue, 21 Apr 2015 12:55:14: 16000000 INFO @ Tue, 21 Apr 2015 12:55:15: 16000000 INFO @ Tue, 21 Apr 2015 12:55:19: 17000000 INFO @ Tue, 21 Apr 2015 12:55:19: 17000000 INFO @ Tue, 21 Apr 2015 12:55:21: 17000000 INFO @ Tue, 21 Apr 2015 12:55:25: 18000000 INFO @ Tue, 21 Apr 2015 12:55:25: 18000000 INFO @ Tue, 21 Apr 2015 12:55:27: 18000000 INFO @ Tue, 21 Apr 2015 12:55:30: 19000000 INFO @ Tue, 21 Apr 2015 12:55:30: 19000000 INFO @ Tue, 21 Apr 2015 12:55:32: 19000000 INFO @ Tue, 21 Apr 2015 12:55:35: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:55:35: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:55:35: #1 total tags in treatment: 19766803 INFO @ Tue, 21 Apr 2015 12:55:35: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:55:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:55:35: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:55:35: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:55:35: #1 total tags in treatment: 19766803 INFO @ Tue, 21 Apr 2015 12:55:35: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:55:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:55:37: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:55:37: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:55:37: #1 total tags in treatment: 19766803 INFO @ Tue, 21 Apr 2015 12:55:37: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:55:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:55:38: #1 tags after filtering in treatment: 19762888 INFO @ Tue, 21 Apr 2015 12:55:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:55:38: #1 finished! INFO @ Tue, 21 Apr 2015 12:55:38: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:55:38: #1 tags after filtering in treatment: 19762888 INFO @ Tue, 21 Apr 2015 12:55:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:55:38: #1 finished! INFO @ Tue, 21 Apr 2015 12:55:38: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:55:40: #1 tags after filtering in treatment: 19762888 INFO @ Tue, 21 Apr 2015 12:55:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:55:40: #1 finished! INFO @ Tue, 21 Apr 2015 12:55:40: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:55:41: #2 number of paired peaks: 559 WARNING @ Tue, 21 Apr 2015 12:55:41: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Tue, 21 Apr 2015 12:55:41: start model_add_line... INFO @ Tue, 21 Apr 2015 12:55:41: #2 number of paired peaks: 559 WARNING @ Tue, 21 Apr 2015 12:55:41: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Tue, 21 Apr 2015 12:55:41: start model_add_line... INFO @ Tue, 21 Apr 2015 12:55:44: #2 number of paired peaks: 559 WARNING @ Tue, 21 Apr 2015 12:55:44: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Tue, 21 Apr 2015 12:55:44: start model_add_line... INFO @ Tue, 21 Apr 2015 12:55:49: start X-correlation... INFO @ Tue, 21 Apr 2015 12:55:49: end of X-cor INFO @ Tue, 21 Apr 2015 12:55:49: #2 finished! INFO @ Tue, 21 Apr 2015 12:55:49: #2 predicted fragment length is 329 bps INFO @ Tue, 21 Apr 2015 12:55:49: #2 alternative fragment length(s) may be 4,34,329 bps INFO @ Tue, 21 Apr 2015 12:55:49: #2.2 Generate R script for model : SRX025476.10_model.r INFO @ Tue, 21 Apr 2015 12:55:49: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:55:49: start X-correlation... INFO @ Tue, 21 Apr 2015 12:55:49: end of X-cor INFO @ Tue, 21 Apr 2015 12:55:49: #2 finished! INFO @ Tue, 21 Apr 2015 12:55:49: #2 predicted fragment length is 329 bps INFO @ Tue, 21 Apr 2015 12:55:49: #2 alternative fragment length(s) may be 4,34,329 bps INFO @ Tue, 21 Apr 2015 12:55:49: #2.2 Generate R script for model : SRX025476.05_model.r INFO @ Tue, 21 Apr 2015 12:55:49: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:55:51: start X-correlation... INFO @ Tue, 21 Apr 2015 12:55:51: end of X-cor INFO @ Tue, 21 Apr 2015 12:55:51: #2 finished! INFO @ Tue, 21 Apr 2015 12:55:51: #2 predicted fragment length is 329 bps INFO @ Tue, 21 Apr 2015 12:55:51: #2 alternative fragment length(s) may be 4,34,329 bps INFO @ Tue, 21 Apr 2015 12:55:51: #2.2 Generate R script for model : SRX025476.20_model.r INFO @ Tue, 21 Apr 2015 12:55:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:55:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:57:45: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:57:47: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:57:49: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:59:06: #4 Write output xls file... SRX025476.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:59:06: #4 Write peak in narrowPeak format file... SRX025476.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:59:06: #4 Write summits bed file... SRX025476.20_summits.bed INFO @ Tue, 21 Apr 2015 12:59:06: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2751 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:59:13: #4 Write output xls file... SRX025476.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:59:13: #4 Write peak in narrowPeak format file... SRX025476.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:59:13: #4 Write summits bed file... SRX025476.10_summits.bed INFO @ Tue, 21 Apr 2015 12:59:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5310 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:59:28: #4 Write output xls file... SRX025476.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:59:28: #4 Write peak in narrowPeak format file... SRX025476.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:59:28: #4 Write summits bed file... SRX025476.05_summits.bed INFO @ Tue, 21 Apr 2015 12:59:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7608 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。