Job ID = 2161351 sra ファイルのダウンロード中... Completed: 1104920K bytes transferred in 12 seconds (753190K 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 6920 0 6920 0 0 12402 0 --:--:-- --:--:-- --:--:-- 18855 100 35384 0 35384 0 0 27647 0 --:--:-- 0:00:01 --:--:-- 32492 100 35384 0 35384 0 0 27631 0 --:--:-- 0:00:01 --:--:-- 32462 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 15519519 spots for /home/okishinya/chipatlas/results/dm3/SRX020700/SRR060783.sra Written 15519519 spots total Written 18830714 spots for /home/okishinya/chipatlas/results/dm3/SRX020700/SRR060782.sra Written 18830714 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: 00:07:40 34350233 reads; of these: 34350233 (100.00%) were unpaired; of these: 19181626 (55.84%) aligned 0 times 10498326 (30.56%) aligned exactly 1 time 4670281 (13.60%) aligned >1 times 44.16% overall alignment rate Time searching: 00:07:40 Overall time: 00:07:40 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_rmdupse_core] 3043442 / 15168607 = 0.2006 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 12:38:36: # Command line: callpeak -t SRX020700.bam -f BAM -g dm -n SRX020700.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX020700.10 # format = BAM # ChIP-seq file = ['SRX020700.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 12:38:36: # Command line: callpeak -t SRX020700.bam -f BAM -g dm -n SRX020700.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX020700.20 # format = BAM # ChIP-seq file = ['SRX020700.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 12:38:36: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:38:36: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:38:36: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:38:36: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:38:36: # Command line: callpeak -t SRX020700.bam -f BAM -g dm -n SRX020700.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX020700.05 # format = BAM # ChIP-seq file = ['SRX020700.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 12:38:36: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:38:36: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:38:42: 1000000 INFO @ Tue, 21 Apr 2015 12:38:42: 1000000 INFO @ Tue, 21 Apr 2015 12:38:42: 1000000 INFO @ Tue, 21 Apr 2015 12:38:47: 2000000 INFO @ Tue, 21 Apr 2015 12:38:47: 2000000 INFO @ Tue, 21 Apr 2015 12:38:47: 2000000 INFO @ Tue, 21 Apr 2015 12:38:52: 3000000 INFO @ Tue, 21 Apr 2015 12:38:52: 3000000 INFO @ Tue, 21 Apr 2015 12:38:52: 3000000 INFO @ Tue, 21 Apr 2015 12:38:58: 4000000 INFO @ Tue, 21 Apr 2015 12:38:58: 4000000 INFO @ Tue, 21 Apr 2015 12:38:58: 4000000 INFO @ Tue, 21 Apr 2015 12:39:03: 5000000 INFO @ Tue, 21 Apr 2015 12:39:03: 5000000 INFO @ Tue, 21 Apr 2015 12:39:03: 5000000 INFO @ Tue, 21 Apr 2015 12:39:08: 6000000 INFO @ Tue, 21 Apr 2015 12:39:09: 6000000 INFO @ Tue, 21 Apr 2015 12:39:09: 6000000 INFO @ Tue, 21 Apr 2015 12:39:14: 7000000 INFO @ Tue, 21 Apr 2015 12:39:14: 7000000 INFO @ Tue, 21 Apr 2015 12:39:14: 7000000 INFO @ Tue, 21 Apr 2015 12:39:19: 8000000 INFO @ Tue, 21 Apr 2015 12:39:20: 8000000 INFO @ Tue, 21 Apr 2015 12:39:20: 8000000 INFO @ Tue, 21 Apr 2015 12:39:24: 9000000 INFO @ Tue, 21 Apr 2015 12:39:25: 9000000 INFO @ Tue, 21 Apr 2015 12:39:25: 9000000 INFO @ Tue, 21 Apr 2015 12:39:30: 10000000 INFO @ Tue, 21 Apr 2015 12:39:31: 10000000 INFO @ Tue, 21 Apr 2015 12:39:31: 10000000 INFO @ Tue, 21 Apr 2015 12:39:35: 11000000 INFO @ Tue, 21 Apr 2015 12:39:36: 11000000 INFO @ Tue, 21 Apr 2015 12:39:37: 11000000 INFO @ Tue, 21 Apr 2015 12:39:40: 12000000 INFO @ Tue, 21 Apr 2015 12:39:41: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:39:41: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:39:41: #1 total tags in treatment: 12125165 INFO @ Tue, 21 Apr 2015 12:39:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:39:41: #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 12:39:42: 12000000 INFO @ Tue, 21 Apr 2015 12:39:42: 12000000 INFO @ Tue, 21 Apr 2015 12:39:43: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:39:43: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:39:43: #1 total tags in treatment: 12125165 INFO @ Tue, 21 Apr 2015 12:39:43: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:39:43: #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 12:39:43: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:39:43: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:39:43: #1 total tags in treatment: 12125165 INFO @ Tue, 21 Apr 2015 12:39:43: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:39:43: #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 12:39:43: #1 tags after filtering in treatment: 12121424 INFO @ Tue, 21 Apr 2015 12:39:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:39:43: #1 finished! INFO @ Tue, 21 Apr 2015 12:39:43: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:39:45: #1 tags after filtering in treatment: 12121424 INFO @ Tue, 21 Apr 2015 12:39:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:39:45: #1 finished! INFO @ Tue, 21 Apr 2015 12:39:45: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:39:45: #2 number of paired peaks: 368 WARNING @ Tue, 21 Apr 2015 12:39:45: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Tue, 21 Apr 2015 12:39:45: start model_add_line... INFO @ Tue, 21 Apr 2015 12:39:45: #1 tags after filtering in treatment: 12121424 INFO @ Tue, 21 Apr 2015 12:39:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:39:45: #1 finished! INFO @ Tue, 21 Apr 2015 12:39:45: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:39:47: #2 number of paired peaks: 368 WARNING @ Tue, 21 Apr 2015 12:39:47: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Tue, 21 Apr 2015 12:39:47: start model_add_line... INFO @ Tue, 21 Apr 2015 12:39:47: #2 number of paired peaks: 368 WARNING @ Tue, 21 Apr 2015 12:39:47: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Tue, 21 Apr 2015 12:39:47: start model_add_line... INFO @ Tue, 21 Apr 2015 12:39:49: start X-correlation... INFO @ Tue, 21 Apr 2015 12:39:49: end of X-cor INFO @ Tue, 21 Apr 2015 12:39:49: #2 finished! INFO @ Tue, 21 Apr 2015 12:39:49: #2 predicted fragment length is 99 bps INFO @ Tue, 21 Apr 2015 12:39:49: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 21 Apr 2015 12:39:49: #2.2 Generate R script for model : SRX020700.05_model.r INFO @ Tue, 21 Apr 2015 12:39:49: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:39:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:39:50: start X-correlation... INFO @ Tue, 21 Apr 2015 12:39:50: end of X-cor INFO @ Tue, 21 Apr 2015 12:39:50: #2 finished! INFO @ Tue, 21 Apr 2015 12:39:50: #2 predicted fragment length is 99 bps INFO @ Tue, 21 Apr 2015 12:39:50: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 21 Apr 2015 12:39:50: #2.2 Generate R script for model : SRX020700.10_model.r INFO @ Tue, 21 Apr 2015 12:39:50: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:39:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:39:51: start X-correlation... INFO @ Tue, 21 Apr 2015 12:39:51: end of X-cor INFO @ Tue, 21 Apr 2015 12:39:51: #2 finished! INFO @ Tue, 21 Apr 2015 12:39:51: #2 predicted fragment length is 99 bps INFO @ Tue, 21 Apr 2015 12:39:51: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 21 Apr 2015 12:39:51: #2.2 Generate R script for model : SRX020700.20_model.r INFO @ Tue, 21 Apr 2015 12:39:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:39:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:40:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:40:57: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:40:57: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:41:46: #4 Write output xls file... SRX020700.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:41:46: #4 Write peak in narrowPeak format file... SRX020700.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:41:46: #4 Write summits bed file... SRX020700.20_summits.bed INFO @ Tue, 21 Apr 2015 12:41:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2328 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:41:53: #4 Write output xls file... SRX020700.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:41:53: #4 Write peak in narrowPeak format file... SRX020700.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:41:53: #4 Write summits bed file... SRX020700.10_summits.bed INFO @ Tue, 21 Apr 2015 12:41:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6355 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:41:53: #4 Write output xls file... SRX020700.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:41:53: #4 Write peak in narrowPeak format file... SRX020700.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:41:54: #4 Write summits bed file... SRX020700.05_summits.bed INFO @ Tue, 21 Apr 2015 12:41:54: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10948 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。