Job ID = 2161285 sra ファイルのダウンロード中... Completed: 233711K bytes transferred in 5 seconds (362634K 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 34341 0 34341 0 0 49237 0 --:--:-- --:--:-- --:--:-- 67867 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 3549680 spots for /home/okishinya/chipatlas/results/dm3/SRX016151/SRR034711.sra Written 3549680 spots total Written 6403468 spots for /home/okishinya/chipatlas/results/dm3/SRX016151/SRR034710.sra Written 6403468 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: 00:02:30 9953148 reads; of these: 9953148 (100.00%) were unpaired; of these: 508459 (5.11%) aligned 0 times 8198328 (82.37%) aligned exactly 1 time 1246361 (12.52%) aligned >1 times 94.89% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 5415865 / 9444689 = 0.5734 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 12:16:37: # Command line: callpeak -t SRX016151.bam -f BAM -g dm -n SRX016151.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX016151.05 # format = BAM # ChIP-seq file = ['SRX016151.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 12:16:37: # Command line: callpeak -t SRX016151.bam -f BAM -g dm -n SRX016151.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX016151.10 # format = BAM # ChIP-seq file = ['SRX016151.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 12:16:37: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:16:37: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:16:37: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:16:37: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:16:37: # Command line: callpeak -t SRX016151.bam -f BAM -g dm -n SRX016151.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX016151.20 # format = BAM # ChIP-seq file = ['SRX016151.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 12:16:37: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:16:37: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:16:42: 1000000 INFO @ Tue, 21 Apr 2015 12:16:42: 1000000 INFO @ Tue, 21 Apr 2015 12:16:42: 1000000 INFO @ Tue, 21 Apr 2015 12:16:47: 2000000 INFO @ Tue, 21 Apr 2015 12:16:47: 2000000 INFO @ Tue, 21 Apr 2015 12:16:47: 2000000 INFO @ Tue, 21 Apr 2015 12:16:52: 3000000 INFO @ Tue, 21 Apr 2015 12:16:52: 3000000 INFO @ Tue, 21 Apr 2015 12:16:52: 3000000 INFO @ Tue, 21 Apr 2015 12:16:57: 4000000 INFO @ Tue, 21 Apr 2015 12:16:57: 4000000 INFO @ Tue, 21 Apr 2015 12:16:57: 4000000 INFO @ Tue, 21 Apr 2015 12:16:57: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:16:57: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:16:57: #1 total tags in treatment: 4028824 INFO @ Tue, 21 Apr 2015 12:16:57: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:16:57: #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 12:16:57: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:16:57: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:16:57: #1 total tags in treatment: 4028824 INFO @ Tue, 21 Apr 2015 12:16:57: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:16:57: #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 12:16:58: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:16:58: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:16:58: #1 total tags in treatment: 4028824 INFO @ Tue, 21 Apr 2015 12:16:58: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:16:58: #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 12:16:58: #1 tags after filtering in treatment: 4028640 INFO @ Tue, 21 Apr 2015 12:16:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:16:58: #1 finished! INFO @ Tue, 21 Apr 2015 12:16:58: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:16:58: #1 tags after filtering in treatment: 4028640 INFO @ Tue, 21 Apr 2015 12:16:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:16:58: #1 finished! INFO @ Tue, 21 Apr 2015 12:16:58: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:16:58: #1 tags after filtering in treatment: 4028640 INFO @ Tue, 21 Apr 2015 12:16:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:16:58: #1 finished! INFO @ Tue, 21 Apr 2015 12:16:58: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:16:59: #2 number of paired peaks: 1432 INFO @ Tue, 21 Apr 2015 12:16:59: start model_add_line... INFO @ Tue, 21 Apr 2015 12:16:59: #2 number of paired peaks: 1432 INFO @ Tue, 21 Apr 2015 12:16:59: start model_add_line... INFO @ Tue, 21 Apr 2015 12:16:59: #2 number of paired peaks: 1432 INFO @ Tue, 21 Apr 2015 12:16:59: start model_add_line... INFO @ Tue, 21 Apr 2015 12:17:02: start X-correlation... INFO @ Tue, 21 Apr 2015 12:17:02: end of X-cor INFO @ Tue, 21 Apr 2015 12:17:02: #2 finished! INFO @ Tue, 21 Apr 2015 12:17:02: #2 predicted fragment length is 155 bps INFO @ Tue, 21 Apr 2015 12:17:02: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 21 Apr 2015 12:17:02: #2.2 Generate R script for model : SRX016151.05_model.r INFO @ Tue, 21 Apr 2015 12:17:02: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:17:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:17:02: start X-correlation... INFO @ Tue, 21 Apr 2015 12:17:02: end of X-cor INFO @ Tue, 21 Apr 2015 12:17:02: #2 finished! INFO @ Tue, 21 Apr 2015 12:17:02: #2 predicted fragment length is 155 bps INFO @ Tue, 21 Apr 2015 12:17:02: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 21 Apr 2015 12:17:02: #2.2 Generate R script for model : SRX016151.20_model.r INFO @ Tue, 21 Apr 2015 12:17:02: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:17:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:17:03: start X-correlation... INFO @ Tue, 21 Apr 2015 12:17:03: end of X-cor INFO @ Tue, 21 Apr 2015 12:17:03: #2 finished! INFO @ Tue, 21 Apr 2015 12:17:03: #2 predicted fragment length is 155 bps INFO @ Tue, 21 Apr 2015 12:17:03: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 21 Apr 2015 12:17:03: #2.2 Generate R script for model : SRX016151.10_model.r INFO @ Tue, 21 Apr 2015 12:17:03: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:17:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:17:25: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:17:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:17:27: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:17:44: #4 Write output xls file... SRX016151.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:17:44: #4 Write peak in narrowPeak format file... SRX016151.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:17:44: #4 Write summits bed file... SRX016151.20_summits.bed INFO @ Tue, 21 Apr 2015 12:17:44: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (525 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:17:45: #4 Write output xls file... SRX016151.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:17:45: #4 Write peak in narrowPeak format file... SRX016151.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:17:45: #4 Write summits bed file... SRX016151.05_summits.bed INFO @ Tue, 21 Apr 2015 12:17:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3789 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:17:46: #4 Write output xls file... SRX016151.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:17:46: #4 Write peak in narrowPeak format file... SRX016151.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:17:46: #4 Write summits bed file... SRX016151.10_summits.bed INFO @ Tue, 21 Apr 2015 12:17:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1565 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。