Job ID = 2161559 sra ファイルのダウンロード中... Completed: 835584K bytes transferred in 12 seconds (555088K 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 --:--:-- --:--:-- --:--:-- 0 101 2540 0 2540 0 0 3696 0 --:--:-- --:--:-- --:--:-- 5120 100 44637 0 44637 0 0 41877 0 --:--:-- 0:00:01 --:--:-- 51013 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 23027607 spots for /home/okishinya/chipatlas/results/dm3/SRX030148/SRR071262.sra Written 23027607 spots total Written 27468934 spots for /home/okishinya/chipatlas/results/dm3/SRX030148/SRR071263.sra Written 27468934 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: 00:17:11 50496541 reads; of these: 50496541 (100.00%) were unpaired; of these: 11826397 (23.42%) aligned 0 times 24899375 (49.31%) aligned exactly 1 time 13770769 (27.27%) aligned >1 times 76.58% overall alignment rate Time searching: 00:17:11 Overall time: 00:17:11 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 12 files... [bam_rmdupse_core] 31191284 / 38670144 = 0.8066 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 13:12:23: # Command line: callpeak -t SRX030148.bam -f BAM -g dm -n SRX030148.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX030148.20 # format = BAM # ChIP-seq file = ['SRX030148.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 13:12:23: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:12:23: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:12:23: # Command line: callpeak -t SRX030148.bam -f BAM -g dm -n SRX030148.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX030148.05 # format = BAM # ChIP-seq file = ['SRX030148.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 13:12:23: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:12:23: # Command line: callpeak -t SRX030148.bam -f BAM -g dm -n SRX030148.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX030148.10 # format = BAM # ChIP-seq file = ['SRX030148.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 13:12:23: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:12:23: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:12:23: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:12:28: 1000000 INFO @ Tue, 21 Apr 2015 13:12:28: 1000000 INFO @ Tue, 21 Apr 2015 13:12:28: 1000000 INFO @ Tue, 21 Apr 2015 13:12:33: 2000000 INFO @ Tue, 21 Apr 2015 13:12:34: 2000000 INFO @ Tue, 21 Apr 2015 13:12:34: 2000000 INFO @ Tue, 21 Apr 2015 13:12:38: 3000000 INFO @ Tue, 21 Apr 2015 13:12:39: 3000000 INFO @ Tue, 21 Apr 2015 13:12:39: 3000000 INFO @ Tue, 21 Apr 2015 13:12:44: 4000000 INFO @ Tue, 21 Apr 2015 13:12:45: 4000000 INFO @ Tue, 21 Apr 2015 13:12:45: 4000000 INFO @ Tue, 21 Apr 2015 13:12:49: 5000000 INFO @ Tue, 21 Apr 2015 13:12:51: 5000000 INFO @ Tue, 21 Apr 2015 13:12:51: 5000000 INFO @ Tue, 21 Apr 2015 13:12:54: 6000000 INFO @ Tue, 21 Apr 2015 13:12:56: 6000000 INFO @ Tue, 21 Apr 2015 13:12:56: 6000000 INFO @ Tue, 21 Apr 2015 13:12:59: 7000000 INFO @ Tue, 21 Apr 2015 13:13:02: 7000000 INFO @ Tue, 21 Apr 2015 13:13:02: 7000000 INFO @ Tue, 21 Apr 2015 13:13:02: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:13:02: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:13:02: #1 total tags in treatment: 7478860 INFO @ Tue, 21 Apr 2015 13:13:02: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:13:02: #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 13:13:03: #1 tags after filtering in treatment: 7476085 INFO @ Tue, 21 Apr 2015 13:13:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:13:03: #1 finished! INFO @ Tue, 21 Apr 2015 13:13:03: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:13:04: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:13:04: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:13:04: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:13:04: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:13:04: #1 total tags in treatment: 7478860 INFO @ Tue, 21 Apr 2015 13:13:04: #1 total tags in treatment: 7478860 INFO @ Tue, 21 Apr 2015 13:13:04: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:13:04: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:13:04: #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 13:13:04: #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 13:13:05: #2 number of paired peaks: 3407 INFO @ Tue, 21 Apr 2015 13:13:05: start model_add_line... INFO @ Tue, 21 Apr 2015 13:13:06: #1 tags after filtering in treatment: 7476085 INFO @ Tue, 21 Apr 2015 13:13:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:13:06: #1 finished! INFO @ Tue, 21 Apr 2015 13:13:06: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:13:06: #1 tags after filtering in treatment: 7476085 INFO @ Tue, 21 Apr 2015 13:13:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:13:06: #1 finished! INFO @ Tue, 21 Apr 2015 13:13:06: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:13:08: #2 number of paired peaks: 3407 INFO @ Tue, 21 Apr 2015 13:13:08: start model_add_line... INFO @ Tue, 21 Apr 2015 13:13:08: #2 number of paired peaks: 3407 INFO @ Tue, 21 Apr 2015 13:13:08: start model_add_line... INFO @ Tue, 21 Apr 2015 13:13:22: start X-correlation... INFO @ Tue, 21 Apr 2015 13:13:22: end of X-cor INFO @ Tue, 21 Apr 2015 13:13:22: #2 finished! INFO @ Tue, 21 Apr 2015 13:13:22: #2 predicted fragment length is 129 bps INFO @ Tue, 21 Apr 2015 13:13:22: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 21 Apr 2015 13:13:22: #2.2 Generate R script for model : SRX030148.10_model.r INFO @ Tue, 21 Apr 2015 13:13:22: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:13:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:13:25: start X-correlation... INFO @ Tue, 21 Apr 2015 13:13:25: end of X-cor INFO @ Tue, 21 Apr 2015 13:13:25: #2 finished! INFO @ Tue, 21 Apr 2015 13:13:25: #2 predicted fragment length is 129 bps INFO @ Tue, 21 Apr 2015 13:13:25: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 21 Apr 2015 13:13:25: #2.2 Generate R script for model : SRX030148.05_model.r INFO @ Tue, 21 Apr 2015 13:13:25: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:13:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:13:26: start X-correlation... INFO @ Tue, 21 Apr 2015 13:13:26: end of X-cor INFO @ Tue, 21 Apr 2015 13:13:26: #2 finished! INFO @ Tue, 21 Apr 2015 13:13:26: #2 predicted fragment length is 129 bps INFO @ Tue, 21 Apr 2015 13:13:26: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 21 Apr 2015 13:13:26: #2.2 Generate R script for model : SRX030148.20_model.r INFO @ Tue, 21 Apr 2015 13:13:26: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:13:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:14:07: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:14:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:14:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:14:43: #4 Write output xls file... SRX030148.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:14:43: #4 Write peak in narrowPeak format file... SRX030148.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:14:43: #4 Write output xls file... SRX030148.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:14:43: #4 Write summits bed file... SRX030148.10_summits.bed INFO @ Tue, 21 Apr 2015 13:14:43: #4 Write peak in narrowPeak format file... SRX030148.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:14:43: Done! INFO @ Tue, 21 Apr 2015 13:14:43: #4 Write summits bed file... SRX030148.20_summits.bed INFO @ Tue, 21 Apr 2015 13:14:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6484 records, 4 fields): 9 millis pass1 - making usageList (15 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (4201 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:14:51: #4 Write output xls file... SRX030148.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:14:51: #4 Write peak in narrowPeak format file... SRX030148.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:14:51: #4 Write summits bed file... SRX030148.05_summits.bed INFO @ Tue, 21 Apr 2015 13:14:51: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11080 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。