Job ID = 2161413 sra ファイルのダウンロード中... Completed: 188212K bytes transferred in 5 seconds (271845K 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 44446 0 44446 0 0 46511 0 --:--:-- --:--:-- --:--:-- 58175 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 1342544 spots for /home/okishinya/chipatlas/results/dm3/SRX025486/SRR063890.sra Written 1342544 spots total Written 6114930 spots for /home/okishinya/chipatlas/results/dm3/SRX025486/SRR063889.sra Written 6114930 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: 00:00:01 Multiseed full-index search: 00:01:52 7457474 reads; of these: 7457474 (100.00%) were unpaired; of these: 539818 (7.24%) aligned 0 times 5615184 (75.30%) aligned exactly 1 time 1302472 (17.47%) aligned >1 times 92.76% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 2450085 / 6917656 = 0.3542 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 12:37:57: # Command line: callpeak -t SRX025486.bam -f BAM -g dm -n SRX025486.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX025486.10 # format = BAM # ChIP-seq file = ['SRX025486.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 12:37:57: # Command line: callpeak -t SRX025486.bam -f BAM -g dm -n SRX025486.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX025486.05 # format = BAM # ChIP-seq file = ['SRX025486.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 12:37:57: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:37:57: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:37:57: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:37:57: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:37:57: # Command line: callpeak -t SRX025486.bam -f BAM -g dm -n SRX025486.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX025486.20 # format = BAM # ChIP-seq file = ['SRX025486.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 12:37:57: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:37:57: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:38:02: 1000000 INFO @ Tue, 21 Apr 2015 12:38:02: 1000000 INFO @ Tue, 21 Apr 2015 12:38:02: 1000000 INFO @ Tue, 21 Apr 2015 12:38:06: 2000000 INFO @ Tue, 21 Apr 2015 12:38:07: 2000000 INFO @ Tue, 21 Apr 2015 12:38:07: 2000000 INFO @ Tue, 21 Apr 2015 12:38:11: 3000000 INFO @ Tue, 21 Apr 2015 12:38:12: 3000000 INFO @ Tue, 21 Apr 2015 12:38:12: 3000000 INFO @ Tue, 21 Apr 2015 12:38:16: 4000000 INFO @ Tue, 21 Apr 2015 12:38:17: 4000000 INFO @ Tue, 21 Apr 2015 12:38:17: 4000000 INFO @ Tue, 21 Apr 2015 12:38:19: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:38:19: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:38:19: #1 total tags in treatment: 4467571 INFO @ Tue, 21 Apr 2015 12:38:19: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:38:19: #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 12:38:19: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:38:19: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:38:19: #1 total tags in treatment: 4467571 INFO @ Tue, 21 Apr 2015 12:38:19: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:38:19: #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 12:38:19: #1 tags after filtering in treatment: 4467198 INFO @ Tue, 21 Apr 2015 12:38:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:38:19: #1 finished! INFO @ Tue, 21 Apr 2015 12:38:19: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:38:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:38:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:38:20: #1 total tags in treatment: 4467571 INFO @ Tue, 21 Apr 2015 12:38:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:38:20: #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 12:38:20: #1 tags after filtering in treatment: 4467198 INFO @ Tue, 21 Apr 2015 12:38:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:38:20: #1 finished! INFO @ Tue, 21 Apr 2015 12:38:20: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:38:20: #1 tags after filtering in treatment: 4467198 INFO @ Tue, 21 Apr 2015 12:38:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:38:20: #1 finished! INFO @ Tue, 21 Apr 2015 12:38:20: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:38:21: #2 number of paired peaks: 5682 INFO @ Tue, 21 Apr 2015 12:38:21: start model_add_line... INFO @ Tue, 21 Apr 2015 12:38:21: #2 number of paired peaks: 5682 INFO @ Tue, 21 Apr 2015 12:38:21: start model_add_line... INFO @ Tue, 21 Apr 2015 12:38:22: #2 number of paired peaks: 5682 INFO @ Tue, 21 Apr 2015 12:38:22: start model_add_line... INFO @ Tue, 21 Apr 2015 12:38:36: start X-correlation... INFO @ Tue, 21 Apr 2015 12:38:36: end of X-cor INFO @ Tue, 21 Apr 2015 12:38:36: #2 finished! INFO @ Tue, 21 Apr 2015 12:38:36: #2 predicted fragment length is 107 bps INFO @ Tue, 21 Apr 2015 12:38:36: #2 alternative fragment length(s) may be 107 bps INFO @ Tue, 21 Apr 2015 12:38:36: #2.2 Generate R script for model : SRX025486.05_model.r INFO @ Tue, 21 Apr 2015 12:38:36: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:38:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:38:37: start X-correlation... INFO @ Tue, 21 Apr 2015 12:38:37: end of X-cor INFO @ Tue, 21 Apr 2015 12:38:37: #2 finished! INFO @ Tue, 21 Apr 2015 12:38:37: #2 predicted fragment length is 107 bps INFO @ Tue, 21 Apr 2015 12:38:37: #2 alternative fragment length(s) may be 107 bps INFO @ Tue, 21 Apr 2015 12:38:37: #2.2 Generate R script for model : SRX025486.10_model.r INFO @ Tue, 21 Apr 2015 12:38:37: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:38:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:38:37: start X-correlation... INFO @ Tue, 21 Apr 2015 12:38:37: end of X-cor INFO @ Tue, 21 Apr 2015 12:38:37: #2 finished! INFO @ Tue, 21 Apr 2015 12:38:37: #2 predicted fragment length is 107 bps INFO @ Tue, 21 Apr 2015 12:38:37: #2 alternative fragment length(s) may be 107 bps INFO @ Tue, 21 Apr 2015 12:38:37: #2.2 Generate R script for model : SRX025486.20_model.r INFO @ Tue, 21 Apr 2015 12:38:37: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:38:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:39:01: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:39:02: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:39:03: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:39:24: #4 Write output xls file... SRX025486.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:39:24: #4 Write peak in narrowPeak format file... SRX025486.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:39:24: #4 Write summits bed file... SRX025486.20_summits.bed INFO @ Tue, 21 Apr 2015 12:39:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2025 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:39:26: #4 Write output xls file... SRX025486.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:39:26: #4 Write peak in narrowPeak format file... SRX025486.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:39:26: #4 Write summits bed file... SRX025486.10_summits.bed INFO @ Tue, 21 Apr 2015 12:39:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5895 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:39:27: #4 Write output xls file... SRX025486.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:39:27: #4 Write peak in narrowPeak format file... SRX025486.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:39:27: #4 Write summits bed file... SRX025486.05_summits.bed INFO @ Tue, 21 Apr 2015 12:39:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8396 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。