Job ID = 2161227 sra ファイルのダウンロード中... Completed: 236863K bytes transferred in 5 seconds (336114K bits/sec), in 1 file, 2 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 13456 0 13456 0 0 24974 0 --:--:-- --:--:-- --:--:-- 38666 100 34472 0 34472 0 0 47328 0 --:--:-- --:--:-- --:--:-- 64074 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 9102392 spots for /home/okishinya/chipatlas/results/dm3/SRX013075/SRR030341.sra Written 9102392 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:02:03 9102392 reads; of these: 9102392 (100.00%) were unpaired; of these: 412563 (4.53%) aligned 0 times 7568340 (83.15%) aligned exactly 1 time 1121489 (12.32%) aligned >1 times 95.47% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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] 1353845 / 8689829 = 0.1558 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 12:08:27: # Command line: callpeak -t SRX013075.bam -f BAM -g dm -n SRX013075.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013075.10 # format = BAM # ChIP-seq file = ['SRX013075.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 12:08:27: # Command line: callpeak -t SRX013075.bam -f BAM -g dm -n SRX013075.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013075.05 # format = BAM # ChIP-seq file = ['SRX013075.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 12:08:27: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:08:27: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:08:27: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:08:27: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:08:27: # Command line: callpeak -t SRX013075.bam -f BAM -g dm -n SRX013075.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013075.20 # format = BAM # ChIP-seq file = ['SRX013075.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 12:08:27: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:08:27: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:08:32: 1000000 INFO @ Tue, 21 Apr 2015 12:08:34: 1000000 INFO @ Tue, 21 Apr 2015 12:08:34: 1000000 INFO @ Tue, 21 Apr 2015 12:08:38: 2000000 INFO @ Tue, 21 Apr 2015 12:08:41: 2000000 INFO @ Tue, 21 Apr 2015 12:08:41: 2000000 INFO @ Tue, 21 Apr 2015 12:08:44: 3000000 INFO @ Tue, 21 Apr 2015 12:08:48: 3000000 INFO @ Tue, 21 Apr 2015 12:08:48: 3000000 INFO @ Tue, 21 Apr 2015 12:08:50: 4000000 INFO @ Tue, 21 Apr 2015 12:08:55: 4000000 INFO @ Tue, 21 Apr 2015 12:08:55: 4000000 INFO @ Tue, 21 Apr 2015 12:08:56: 5000000 INFO @ Tue, 21 Apr 2015 12:09:01: 6000000 INFO @ Tue, 21 Apr 2015 12:09:03: 5000000 INFO @ Tue, 21 Apr 2015 12:09:03: 5000000 INFO @ Tue, 21 Apr 2015 12:09:07: 7000000 INFO @ Tue, 21 Apr 2015 12:09:09: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:09: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:09: #1 total tags in treatment: 7335984 INFO @ Tue, 21 Apr 2015 12:09:09: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:09: #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 12:09:10: 6000000 INFO @ Tue, 21 Apr 2015 12:09:10: 6000000 INFO @ Tue, 21 Apr 2015 12:09:10: #1 tags after filtering in treatment: 7335689 INFO @ Tue, 21 Apr 2015 12:09:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:10: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:10: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:12: #2 number of paired peaks: 2005 INFO @ Tue, 21 Apr 2015 12:09:12: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:17: 7000000 INFO @ Tue, 21 Apr 2015 12:09:17: 7000000 INFO @ Tue, 21 Apr 2015 12:09:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:20: #1 total tags in treatment: 7335984 INFO @ Tue, 21 Apr 2015 12:09:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:20: #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 12:09:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:20: #1 total tags in treatment: 7335984 INFO @ Tue, 21 Apr 2015 12:09:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:20: #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 12:09:20: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:20: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:20: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:20: #2 predicted fragment length is 114 bps INFO @ Tue, 21 Apr 2015 12:09:20: #2 alternative fragment length(s) may be 114 bps INFO @ Tue, 21 Apr 2015 12:09:20: #2.2 Generate R script for model : SRX013075.20_model.r INFO @ Tue, 21 Apr 2015 12:09:20: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:21: #1 tags after filtering in treatment: 7335689 INFO @ Tue, 21 Apr 2015 12:09:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:21: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:21: #1 tags after filtering in treatment: 7335689 INFO @ Tue, 21 Apr 2015 12:09:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:21: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:22: #2 number of paired peaks: 2005 INFO @ Tue, 21 Apr 2015 12:09:22: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:23: #2 number of paired peaks: 2005 INFO @ Tue, 21 Apr 2015 12:09:23: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:30: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:30: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:30: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:30: #2 predicted fragment length is 114 bps INFO @ Tue, 21 Apr 2015 12:09:30: #2 alternative fragment length(s) may be 114 bps INFO @ Tue, 21 Apr 2015 12:09:30: #2.2 Generate R script for model : SRX013075.10_model.r INFO @ Tue, 21 Apr 2015 12:09:30: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:30: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:30: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:30: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:30: #2 predicted fragment length is 114 bps INFO @ Tue, 21 Apr 2015 12:09:30: #2 alternative fragment length(s) may be 114 bps INFO @ Tue, 21 Apr 2015 12:09:30: #2.2 Generate R script for model : SRX013075.05_model.r INFO @ Tue, 21 Apr 2015 12:09:30: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:10:01: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:11: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:34: #4 Write output xls file... SRX013075.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:34: #4 Write peak in narrowPeak format file... SRX013075.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:34: #4 Write summits bed file... SRX013075.20_summits.bed INFO @ Tue, 21 Apr 2015 12:10:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2592 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:10:43: #4 Write output xls file... SRX013075.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:43: #4 Write peak in narrowPeak format file... SRX013075.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:43: #4 Write summits bed file... SRX013075.10_summits.bed INFO @ Tue, 21 Apr 2015 12:10:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5080 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:10:47: #4 Write output xls file... SRX013075.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:47: #4 Write peak in narrowPeak format file... SRX013075.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:47: #4 Write summits bed file... SRX013075.05_summits.bed INFO @ Tue, 21 Apr 2015 12:10:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7239 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。