Job ID = 2161222 sra ファイルのダウンロード中... Completed: 131264K bytes transferred in 4 seconds (222863K 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 34447 0 34447 0 0 46534 0 --:--:-- --:--:-- --:--:-- 62744 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 5088120 spots for /home/okishinya/chipatlas/results/dm3/SRX013070/SRR030336.sra Written 5088120 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: 00:01:06 5088120 reads; of these: 5088120 (100.00%) were unpaired; of these: 362322 (7.12%) aligned 0 times 4289623 (84.31%) aligned exactly 1 time 436175 (8.57%) aligned >1 times 92.88% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 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] 1623235 / 4725798 = 0.3435 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 12:06:01: # Command line: callpeak -t SRX013070.bam -f BAM -g dm -n SRX013070.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013070.10 # format = BAM # ChIP-seq file = ['SRX013070.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 12:06:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:06:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:06:01: # Command line: callpeak -t SRX013070.bam -f BAM -g dm -n SRX013070.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013070.05 # format = BAM # ChIP-seq file = ['SRX013070.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 12:06:01: # Command line: callpeak -t SRX013070.bam -f BAM -g dm -n SRX013070.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013070.20 # format = BAM # ChIP-seq file = ['SRX013070.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 12:06:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:06:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:06:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:06:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:06:06: 1000000 INFO @ Tue, 21 Apr 2015 12:06:07: 1000000 INFO @ Tue, 21 Apr 2015 12:06:07: 1000000 INFO @ Tue, 21 Apr 2015 12:06:12: 2000000 INFO @ Tue, 21 Apr 2015 12:06:14: 2000000 INFO @ Tue, 21 Apr 2015 12:06:14: 2000000 INFO @ Tue, 21 Apr 2015 12:06:18: 3000000 INFO @ Tue, 21 Apr 2015 12:06:18: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:06:18: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:06:18: #1 total tags in treatment: 3102563 INFO @ Tue, 21 Apr 2015 12:06:18: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:06:18: #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 12:06:19: #1 tags after filtering in treatment: 3102190 INFO @ Tue, 21 Apr 2015 12:06:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:06:19: #1 finished! INFO @ Tue, 21 Apr 2015 12:06:19: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:06:20: #2 number of paired peaks: 2058 INFO @ Tue, 21 Apr 2015 12:06:20: start model_add_line... INFO @ Tue, 21 Apr 2015 12:06:20: 3000000 INFO @ Tue, 21 Apr 2015 12:06:20: 3000000 INFO @ Tue, 21 Apr 2015 12:06:21: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:06:21: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:06:21: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:06:21: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:06:21: #1 total tags in treatment: 3102563 INFO @ Tue, 21 Apr 2015 12:06:21: #1 total tags in treatment: 3102563 INFO @ Tue, 21 Apr 2015 12:06:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:06:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:06:21: #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 12:06:21: #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 12:06:21: #1 tags after filtering in treatment: 3102190 INFO @ Tue, 21 Apr 2015 12:06:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:06:21: #1 finished! INFO @ Tue, 21 Apr 2015 12:06:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:06:22: #1 tags after filtering in treatment: 3102190 INFO @ Tue, 21 Apr 2015 12:06:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:06:22: #1 finished! INFO @ Tue, 21 Apr 2015 12:06:22: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:06:22: #2 number of paired peaks: 2058 INFO @ Tue, 21 Apr 2015 12:06:22: start model_add_line... INFO @ Tue, 21 Apr 2015 12:06:22: #2 number of paired peaks: 2058 INFO @ Tue, 21 Apr 2015 12:06:22: start model_add_line... INFO @ Tue, 21 Apr 2015 12:06:23: start X-correlation... INFO @ Tue, 21 Apr 2015 12:06:23: end of X-cor INFO @ Tue, 21 Apr 2015 12:06:23: #2 finished! INFO @ Tue, 21 Apr 2015 12:06:23: #2 predicted fragment length is 210 bps INFO @ Tue, 21 Apr 2015 12:06:23: #2 alternative fragment length(s) may be 210 bps INFO @ Tue, 21 Apr 2015 12:06:23: #2.2 Generate R script for model : SRX013070.20_model.r INFO @ Tue, 21 Apr 2015 12:06:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:06:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:06:26: start X-correlation... INFO @ Tue, 21 Apr 2015 12:06:26: end of X-cor INFO @ Tue, 21 Apr 2015 12:06:26: #2 finished! INFO @ Tue, 21 Apr 2015 12:06:26: #2 predicted fragment length is 210 bps INFO @ Tue, 21 Apr 2015 12:06:26: #2 alternative fragment length(s) may be 210 bps INFO @ Tue, 21 Apr 2015 12:06:26: #2.2 Generate R script for model : SRX013070.10_model.r INFO @ Tue, 21 Apr 2015 12:06:26: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:06:26: start X-correlation... INFO @ Tue, 21 Apr 2015 12:06:26: end of X-cor INFO @ Tue, 21 Apr 2015 12:06:26: #2 finished! INFO @ Tue, 21 Apr 2015 12:06:26: #2 predicted fragment length is 210 bps INFO @ Tue, 21 Apr 2015 12:06:26: #2 alternative fragment length(s) may be 210 bps INFO @ Tue, 21 Apr 2015 12:06:26: #2.2 Generate R script for model : SRX013070.05_model.r INFO @ Tue, 21 Apr 2015 12:06:26: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:06:41: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:06:44: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:06:44: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:06:55: #4 Write output xls file... SRX013070.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:06:55: #4 Write peak in narrowPeak format file... SRX013070.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:06:55: #4 Write summits bed file... SRX013070.20_summits.bed INFO @ Tue, 21 Apr 2015 12:06:55: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (340 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:06:58: #4 Write output xls file... SRX013070.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:06:58: #4 Write peak in narrowPeak format file... SRX013070.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:06:58: #4 Write summits bed file... SRX013070.10_summits.bed INFO @ Tue, 21 Apr 2015 12:06:58: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1345 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:07:00: #4 Write output xls file... SRX013070.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:07:00: #4 Write peak in narrowPeak format file... SRX013070.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:07:00: #4 Write summits bed file... SRX013070.05_summits.bed INFO @ Tue, 21 Apr 2015 12:07:00: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (3012 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。