Job ID = 2161218 sra ファイルのダウンロード中... Completed: 247162K bytes transferred in 5 seconds (343084K 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 4000 0 4000 0 0 7535 0 --:--:-- --:--:-- --:--:-- 11764 100 34478 0 34478 0 0 47699 0 --:--:-- --:--:-- --:--:-- 64808 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 9192292 spots for /home/okishinya/chipatlas/results/dm3/SRX013066/SRR030332.sra Written 9192292 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: 00:02:00 9192292 reads; of these: 9192292 (100.00%) were unpaired; of these: 415740 (4.52%) aligned 0 times 7873080 (85.65%) aligned exactly 1 time 903472 (9.83%) aligned >1 times 95.48% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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] 747332 / 8776552 = 0.0852 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 12:07:52: # Command line: callpeak -t SRX013066.bam -f BAM -g dm -n SRX013066.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013066.05 # format = BAM # ChIP-seq file = ['SRX013066.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 12:07:52: # Command line: callpeak -t SRX013066.bam -f BAM -g dm -n SRX013066.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013066.20 # format = BAM # ChIP-seq file = ['SRX013066.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 12:07:52: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:07:52: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:07:52: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:07:52: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:07:52: # Command line: callpeak -t SRX013066.bam -f BAM -g dm -n SRX013066.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013066.10 # format = BAM # ChIP-seq file = ['SRX013066.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 12:07:52: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:07:52: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:07:57: 1000000 INFO @ Tue, 21 Apr 2015 12:07:57: 1000000 INFO @ Tue, 21 Apr 2015 12:07:57: 1000000 INFO @ Tue, 21 Apr 2015 12:08:02: 2000000 INFO @ Tue, 21 Apr 2015 12:08:02: 2000000 INFO @ Tue, 21 Apr 2015 12:08:03: 2000000 INFO @ Tue, 21 Apr 2015 12:08:08: 3000000 INFO @ Tue, 21 Apr 2015 12:08:08: 3000000 INFO @ Tue, 21 Apr 2015 12:08:08: 3000000 INFO @ Tue, 21 Apr 2015 12:08:13: 4000000 INFO @ Tue, 21 Apr 2015 12:08:13: 4000000 INFO @ Tue, 21 Apr 2015 12:08:13: 4000000 INFO @ Tue, 21 Apr 2015 12:08:18: 5000000 INFO @ Tue, 21 Apr 2015 12:08:18: 5000000 INFO @ Tue, 21 Apr 2015 12:08:19: 5000000 INFO @ Tue, 21 Apr 2015 12:08:23: 6000000 INFO @ Tue, 21 Apr 2015 12:08:23: 6000000 INFO @ Tue, 21 Apr 2015 12:08:24: 6000000 INFO @ Tue, 21 Apr 2015 12:08:28: 7000000 INFO @ Tue, 21 Apr 2015 12:08:29: 7000000 INFO @ Tue, 21 Apr 2015 12:08:30: 7000000 INFO @ Tue, 21 Apr 2015 12:08:34: 8000000 INFO @ Tue, 21 Apr 2015 12:08:34: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:08:34: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:08:34: #1 total tags in treatment: 8029220 INFO @ Tue, 21 Apr 2015 12:08:34: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:08:34: #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 12:08:34: 8000000 INFO @ Tue, 21 Apr 2015 12:08:34: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:08:34: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:08:34: #1 total tags in treatment: 8029220 INFO @ Tue, 21 Apr 2015 12:08:34: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:08:34: #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 12:08:35: 8000000 INFO @ Tue, 21 Apr 2015 12:08:35: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:08:35: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:08:35: #1 total tags in treatment: 8029220 INFO @ Tue, 21 Apr 2015 12:08:35: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:08:35: #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 12:08:35: #1 tags after filtering in treatment: 8028868 INFO @ Tue, 21 Apr 2015 12:08:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:08:35: #1 finished! INFO @ Tue, 21 Apr 2015 12:08:35: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:08:36: #1 tags after filtering in treatment: 8028868 INFO @ Tue, 21 Apr 2015 12:08:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:08:36: #1 finished! INFO @ Tue, 21 Apr 2015 12:08:36: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:08:37: #1 tags after filtering in treatment: 8028868 INFO @ Tue, 21 Apr 2015 12:08:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:08:37: #1 finished! INFO @ Tue, 21 Apr 2015 12:08:37: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:08:37: #2 number of paired peaks: 1779 INFO @ Tue, 21 Apr 2015 12:08:37: start model_add_line... INFO @ Tue, 21 Apr 2015 12:08:37: #2 number of paired peaks: 1779 INFO @ Tue, 21 Apr 2015 12:08:37: start model_add_line... INFO @ Tue, 21 Apr 2015 12:08:38: #2 number of paired peaks: 1779 INFO @ Tue, 21 Apr 2015 12:08:38: start model_add_line... INFO @ Tue, 21 Apr 2015 12:08:45: start X-correlation... INFO @ Tue, 21 Apr 2015 12:08:45: end of X-cor INFO @ Tue, 21 Apr 2015 12:08:45: #2 finished! INFO @ Tue, 21 Apr 2015 12:08:45: #2 predicted fragment length is 150 bps INFO @ Tue, 21 Apr 2015 12:08:45: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 21 Apr 2015 12:08:45: #2.2 Generate R script for model : SRX013066.05_model.r INFO @ Tue, 21 Apr 2015 12:08:45: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:08:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:08:45: start X-correlation... INFO @ Tue, 21 Apr 2015 12:08:45: end of X-cor INFO @ Tue, 21 Apr 2015 12:08:45: #2 finished! INFO @ Tue, 21 Apr 2015 12:08:45: #2 predicted fragment length is 150 bps INFO @ Tue, 21 Apr 2015 12:08:45: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 21 Apr 2015 12:08:45: #2.2 Generate R script for model : SRX013066.20_model.r INFO @ Tue, 21 Apr 2015 12:08:45: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:08:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:08:46: start X-correlation... INFO @ Tue, 21 Apr 2015 12:08:46: end of X-cor INFO @ Tue, 21 Apr 2015 12:08:46: #2 finished! INFO @ Tue, 21 Apr 2015 12:08:46: #2 predicted fragment length is 150 bps INFO @ Tue, 21 Apr 2015 12:08:46: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 21 Apr 2015 12:08:46: #2.2 Generate R script for model : SRX013066.10_model.r INFO @ Tue, 21 Apr 2015 12:08:46: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:08:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:29: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:31: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:35: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:05: #4 Write output xls file... SRX013066.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:05: #4 Write peak in narrowPeak format file... SRX013066.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:05: #4 Write summits bed file... SRX013066.20_summits.bed INFO @ Tue, 21 Apr 2015 12:10:05: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1871 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:10:09: #4 Write output xls file... SRX013066.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:09: #4 Write peak in narrowPeak format file... SRX013066.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:09: #4 Write summits bed file... SRX013066.05_summits.bed INFO @ Tue, 21 Apr 2015 12:10:09: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7303 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:10:13: #4 Write output xls file... SRX013066.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:13: #4 Write peak in narrowPeak format file... SRX013066.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:13: #4 Write summits bed file... SRX013066.10_summits.bed INFO @ Tue, 21 Apr 2015 12:10:13: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4663 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。