Job ID = 2162375 sra ファイルのダウンロード中... Completed: 425958K bytes transferred in 7 seconds (468465K 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 12008 0 12008 0 0 22194 0 --:--:-- --:--:-- --:--:-- 34308 100 34901 0 34901 0 0 47769 0 --:--:-- --:--:-- --:--:-- 64631 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 22573162 spots for /home/okishinya/chipatlas/results/dm3/SRX050608/SRR139090.sra Written 22573162 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: 00:04:09 22573162 reads; of these: 22573162 (100.00%) were unpaired; of these: 5991267 (26.54%) aligned 0 times 14984252 (66.38%) aligned exactly 1 time 1597643 (7.08%) aligned >1 times 73.46% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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 8 files... [bam_rmdupse_core] 6977350 / 16581895 = 0.4208 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 13:44:55: # Command line: callpeak -t SRX050608.bam -f BAM -g dm -n SRX050608.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX050608.20 # format = BAM # ChIP-seq file = ['SRX050608.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 13:44:55: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:44:55: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:44:55: # Command line: callpeak -t SRX050608.bam -f BAM -g dm -n SRX050608.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX050608.05 # format = BAM # ChIP-seq file = ['SRX050608.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 13:44:55: # Command line: callpeak -t SRX050608.bam -f BAM -g dm -n SRX050608.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX050608.10 # format = BAM # ChIP-seq file = ['SRX050608.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 13:44:55: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:44:55: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:44:55: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:44:55: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:45:00: 1000000 INFO @ Tue, 21 Apr 2015 13:45:00: 1000000 INFO @ Tue, 21 Apr 2015 13:45:00: 1000000 INFO @ Tue, 21 Apr 2015 13:45:05: 2000000 INFO @ Tue, 21 Apr 2015 13:45:05: 2000000 INFO @ Tue, 21 Apr 2015 13:45:05: 2000000 INFO @ Tue, 21 Apr 2015 13:45:10: 3000000 INFO @ Tue, 21 Apr 2015 13:45:10: 3000000 INFO @ Tue, 21 Apr 2015 13:45:10: 3000000 INFO @ Tue, 21 Apr 2015 13:45:15: 4000000 INFO @ Tue, 21 Apr 2015 13:45:15: 4000000 INFO @ Tue, 21 Apr 2015 13:45:15: 4000000 INFO @ Tue, 21 Apr 2015 13:45:20: 5000000 INFO @ Tue, 21 Apr 2015 13:45:20: 5000000 INFO @ Tue, 21 Apr 2015 13:45:20: 5000000 INFO @ Tue, 21 Apr 2015 13:45:25: 6000000 INFO @ Tue, 21 Apr 2015 13:45:25: 6000000 INFO @ Tue, 21 Apr 2015 13:45:25: 6000000 INFO @ Tue, 21 Apr 2015 13:45:30: 7000000 INFO @ Tue, 21 Apr 2015 13:45:30: 7000000 INFO @ Tue, 21 Apr 2015 13:45:30: 7000000 INFO @ Tue, 21 Apr 2015 13:45:35: 8000000 INFO @ Tue, 21 Apr 2015 13:45:35: 8000000 INFO @ Tue, 21 Apr 2015 13:45:35: 8000000 INFO @ Tue, 21 Apr 2015 13:45:39: 9000000 INFO @ Tue, 21 Apr 2015 13:45:40: 9000000 INFO @ Tue, 21 Apr 2015 13:45:40: 9000000 INFO @ Tue, 21 Apr 2015 13:45:42: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:45:42: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:45:42: #1 total tags in treatment: 9604545 INFO @ Tue, 21 Apr 2015 13:45:42: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:45:42: #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 13:45:43: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:45:43: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:45:43: #1 total tags in treatment: 9604545 INFO @ Tue, 21 Apr 2015 13:45:43: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:45:43: #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 13:45:44: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:45:44: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:45:44: #1 total tags in treatment: 9604545 INFO @ Tue, 21 Apr 2015 13:45:44: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:45:44: #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 13:45:44: #1 tags after filtering in treatment: 9603309 INFO @ Tue, 21 Apr 2015 13:45:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:45:44: #1 finished! INFO @ Tue, 21 Apr 2015 13:45:44: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:45:45: #1 tags after filtering in treatment: 9603309 INFO @ Tue, 21 Apr 2015 13:45:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:45:45: #1 finished! INFO @ Tue, 21 Apr 2015 13:45:45: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:45:45: #1 tags after filtering in treatment: 9603309 INFO @ Tue, 21 Apr 2015 13:45:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:45:45: #1 finished! INFO @ Tue, 21 Apr 2015 13:45:45: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:45:46: #2 number of paired peaks: 1479 INFO @ Tue, 21 Apr 2015 13:45:46: start model_add_line... INFO @ Tue, 21 Apr 2015 13:45:47: #2 number of paired peaks: 1479 INFO @ Tue, 21 Apr 2015 13:45:47: start model_add_line... INFO @ Tue, 21 Apr 2015 13:45:47: #2 number of paired peaks: 1479 INFO @ Tue, 21 Apr 2015 13:45:47: start model_add_line... INFO @ Tue, 21 Apr 2015 13:45:55: start X-correlation... INFO @ Tue, 21 Apr 2015 13:45:55: end of X-cor INFO @ Tue, 21 Apr 2015 13:45:55: #2 finished! INFO @ Tue, 21 Apr 2015 13:45:55: #2 predicted fragment length is 136 bps INFO @ Tue, 21 Apr 2015 13:45:55: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 21 Apr 2015 13:45:55: #2.2 Generate R script for model : SRX050608.05_model.r INFO @ Tue, 21 Apr 2015 13:45:55: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:45:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:45:55: start X-correlation... INFO @ Tue, 21 Apr 2015 13:45:55: end of X-cor INFO @ Tue, 21 Apr 2015 13:45:55: #2 finished! INFO @ Tue, 21 Apr 2015 13:45:55: #2 predicted fragment length is 136 bps INFO @ Tue, 21 Apr 2015 13:45:55: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 21 Apr 2015 13:45:55: #2.2 Generate R script for model : SRX050608.20_model.r INFO @ Tue, 21 Apr 2015 13:45:55: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:45:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:45:55: start X-correlation... INFO @ Tue, 21 Apr 2015 13:45:55: end of X-cor INFO @ Tue, 21 Apr 2015 13:45:55: #2 finished! INFO @ Tue, 21 Apr 2015 13:45:55: #2 predicted fragment length is 136 bps INFO @ Tue, 21 Apr 2015 13:45:55: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 21 Apr 2015 13:45:55: #2.2 Generate R script for model : SRX050608.10_model.r INFO @ Tue, 21 Apr 2015 13:45:55: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:45:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:46:48: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:46:49: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:46:52: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:47:29: #4 Write output xls file... SRX050608.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:47:29: #4 Write peak in narrowPeak format file... SRX050608.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:47:29: #4 Write summits bed file... SRX050608.20_summits.bed INFO @ Tue, 21 Apr 2015 13:47:29: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2408 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:47:31: #4 Write output xls file... SRX050608.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:47:31: #4 Write peak in narrowPeak format file... SRX050608.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:47:31: #4 Write summits bed file... SRX050608.10_summits.bed INFO @ Tue, 21 Apr 2015 13:47:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4688 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:47:39: #4 Write output xls file... SRX050608.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:47:40: #4 Write peak in narrowPeak format file... SRX050608.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:47:40: #4 Write summits bed file... SRX050608.05_summits.bed INFO @ Tue, 21 Apr 2015 13:47:40: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7085 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。