Job ID = 2161551 sra ファイルのダウンロード中... Completed: 6996603K bytes transferred in 96 seconds (591390K 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 4007 0 4007 0 0 7049 0 --:--:-- --:--:-- --:--:-- 10600 100 37096 0 37096 0 0 48913 0 --:--:-- --:--:-- --:--:-- 65309 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 11712269 spots for /home/okishinya/chipatlas/results/dm3/SRX027827/SRR067910.sra Written 11712269 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:00 11712269 reads; of these: 11712269 (100.00%) were unpaired; of these: 3577360 (30.54%) aligned 0 times 5686598 (48.55%) aligned exactly 1 time 2448311 (20.90%) aligned >1 times 69.46% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 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] 1824308 / 8134909 = 0.2243 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 12:52:13: # Command line: callpeak -t SRX027827.bam -f BAM -g dm -n SRX027827.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX027827.05 # format = BAM # ChIP-seq file = ['SRX027827.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 12:52:13: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:52:13: # Command line: callpeak -t SRX027827.bam -f BAM -g dm -n SRX027827.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX027827.10 # format = BAM # ChIP-seq file = ['SRX027827.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 12:52:13: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:52:13: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:52:13: # Command line: callpeak -t SRX027827.bam -f BAM -g dm -n SRX027827.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX027827.20 # format = BAM # ChIP-seq file = ['SRX027827.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 12:52:13: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:52:13: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:52:13: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:52:19: 1000000 INFO @ Tue, 21 Apr 2015 12:52:19: 1000000 INFO @ Tue, 21 Apr 2015 12:52:19: 1000000 INFO @ Tue, 21 Apr 2015 12:52:24: 2000000 INFO @ Tue, 21 Apr 2015 12:52:24: 2000000 INFO @ Tue, 21 Apr 2015 12:52:24: 2000000 INFO @ Tue, 21 Apr 2015 12:52:29: 3000000 INFO @ Tue, 21 Apr 2015 12:52:30: 3000000 INFO @ Tue, 21 Apr 2015 12:52:30: 3000000 INFO @ Tue, 21 Apr 2015 12:52:34: 4000000 INFO @ Tue, 21 Apr 2015 12:52:35: 4000000 INFO @ Tue, 21 Apr 2015 12:52:36: 4000000 INFO @ Tue, 21 Apr 2015 12:52:39: 5000000 INFO @ Tue, 21 Apr 2015 12:52:41: 5000000 INFO @ Tue, 21 Apr 2015 12:52:41: 5000000 INFO @ Tue, 21 Apr 2015 12:52:45: 6000000 INFO @ Tue, 21 Apr 2015 12:52:46: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:52:46: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:52:46: #1 total tags in treatment: 6310601 INFO @ Tue, 21 Apr 2015 12:52:46: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:52:46: #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 12:52:46: 6000000 INFO @ Tue, 21 Apr 2015 12:52:47: 6000000 INFO @ Tue, 21 Apr 2015 12:52:47: #1 tags after filtering in treatment: 6309952 INFO @ Tue, 21 Apr 2015 12:52:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:52:47: #1 finished! INFO @ Tue, 21 Apr 2015 12:52:47: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:52:48: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:52:48: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:52:48: #1 total tags in treatment: 6310601 INFO @ Tue, 21 Apr 2015 12:52:48: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:52:48: #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 12:52:49: #2 number of paired peaks: 2016 INFO @ Tue, 21 Apr 2015 12:52:49: start model_add_line... INFO @ Tue, 21 Apr 2015 12:52:49: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:52:49: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:52:49: #1 total tags in treatment: 6310601 INFO @ Tue, 21 Apr 2015 12:52:49: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:52:49: #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 12:52:49: #1 tags after filtering in treatment: 6309952 INFO @ Tue, 21 Apr 2015 12:52:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:52:49: #1 finished! INFO @ Tue, 21 Apr 2015 12:52:49: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:52:50: #1 tags after filtering in treatment: 6309952 INFO @ Tue, 21 Apr 2015 12:52:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:52:50: #1 finished! INFO @ Tue, 21 Apr 2015 12:52:50: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:52:51: #2 number of paired peaks: 2016 INFO @ Tue, 21 Apr 2015 12:52:51: start model_add_line... INFO @ Tue, 21 Apr 2015 12:52:52: #2 number of paired peaks: 2016 INFO @ Tue, 21 Apr 2015 12:52:52: start model_add_line... INFO @ Tue, 21 Apr 2015 12:52:58: start X-correlation... INFO @ Tue, 21 Apr 2015 12:52:58: end of X-cor INFO @ Tue, 21 Apr 2015 12:52:58: #2 finished! INFO @ Tue, 21 Apr 2015 12:52:58: #2 predicted fragment length is 75 bps INFO @ Tue, 21 Apr 2015 12:52:58: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 21 Apr 2015 12:52:58: #2.2 Generate R script for model : SRX027827.20_model.r INFO @ Tue, 21 Apr 2015 12:52:58: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:52:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:53:00: start X-correlation... INFO @ Tue, 21 Apr 2015 12:53:00: end of X-cor INFO @ Tue, 21 Apr 2015 12:53:00: #2 finished! INFO @ Tue, 21 Apr 2015 12:53:00: #2 predicted fragment length is 75 bps INFO @ Tue, 21 Apr 2015 12:53:00: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 21 Apr 2015 12:53:00: #2.2 Generate R script for model : SRX027827.10_model.r INFO @ Tue, 21 Apr 2015 12:53:00: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:53:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:53:00: start X-correlation... INFO @ Tue, 21 Apr 2015 12:53:00: end of X-cor INFO @ Tue, 21 Apr 2015 12:53:00: #2 finished! INFO @ Tue, 21 Apr 2015 12:53:00: #2 predicted fragment length is 75 bps INFO @ Tue, 21 Apr 2015 12:53:00: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 21 Apr 2015 12:53:00: #2.2 Generate R script for model : SRX027827.05_model.r INFO @ Tue, 21 Apr 2015 12:53:00: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:53:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:53:35: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:53:35: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:53:37: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:54:02: #4 Write output xls file... SRX027827.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:54:02: #4 Write peak in narrowPeak format file... SRX027827.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:54:02: #4 Write summits bed file... SRX027827.10_summits.bed INFO @ Tue, 21 Apr 2015 12:54:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3089 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:54:03: #4 Write output xls file... SRX027827.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:54:03: #4 Write peak in narrowPeak format file... SRX027827.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:54:03: #4 Write output xls file... SRX027827.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:54:03: #4 Write summits bed file... SRX027827.05_summits.bed INFO @ Tue, 21 Apr 2015 12:54:03: #4 Write peak in narrowPeak format file... SRX027827.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:54:03: #4 Write summits bed file... SRX027827.20_summits.bed INFO @ Tue, 21 Apr 2015 12:54:03: Done! INFO @ Tue, 21 Apr 2015 12:54:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1427 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5118 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。