Job ID = 2161423 sra ファイルのダウンロード中... Completed: 395641K bytes transferred in 6 seconds (490295K 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 23619 0 --:--:-- --:--:-- --:--:-- 35503 100 35840 0 35840 0 0 47193 0 --:--:-- --:--:-- --:--:-- 62987 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 15350276 spots for /home/okishinya/chipatlas/results/dm3/SRX026741/SRR065627.sra Written 15350276 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: 00:00:01 Multiseed full-index search: 00:02:40 15350276 reads; of these: 15350276 (100.00%) were unpaired; of these: 5908130 (38.49%) aligned 0 times 8237838 (53.67%) aligned exactly 1 time 1204308 (7.85%) aligned >1 times 61.51% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 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] 2044172 / 9442146 = 0.2165 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 12:42:50: # Command line: callpeak -t SRX026741.bam -f BAM -g dm -n SRX026741.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX026741.05 # format = BAM # ChIP-seq file = ['SRX026741.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 12:42:50: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:42:50: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:42:50: # Command line: callpeak -t SRX026741.bam -f BAM -g dm -n SRX026741.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX026741.10 # format = BAM # ChIP-seq file = ['SRX026741.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 12:42:50: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:42:50: # Command line: callpeak -t SRX026741.bam -f BAM -g dm -n SRX026741.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX026741.20 # format = BAM # ChIP-seq file = ['SRX026741.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 12:42:50: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:42:50: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:42:50: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:42:56: 1000000 INFO @ Tue, 21 Apr 2015 12:42:56: 1000000 INFO @ Tue, 21 Apr 2015 12:42:56: 1000000 INFO @ Tue, 21 Apr 2015 12:43:01: 2000000 INFO @ Tue, 21 Apr 2015 12:43:01: 2000000 INFO @ Tue, 21 Apr 2015 12:43:03: 2000000 INFO @ Tue, 21 Apr 2015 12:43:07: 3000000 INFO @ Tue, 21 Apr 2015 12:43:07: 3000000 INFO @ Tue, 21 Apr 2015 12:43:10: 3000000 INFO @ Tue, 21 Apr 2015 12:43:13: 4000000 INFO @ Tue, 21 Apr 2015 12:43:13: 4000000 INFO @ Tue, 21 Apr 2015 12:43:16: 4000000 INFO @ Tue, 21 Apr 2015 12:43:19: 5000000 INFO @ Tue, 21 Apr 2015 12:43:19: 5000000 INFO @ Tue, 21 Apr 2015 12:43:23: 5000000 INFO @ Tue, 21 Apr 2015 12:43:25: 6000000 INFO @ Tue, 21 Apr 2015 12:43:25: 6000000 INFO @ Tue, 21 Apr 2015 12:43:30: 6000000 INFO @ Tue, 21 Apr 2015 12:43:31: 7000000 INFO @ Tue, 21 Apr 2015 12:43:31: 7000000 INFO @ Tue, 21 Apr 2015 12:43:33: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:43:33: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:43:33: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:43:33: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:43:33: #1 total tags in treatment: 7397974 INFO @ Tue, 21 Apr 2015 12:43:33: #1 total tags in treatment: 7397974 INFO @ Tue, 21 Apr 2015 12:43:33: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:43:33: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:43:33: #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 12:43:33: #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 12:43:34: #1 tags after filtering in treatment: 7397281 INFO @ Tue, 21 Apr 2015 12:43:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:43:34: #1 finished! INFO @ Tue, 21 Apr 2015 12:43:34: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:43:34: #1 tags after filtering in treatment: 7397281 INFO @ Tue, 21 Apr 2015 12:43:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:43:34: #1 finished! INFO @ Tue, 21 Apr 2015 12:43:34: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:43:36: 7000000 INFO @ Tue, 21 Apr 2015 12:43:36: #2 number of paired peaks: 6498 INFO @ Tue, 21 Apr 2015 12:43:36: start model_add_line... INFO @ Tue, 21 Apr 2015 12:43:37: #2 number of paired peaks: 6498 INFO @ Tue, 21 Apr 2015 12:43:37: start model_add_line... INFO @ Tue, 21 Apr 2015 12:43:39: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:43:39: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:43:39: #1 total tags in treatment: 7397974 INFO @ Tue, 21 Apr 2015 12:43:39: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:43:39: #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 12:43:40: #1 tags after filtering in treatment: 7397281 INFO @ Tue, 21 Apr 2015 12:43:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:43:40: #1 finished! INFO @ Tue, 21 Apr 2015 12:43:40: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:43:42: #2 number of paired peaks: 6498 INFO @ Tue, 21 Apr 2015 12:43:42: start model_add_line... INFO @ Tue, 21 Apr 2015 12:44:02: start X-correlation... INFO @ Tue, 21 Apr 2015 12:44:02: end of X-cor INFO @ Tue, 21 Apr 2015 12:44:02: #2 finished! INFO @ Tue, 21 Apr 2015 12:44:02: #2 predicted fragment length is 298 bps INFO @ Tue, 21 Apr 2015 12:44:02: #2 alternative fragment length(s) may be 298 bps INFO @ Tue, 21 Apr 2015 12:44:02: #2.2 Generate R script for model : SRX026741.20_model.r INFO @ Tue, 21 Apr 2015 12:44:02: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:44:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:44:03: start X-correlation... INFO @ Tue, 21 Apr 2015 12:44:03: end of X-cor INFO @ Tue, 21 Apr 2015 12:44:03: #2 finished! INFO @ Tue, 21 Apr 2015 12:44:03: #2 predicted fragment length is 298 bps INFO @ Tue, 21 Apr 2015 12:44:03: #2 alternative fragment length(s) may be 298 bps INFO @ Tue, 21 Apr 2015 12:44:03: #2.2 Generate R script for model : SRX026741.10_model.r INFO @ Tue, 21 Apr 2015 12:44:03: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:44:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:44:08: start X-correlation... INFO @ Tue, 21 Apr 2015 12:44:08: end of X-cor INFO @ Tue, 21 Apr 2015 12:44:08: #2 finished! INFO @ Tue, 21 Apr 2015 12:44:08: #2 predicted fragment length is 298 bps INFO @ Tue, 21 Apr 2015 12:44:08: #2 alternative fragment length(s) may be 298 bps INFO @ Tue, 21 Apr 2015 12:44:08: #2.2 Generate R script for model : SRX026741.05_model.r INFO @ Tue, 21 Apr 2015 12:44:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:44:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:44:49: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:44:49: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:44:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:45:25: #4 Write output xls file... SRX026741.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:45:26: #4 Write peak in narrowPeak format file... SRX026741.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:45:26: #4 Write summits bed file... SRX026741.20_summits.bed INFO @ Tue, 21 Apr 2015 12:45:26: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2837 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:45:32: #4 Write output xls file... SRX026741.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:45:32: #4 Write peak in narrowPeak format file... SRX026741.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:45:32: #4 Write summits bed file... SRX026741.10_summits.bed INFO @ Tue, 21 Apr 2015 12:45:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5916 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 21 Apr 2015 12:45:47: #4 Write output xls file... SRX026741.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:45:47: #4 Write peak in narrowPeak format file... SRX026741.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:45:47: #4 Write summits bed file... SRX026741.05_summits.bed INFO @ Tue, 21 Apr 2015 12:45:47: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8863 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。