Job ID = 2161347 sra ファイルのダウンロード中... Completed: 823762K bytes transferred in 8 seconds (788722K bits/sec), in 3 files, 4 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 101 5467 0 5467 0 0 9976 0 --:--:-- --:--:-- --:--:-- 15313 100 35353 0 35353 0 0 47922 0 --:--:-- --:--:-- --:--:-- 64630 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 12048361 spots for /home/okishinya/chipatlas/results/dm3/SRX020696/SRR060774.sra Written 12048361 spots total Written 12583034 spots for /home/okishinya/chipatlas/results/dm3/SRX020696/SRR060772.sra Written 12583034 spots total Written 13683143 spots for /home/okishinya/chipatlas/results/dm3/SRX020696/SRR060773.sra Written 13683143 spots total 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:01 38314538 reads; of these: 38314538 (100.00%) were unpaired; of these: 24230809 (63.24%) aligned 0 times 10289922 (26.86%) aligned exactly 1 time 3793807 (9.90%) aligned >1 times 36.76% overall alignment rate Time searching: 00:07:02 Overall time: 00:07:02 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] 5700553 / 14083729 = 0.4048 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 12:36:08: # Command line: callpeak -t SRX020696.bam -f BAM -g dm -n SRX020696.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX020696.20 # format = BAM # ChIP-seq file = ['SRX020696.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 12:36:08: # Command line: callpeak -t SRX020696.bam -f BAM -g dm -n SRX020696.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX020696.05 # format = BAM # ChIP-seq file = ['SRX020696.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 12:36:08: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:36:08: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:36:08: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:36:08: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:36:08: # Command line: callpeak -t SRX020696.bam -f BAM -g dm -n SRX020696.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX020696.10 # format = BAM # ChIP-seq file = ['SRX020696.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 12:36:08: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:36:08: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:36:14: 1000000 INFO @ Tue, 21 Apr 2015 12:36:14: 1000000 INFO @ Tue, 21 Apr 2015 12:36:14: 1000000 INFO @ Tue, 21 Apr 2015 12:36:19: 2000000 INFO @ Tue, 21 Apr 2015 12:36:20: 2000000 INFO @ Tue, 21 Apr 2015 12:36:20: 2000000 INFO @ Tue, 21 Apr 2015 12:36:25: 3000000 INFO @ Tue, 21 Apr 2015 12:36:26: 3000000 INFO @ Tue, 21 Apr 2015 12:36:26: 3000000 INFO @ Tue, 21 Apr 2015 12:36:31: 4000000 INFO @ Tue, 21 Apr 2015 12:36:32: 4000000 INFO @ Tue, 21 Apr 2015 12:36:32: 4000000 INFO @ Tue, 21 Apr 2015 12:36:36: 5000000 INFO @ Tue, 21 Apr 2015 12:36:37: 5000000 INFO @ Tue, 21 Apr 2015 12:36:37: 5000000 INFO @ Tue, 21 Apr 2015 12:36:42: 6000000 INFO @ Tue, 21 Apr 2015 12:36:43: 6000000 INFO @ Tue, 21 Apr 2015 12:36:43: 6000000 INFO @ Tue, 21 Apr 2015 12:36:47: 7000000 INFO @ Tue, 21 Apr 2015 12:36:49: 7000000 INFO @ Tue, 21 Apr 2015 12:36:49: 7000000 INFO @ Tue, 21 Apr 2015 12:36:53: 8000000 INFO @ Tue, 21 Apr 2015 12:36:54: 8000000 INFO @ Tue, 21 Apr 2015 12:36:54: 8000000 INFO @ Tue, 21 Apr 2015 12:36:55: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:36:55: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:36:55: #1 total tags in treatment: 8383176 INFO @ Tue, 21 Apr 2015 12:36:55: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:36:55: #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 12:36:56: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:36:56: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:36:56: #1 total tags in treatment: 8383176 INFO @ Tue, 21 Apr 2015 12:36:56: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:36:56: #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 12:36:56: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:36:56: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:36:56: #1 total tags in treatment: 8383176 INFO @ Tue, 21 Apr 2015 12:36:56: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:36:56: #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 12:36:57: #1 tags after filtering in treatment: 8378678 INFO @ Tue, 21 Apr 2015 12:36:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:36:57: #1 finished! INFO @ Tue, 21 Apr 2015 12:36:57: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:36:58: #1 tags after filtering in treatment: 8378678 INFO @ Tue, 21 Apr 2015 12:36:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:36:58: #1 finished! INFO @ Tue, 21 Apr 2015 12:36:58: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:36:58: #1 tags after filtering in treatment: 8378678 INFO @ Tue, 21 Apr 2015 12:36:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:36:58: #1 finished! INFO @ Tue, 21 Apr 2015 12:36:58: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:36:58: #2 number of paired peaks: 1605 INFO @ Tue, 21 Apr 2015 12:36:58: start model_add_line... INFO @ Tue, 21 Apr 2015 12:37:00: #2 number of paired peaks: 1605 INFO @ Tue, 21 Apr 2015 12:37:00: start model_add_line... INFO @ Tue, 21 Apr 2015 12:37:00: #2 number of paired peaks: 1605 INFO @ Tue, 21 Apr 2015 12:37:00: start model_add_line... INFO @ Tue, 21 Apr 2015 12:37:06: start X-correlation... INFO @ Tue, 21 Apr 2015 12:37:06: end of X-cor INFO @ Tue, 21 Apr 2015 12:37:06: #2 finished! INFO @ Tue, 21 Apr 2015 12:37:06: #2 predicted fragment length is 78 bps INFO @ Tue, 21 Apr 2015 12:37:06: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 21 Apr 2015 12:37:06: #2.2 Generate R script for model : SRX020696.10_model.r INFO @ Tue, 21 Apr 2015 12:37:06: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:37:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:37:07: start X-correlation... INFO @ Tue, 21 Apr 2015 12:37:07: end of X-cor INFO @ Tue, 21 Apr 2015 12:37:07: #2 finished! INFO @ Tue, 21 Apr 2015 12:37:07: #2 predicted fragment length is 78 bps INFO @ Tue, 21 Apr 2015 12:37:07: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 21 Apr 2015 12:37:07: #2.2 Generate R script for model : SRX020696.05_model.r INFO @ Tue, 21 Apr 2015 12:37:07: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:37:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:37:08: start X-correlation... INFO @ Tue, 21 Apr 2015 12:37:08: end of X-cor INFO @ Tue, 21 Apr 2015 12:37:08: #2 finished! INFO @ Tue, 21 Apr 2015 12:37:08: #2 predicted fragment length is 78 bps INFO @ Tue, 21 Apr 2015 12:37:08: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 21 Apr 2015 12:37:08: #2.2 Generate R script for model : SRX020696.20_model.r INFO @ Tue, 21 Apr 2015 12:37:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:37:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:37:51: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:37:53: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:37:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:38:27: #4 Write output xls file... SRX020696.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:38:27: #4 Write peak in narrowPeak format file... SRX020696.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:38:27: #4 Write summits bed file... SRX020696.10_summits.bed INFO @ Tue, 21 Apr 2015 12:38:27: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5548 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:38:30: #4 Write output xls file... SRX020696.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:38:30: #4 Write peak in narrowPeak format file... SRX020696.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:38:30: #4 Write summits bed file... SRX020696.20_summits.bed INFO @ Tue, 21 Apr 2015 12:38:30: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2571 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:38:33: #4 Write output xls file... SRX020696.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:38:33: #4 Write peak in narrowPeak format file... SRX020696.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:38:33: #4 Write summits bed file... SRX020696.05_summits.bed INFO @ Tue, 21 Apr 2015 12:38:33: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10983 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。