Job ID = 2161390 sra ファイルのダウンロード中... Completed: 862922K bytes transferred in 10 seconds (702968K bits/sec), in 2 files, 3 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 19288 0 19288 0 0 25681 0 --:--:-- --:--:-- --:--:-- 34442 100 44990 0 44990 0 0 47840 0 --:--:-- --:--:-- --:--:-- 59986 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 23787659 spots for /home/okishinya/chipatlas/results/dm3/SRX025478/SRR063879.sra Written 23787659 spots total Written 26376652 spots for /home/okishinya/chipatlas/results/dm3/SRX025478/SRR063878.sra Written 26376652 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:35 50164311 reads; of these: 50164311 (100.00%) were unpaired; of these: 706683 (1.41%) aligned 0 times 39735257 (79.21%) aligned exactly 1 time 9722371 (19.38%) aligned >1 times 98.59% overall alignment rate Time searching: 00:16:35 Overall time: 00:16:35 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 16 files... [bam_rmdupse_core] 35096892 / 49457628 = 0.7096 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 12:57:52: # Command line: callpeak -t SRX025478.bam -f BAM -g dm -n SRX025478.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX025478.10 # format = BAM # ChIP-seq file = ['SRX025478.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 12:57:52: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:57:52: # Command line: callpeak -t SRX025478.bam -f BAM -g dm -n SRX025478.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX025478.05 # format = BAM # ChIP-seq file = ['SRX025478.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 12:57:52: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:57:52: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:57:52: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:57:52: # Command line: callpeak -t SRX025478.bam -f BAM -g dm -n SRX025478.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX025478.20 # format = BAM # ChIP-seq file = ['SRX025478.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 12:57:52: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:57:52: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:57:58: 1000000 INFO @ Tue, 21 Apr 2015 12:57:58: 1000000 INFO @ Tue, 21 Apr 2015 12:57:58: 1000000 INFO @ Tue, 21 Apr 2015 12:58:04: 2000000 INFO @ Tue, 21 Apr 2015 12:58:04: 2000000 INFO @ Tue, 21 Apr 2015 12:58:04: 2000000 INFO @ Tue, 21 Apr 2015 12:58:10: 3000000 INFO @ Tue, 21 Apr 2015 12:58:10: 3000000 INFO @ Tue, 21 Apr 2015 12:58:10: 3000000 INFO @ Tue, 21 Apr 2015 12:58:15: 4000000 INFO @ Tue, 21 Apr 2015 12:58:16: 4000000 INFO @ Tue, 21 Apr 2015 12:58:16: 4000000 INFO @ Tue, 21 Apr 2015 12:58:21: 5000000 INFO @ Tue, 21 Apr 2015 12:58:22: 5000000 INFO @ Tue, 21 Apr 2015 12:58:22: 5000000 INFO @ Tue, 21 Apr 2015 12:58:27: 6000000 INFO @ Tue, 21 Apr 2015 12:58:28: 6000000 INFO @ Tue, 21 Apr 2015 12:58:28: 6000000 INFO @ Tue, 21 Apr 2015 12:58:32: 7000000 INFO @ Tue, 21 Apr 2015 12:58:34: 7000000 INFO @ Tue, 21 Apr 2015 12:58:35: 7000000 INFO @ Tue, 21 Apr 2015 12:58:38: 8000000 INFO @ Tue, 21 Apr 2015 12:58:40: 8000000 INFO @ Tue, 21 Apr 2015 12:58:41: 8000000 INFO @ Tue, 21 Apr 2015 12:58:44: 9000000 INFO @ Tue, 21 Apr 2015 12:58:46: 9000000 INFO @ Tue, 21 Apr 2015 12:58:47: 9000000 INFO @ Tue, 21 Apr 2015 12:58:49: 10000000 INFO @ Tue, 21 Apr 2015 12:58:52: 10000000 INFO @ Tue, 21 Apr 2015 12:58:53: 10000000 INFO @ Tue, 21 Apr 2015 12:58:55: 11000000 INFO @ Tue, 21 Apr 2015 12:58:59: 11000000 INFO @ Tue, 21 Apr 2015 12:59:00: 11000000 INFO @ Tue, 21 Apr 2015 12:59:00: 12000000 INFO @ Tue, 21 Apr 2015 12:59:05: 12000000 INFO @ Tue, 21 Apr 2015 12:59:06: 12000000 INFO @ Tue, 21 Apr 2015 12:59:06: 13000000 INFO @ Tue, 21 Apr 2015 12:59:11: 13000000 INFO @ Tue, 21 Apr 2015 12:59:12: 14000000 INFO @ Tue, 21 Apr 2015 12:59:12: 13000000 INFO @ Tue, 21 Apr 2015 12:59:14: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:59:14: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:59:14: #1 total tags in treatment: 14360736 INFO @ Tue, 21 Apr 2015 12:59:14: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:59:14: #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 12:59:16: #1 tags after filtering in treatment: 14357472 INFO @ Tue, 21 Apr 2015 12:59:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:59:16: #1 finished! INFO @ Tue, 21 Apr 2015 12:59:16: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:59:17: 14000000 INFO @ Tue, 21 Apr 2015 12:59:18: 14000000 INFO @ Tue, 21 Apr 2015 12:59:19: #2 number of paired peaks: 3392 INFO @ Tue, 21 Apr 2015 12:59:19: start model_add_line... INFO @ Tue, 21 Apr 2015 12:59:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:59:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:59:20: #1 total tags in treatment: 14360736 INFO @ Tue, 21 Apr 2015 12:59:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:59:20: #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 12:59:21: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:59:21: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:59:21: #1 total tags in treatment: 14360736 INFO @ Tue, 21 Apr 2015 12:59:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:59:21: #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 12:59:22: #1 tags after filtering in treatment: 14357472 INFO @ Tue, 21 Apr 2015 12:59:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:59:22: #1 finished! INFO @ Tue, 21 Apr 2015 12:59:22: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:59:23: #1 tags after filtering in treatment: 14357472 INFO @ Tue, 21 Apr 2015 12:59:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:59:23: #1 finished! INFO @ Tue, 21 Apr 2015 12:59:23: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:59:25: #2 number of paired peaks: 3392 INFO @ Tue, 21 Apr 2015 12:59:25: start model_add_line... INFO @ Tue, 21 Apr 2015 12:59:26: #2 number of paired peaks: 3392 INFO @ Tue, 21 Apr 2015 12:59:26: start model_add_line... INFO @ Tue, 21 Apr 2015 12:59:49: start X-correlation... INFO @ Tue, 21 Apr 2015 12:59:49: end of X-cor INFO @ Tue, 21 Apr 2015 12:59:49: #2 finished! INFO @ Tue, 21 Apr 2015 12:59:49: #2 predicted fragment length is 252 bps INFO @ Tue, 21 Apr 2015 12:59:49: #2 alternative fragment length(s) may be 252 bps INFO @ Tue, 21 Apr 2015 12:59:49: #2.2 Generate R script for model : SRX025478.20_model.r INFO @ Tue, 21 Apr 2015 12:59:49: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:59:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:59:56: start X-correlation... INFO @ Tue, 21 Apr 2015 12:59:56: end of X-cor INFO @ Tue, 21 Apr 2015 12:59:56: #2 finished! INFO @ Tue, 21 Apr 2015 12:59:56: #2 predicted fragment length is 252 bps INFO @ Tue, 21 Apr 2015 12:59:56: #2 alternative fragment length(s) may be 252 bps INFO @ Tue, 21 Apr 2015 12:59:56: #2.2 Generate R script for model : SRX025478.10_model.r INFO @ Tue, 21 Apr 2015 12:59:56: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:59:58: start X-correlation... INFO @ Tue, 21 Apr 2015 12:59:58: end of X-cor INFO @ Tue, 21 Apr 2015 12:59:58: #2 finished! INFO @ Tue, 21 Apr 2015 12:59:58: #2 predicted fragment length is 252 bps INFO @ Tue, 21 Apr 2015 12:59:58: #2 alternative fragment length(s) may be 252 bps INFO @ Tue, 21 Apr 2015 12:59:58: #2.2 Generate R script for model : SRX025478.05_model.r INFO @ Tue, 21 Apr 2015 12:59:58: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:59:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:01:20: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:01:30: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:01:34: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:02:28: #4 Write output xls file... SRX025478.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:02:28: #4 Write peak in narrowPeak format file... SRX025478.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:02:28: #4 Write summits bed file... SRX025478.20_summits.bed INFO @ Tue, 21 Apr 2015 13:02:28: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5387 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:02:38: #4 Write output xls file... SRX025478.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:02:38: #4 Write peak in narrowPeak format file... SRX025478.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:02:38: #4 Write summits bed file... SRX025478.10_summits.bed INFO @ Tue, 21 Apr 2015 13:02:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6760 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:02:48: #4 Write output xls file... SRX025478.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:02:49: #4 Write peak in narrowPeak format file... SRX025478.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:02:49: #4 Write summits bed file... SRX025478.05_summits.bed INFO @ Tue, 21 Apr 2015 13:02:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8102 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。