Job ID = 2161345 sra ファイルのダウンロード中... Completed: 1658529K bytes transferred in 15 seconds (870132K bits/sec), in 5 files, 6 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 7156 0 --:--:-- --:--:-- --:--:-- 10859 100 35363 0 35363 0 0 47180 0 --:--:-- --:--:-- --:--:-- 63261 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 12709970 spots for /home/okishinya/chipatlas/results/dm3/SRX020694/SRR060801.sra Written 12709970 spots total Written 12652502 spots for /home/okishinya/chipatlas/results/dm3/SRX020694/SRR060805.sra Written 12652502 spots total Written 12995670 spots for /home/okishinya/chipatlas/results/dm3/SRX020694/SRR060802.sra Written 12995670 spots total Written 13117930 spots for /home/okishinya/chipatlas/results/dm3/SRX020694/SRR060804.sra Written 13117930 spots total Written 13335981 spots for /home/okishinya/chipatlas/results/dm3/SRX020694/SRR060803.sra Written 13335981 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: 00:08:31 64812053 reads; of these: 64812053 (100.00%) were unpaired; of these: 41244792 (63.64%) aligned 0 times 18933962 (29.21%) aligned exactly 1 time 4633299 (7.15%) aligned >1 times 36.36% overall alignment rate Time searching: 00:08:32 Overall time: 00:08:32 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] 9015606 / 23567261 = 0.3825 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 12:38:46: # Command line: callpeak -t SRX020694.bam -f BAM -g dm -n SRX020694.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX020694.20 # format = BAM # ChIP-seq file = ['SRX020694.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 12:38:46: # Command line: callpeak -t SRX020694.bam -f BAM -g dm -n SRX020694.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX020694.10 # format = BAM # ChIP-seq file = ['SRX020694.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 12:38:46: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:38:46: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:38:46: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:38:46: # Command line: callpeak -t SRX020694.bam -f BAM -g dm -n SRX020694.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX020694.05 # format = BAM # ChIP-seq file = ['SRX020694.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 12:38:46: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:38:46: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:38:46: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:38:51: 1000000 INFO @ Tue, 21 Apr 2015 12:38:51: 1000000 INFO @ Tue, 21 Apr 2015 12:38:51: 1000000 INFO @ Tue, 21 Apr 2015 12:38:56: 2000000 INFO @ Tue, 21 Apr 2015 12:38:56: 2000000 INFO @ Tue, 21 Apr 2015 12:38:56: 2000000 INFO @ Tue, 21 Apr 2015 12:39:00: 3000000 INFO @ Tue, 21 Apr 2015 12:39:01: 3000000 INFO @ Tue, 21 Apr 2015 12:39:01: 3000000 INFO @ Tue, 21 Apr 2015 12:39:05: 4000000 INFO @ Tue, 21 Apr 2015 12:39:06: 4000000 INFO @ Tue, 21 Apr 2015 12:39:06: 4000000 INFO @ Tue, 21 Apr 2015 12:39:09: 5000000 INFO @ Tue, 21 Apr 2015 12:39:11: 5000000 INFO @ Tue, 21 Apr 2015 12:39:11: 5000000 INFO @ Tue, 21 Apr 2015 12:39:14: 6000000 INFO @ Tue, 21 Apr 2015 12:39:15: 6000000 INFO @ Tue, 21 Apr 2015 12:39:15: 6000000 INFO @ Tue, 21 Apr 2015 12:39:19: 7000000 INFO @ Tue, 21 Apr 2015 12:39:20: 7000000 INFO @ Tue, 21 Apr 2015 12:39:20: 7000000 INFO @ Tue, 21 Apr 2015 12:39:23: 8000000 INFO @ Tue, 21 Apr 2015 12:39:25: 8000000 INFO @ Tue, 21 Apr 2015 12:39:25: 8000000 INFO @ Tue, 21 Apr 2015 12:39:28: 9000000 INFO @ Tue, 21 Apr 2015 12:39:30: 9000000 INFO @ Tue, 21 Apr 2015 12:39:30: 9000000 INFO @ Tue, 21 Apr 2015 12:39:33: 10000000 INFO @ Tue, 21 Apr 2015 12:39:35: 10000000 INFO @ Tue, 21 Apr 2015 12:39:35: 10000000 INFO @ Tue, 21 Apr 2015 12:39:37: 11000000 INFO @ Tue, 21 Apr 2015 12:39:40: 11000000 INFO @ Tue, 21 Apr 2015 12:39:40: 11000000 INFO @ Tue, 21 Apr 2015 12:39:42: 12000000 INFO @ Tue, 21 Apr 2015 12:39:45: 12000000 INFO @ Tue, 21 Apr 2015 12:39:45: 12000000 INFO @ Tue, 21 Apr 2015 12:39:47: 13000000 INFO @ Tue, 21 Apr 2015 12:39:50: 13000000 INFO @ Tue, 21 Apr 2015 12:39:50: 13000000 INFO @ Tue, 21 Apr 2015 12:39:51: 14000000 INFO @ Tue, 21 Apr 2015 12:39:54: #1 tag size is determined as 28 bps INFO @ Tue, 21 Apr 2015 12:39:54: #1 tag size = 28 INFO @ Tue, 21 Apr 2015 12:39:54: #1 total tags in treatment: 14551655 INFO @ Tue, 21 Apr 2015 12:39:54: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:39:54: #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 12:39:55: 14000000 INFO @ Tue, 21 Apr 2015 12:39:55: 14000000 INFO @ Tue, 21 Apr 2015 12:39:57: #1 tags after filtering in treatment: 14551315 INFO @ Tue, 21 Apr 2015 12:39:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:39:57: #1 finished! INFO @ Tue, 21 Apr 2015 12:39:57: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:39:58: #1 tag size is determined as 28 bps INFO @ Tue, 21 Apr 2015 12:39:58: #1 tag size = 28 INFO @ Tue, 21 Apr 2015 12:39:58: #1 total tags in treatment: 14551655 INFO @ Tue, 21 Apr 2015 12:39:58: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:39:58: #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 12:39:58: #1 tag size is determined as 28 bps INFO @ Tue, 21 Apr 2015 12:39:58: #1 tag size = 28 INFO @ Tue, 21 Apr 2015 12:39:58: #1 total tags in treatment: 14551655 INFO @ Tue, 21 Apr 2015 12:39:58: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:39:58: #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 12:39:59: #2 number of paired peaks: 2309 INFO @ Tue, 21 Apr 2015 12:39:59: start model_add_line... INFO @ Tue, 21 Apr 2015 12:40:00: #1 tags after filtering in treatment: 14551315 INFO @ Tue, 21 Apr 2015 12:40:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:40:00: #1 finished! INFO @ Tue, 21 Apr 2015 12:40:00: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:40:00: #1 tags after filtering in treatment: 14551315 INFO @ Tue, 21 Apr 2015 12:40:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:40:00: #1 finished! INFO @ Tue, 21 Apr 2015 12:40:00: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:40:03: #2 number of paired peaks: 2309 INFO @ Tue, 21 Apr 2015 12:40:03: start model_add_line... INFO @ Tue, 21 Apr 2015 12:40:03: #2 number of paired peaks: 2309 INFO @ Tue, 21 Apr 2015 12:40:03: start model_add_line... INFO @ Tue, 21 Apr 2015 12:40:19: start X-correlation... INFO @ Tue, 21 Apr 2015 12:40:19: end of X-cor INFO @ Tue, 21 Apr 2015 12:40:19: #2 finished! INFO @ Tue, 21 Apr 2015 12:40:19: #2 predicted fragment length is 64 bps INFO @ Tue, 21 Apr 2015 12:40:19: #2 alternative fragment length(s) may be 64 bps INFO @ Tue, 21 Apr 2015 12:40:19: #2.2 Generate R script for model : SRX020694.05_model.r INFO @ Tue, 21 Apr 2015 12:40:19: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:40:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:40:23: start X-correlation... INFO @ Tue, 21 Apr 2015 12:40:23: end of X-cor INFO @ Tue, 21 Apr 2015 12:40:23: #2 finished! INFO @ Tue, 21 Apr 2015 12:40:23: #2 predicted fragment length is 64 bps INFO @ Tue, 21 Apr 2015 12:40:23: #2 alternative fragment length(s) may be 64 bps INFO @ Tue, 21 Apr 2015 12:40:23: #2.2 Generate R script for model : SRX020694.20_model.r INFO @ Tue, 21 Apr 2015 12:40:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:40:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:40:23: start X-correlation... INFO @ Tue, 21 Apr 2015 12:40:23: end of X-cor INFO @ Tue, 21 Apr 2015 12:40:23: #2 finished! INFO @ Tue, 21 Apr 2015 12:40:23: #2 predicted fragment length is 64 bps INFO @ Tue, 21 Apr 2015 12:40:23: #2 alternative fragment length(s) may be 64 bps INFO @ Tue, 21 Apr 2015 12:40:23: #2.2 Generate R script for model : SRX020694.10_model.r INFO @ Tue, 21 Apr 2015 12:40:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:40:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:41:33: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:41:37: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:41:41: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:42:33: #4 Write output xls file... SRX020694.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:42:33: #4 Write peak in narrowPeak format file... SRX020694.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:42:33: #4 Write summits bed file... SRX020694.20_summits.bed INFO @ Tue, 21 Apr 2015 12:42:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4302 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:42:39: #4 Write output xls file... SRX020694.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:42:40: #4 Write peak in narrowPeak format file... SRX020694.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:42:40: #4 Write summits bed file... SRX020694.05_summits.bed INFO @ Tue, 21 Apr 2015 12:42:40: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (17391 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:42:44: #4 Write output xls file... SRX020694.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:42:44: #4 Write peak in narrowPeak format file... SRX020694.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:42:44: #4 Write summits bed file... SRX020694.10_summits.bed INFO @ Tue, 21 Apr 2015 12:42:44: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10640 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。