Job ID = 2161549 sra ファイルのダウンロード中... Completed: 7632981K bytes transferred in 100 seconds (623252K 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 --:--:-- --:--:-- --:--:-- 0 101 5467 0 5467 0 0 10034 0 --:--:-- --:--:-- --:--:-- 15443 100 37094 0 37094 0 0 50476 0 --:--:-- --:--:-- --:--:-- 68187 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 12718721 spots for /home/okishinya/chipatlas/results/dm3/SRX027825/SRR067908.sra Written 12718721 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: 00:03:07 12718721 reads; of these: 12718721 (100.00%) were unpaired; of these: 3549455 (27.91%) aligned 0 times 6734065 (52.95%) aligned exactly 1 time 2435201 (19.15%) aligned >1 times 72.09% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 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] 1599439 / 9169266 = 0.1744 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 12:52:33: # Command line: callpeak -t SRX027825.bam -f BAM -g dm -n SRX027825.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX027825.05 # format = BAM # ChIP-seq file = ['SRX027825.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 12:52:33: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:52:33: # Command line: callpeak -t SRX027825.bam -f BAM -g dm -n SRX027825.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX027825.20 # format = BAM # ChIP-seq file = ['SRX027825.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 12:52:33: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:52:33: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:52:33: # Command line: callpeak -t SRX027825.bam -f BAM -g dm -n SRX027825.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX027825.10 # format = BAM # ChIP-seq file = ['SRX027825.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 12:52:33: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:52:33: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:52:33: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:52:38: 1000000 INFO @ Tue, 21 Apr 2015 12:52:39: 1000000 INFO @ Tue, 21 Apr 2015 12:52:39: 1000000 INFO @ Tue, 21 Apr 2015 12:52:44: 2000000 INFO @ Tue, 21 Apr 2015 12:52:45: 2000000 INFO @ Tue, 21 Apr 2015 12:52:45: 2000000 INFO @ Tue, 21 Apr 2015 12:52:49: 3000000 INFO @ Tue, 21 Apr 2015 12:52:51: 3000000 INFO @ Tue, 21 Apr 2015 12:52:51: 3000000 INFO @ Tue, 21 Apr 2015 12:52:55: 4000000 INFO @ Tue, 21 Apr 2015 12:52:58: 4000000 INFO @ Tue, 21 Apr 2015 12:52:58: 4000000 INFO @ Tue, 21 Apr 2015 12:53:00: 5000000 INFO @ Tue, 21 Apr 2015 12:53:04: 5000000 INFO @ Tue, 21 Apr 2015 12:53:04: 5000000 INFO @ Tue, 21 Apr 2015 12:53:05: 6000000 INFO @ Tue, 21 Apr 2015 12:53:10: 6000000 INFO @ Tue, 21 Apr 2015 12:53:10: 6000000 INFO @ Tue, 21 Apr 2015 12:53:11: 7000000 INFO @ Tue, 21 Apr 2015 12:53:14: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:53:14: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:53:14: #1 total tags in treatment: 7569827 INFO @ Tue, 21 Apr 2015 12:53:14: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:53:14: #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 12:53:15: #1 tags after filtering in treatment: 7569208 INFO @ Tue, 21 Apr 2015 12:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:53:15: #1 finished! INFO @ Tue, 21 Apr 2015 12:53:15: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:53:16: 7000000 INFO @ Tue, 21 Apr 2015 12:53:16: 7000000 INFO @ Tue, 21 Apr 2015 12:53:17: #2 number of paired peaks: 1646 INFO @ Tue, 21 Apr 2015 12:53:17: start model_add_line... INFO @ Tue, 21 Apr 2015 12:53:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:53:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:53:20: #1 total tags in treatment: 7569827 INFO @ Tue, 21 Apr 2015 12:53:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:53:20: #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 12:53:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:53:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:53:20: #1 total tags in treatment: 7569827 INFO @ Tue, 21 Apr 2015 12:53:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:53:20: #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 12:53:21: #1 tags after filtering in treatment: 7569208 INFO @ Tue, 21 Apr 2015 12:53:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:53:21: #1 finished! INFO @ Tue, 21 Apr 2015 12:53:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:53:21: #1 tags after filtering in treatment: 7569208 INFO @ Tue, 21 Apr 2015 12:53:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:53:21: #1 finished! INFO @ Tue, 21 Apr 2015 12:53:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:53:23: #2 number of paired peaks: 1646 INFO @ Tue, 21 Apr 2015 12:53:23: start model_add_line... INFO @ Tue, 21 Apr 2015 12:53:23: #2 number of paired peaks: 1646 INFO @ Tue, 21 Apr 2015 12:53:23: start model_add_line... INFO @ Tue, 21 Apr 2015 12:53:26: start X-correlation... INFO @ Tue, 21 Apr 2015 12:53:26: end of X-cor INFO @ Tue, 21 Apr 2015 12:53:26: #2 finished! INFO @ Tue, 21 Apr 2015 12:53:26: #2 predicted fragment length is 89 bps INFO @ Tue, 21 Apr 2015 12:53:26: #2 alternative fragment length(s) may be 89 bps INFO @ Tue, 21 Apr 2015 12:53:26: #2.2 Generate R script for model : SRX027825.20_model.r INFO @ Tue, 21 Apr 2015 12:53:26: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:53:32: start X-correlation... INFO @ Tue, 21 Apr 2015 12:53:32: end of X-cor INFO @ Tue, 21 Apr 2015 12:53:32: #2 finished! INFO @ Tue, 21 Apr 2015 12:53:32: #2 predicted fragment length is 89 bps INFO @ Tue, 21 Apr 2015 12:53:32: #2 alternative fragment length(s) may be 89 bps INFO @ Tue, 21 Apr 2015 12:53:32: #2.2 Generate R script for model : SRX027825.10_model.r INFO @ Tue, 21 Apr 2015 12:53:32: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:53:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:53:33: start X-correlation... INFO @ Tue, 21 Apr 2015 12:53:33: end of X-cor INFO @ Tue, 21 Apr 2015 12:53:33: #2 finished! INFO @ Tue, 21 Apr 2015 12:53:33: #2 predicted fragment length is 89 bps INFO @ Tue, 21 Apr 2015 12:53:33: #2 alternative fragment length(s) may be 89 bps INFO @ Tue, 21 Apr 2015 12:53:33: #2.2 Generate R script for model : SRX027825.05_model.r INFO @ Tue, 21 Apr 2015 12:53:33: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:54:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:54:15: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:54:15: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:54:42: #4 Write output xls file... SRX027825.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:54:42: #4 Write peak in narrowPeak format file... SRX027825.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:54:42: #4 Write summits bed file... SRX027825.20_summits.bed INFO @ Tue, 21 Apr 2015 12:54:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1826 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:54:47: #4 Write output xls file... SRX027825.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:54:47: #4 Write peak in narrowPeak format file... SRX027825.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:54:47: #4 Write summits bed file... SRX027825.10_summits.bed INFO @ Tue, 21 Apr 2015 12:54:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3242 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:54:49: #4 Write output xls file... SRX027825.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:54:49: #4 Write peak in narrowPeak format file... SRX027825.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:54:49: #4 Write summits bed file... SRX027825.05_summits.bed INFO @ Tue, 21 Apr 2015 12:54:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5021 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。