Job ID = 2161905 sra ファイルのダウンロード中... Completed: 450982K bytes transferred in 7 seconds (506781K 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 35596 0 35596 0 0 48285 0 --:--:-- --:--:-- --:--:-- 65194 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 15781499 spots for /home/okishinya/chipatlas/results/dm3/SRX040609/SRR097978.sra Written 15781499 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: 00:00:00 Multiseed full-index search: 00:03:10 15781499 reads; of these: 15781499 (100.00%) were unpaired; of these: 880682 (5.58%) aligned 0 times 14249368 (90.29%) aligned exactly 1 time 651449 (4.13%) aligned >1 times 94.42% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 7894213 / 14900817 = 0.5298 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 13:14:24: # Command line: callpeak -t SRX040609.bam -f BAM -g dm -n SRX040609.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX040609.10 # format = BAM # ChIP-seq file = ['SRX040609.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 13:14:24: # Command line: callpeak -t SRX040609.bam -f BAM -g dm -n SRX040609.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX040609.20 # format = BAM # ChIP-seq file = ['SRX040609.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 13:14:24: # Command line: callpeak -t SRX040609.bam -f BAM -g dm -n SRX040609.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX040609.05 # format = BAM # ChIP-seq file = ['SRX040609.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 13:14:24: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:14:24: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:14:24: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:14:24: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:14:24: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:14:24: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:14:30: 1000000 INFO @ Tue, 21 Apr 2015 13:14:31: 1000000 INFO @ Tue, 21 Apr 2015 13:14:31: 1000000 INFO @ Tue, 21 Apr 2015 13:14:36: 2000000 INFO @ Tue, 21 Apr 2015 13:14:37: 2000000 INFO @ Tue, 21 Apr 2015 13:14:37: 2000000 INFO @ Tue, 21 Apr 2015 13:14:43: 3000000 INFO @ Tue, 21 Apr 2015 13:14:44: 3000000 INFO @ Tue, 21 Apr 2015 13:14:44: 3000000 INFO @ Tue, 21 Apr 2015 13:14:49: 4000000 INFO @ Tue, 21 Apr 2015 13:14:50: 4000000 INFO @ Tue, 21 Apr 2015 13:14:50: 4000000 INFO @ Tue, 21 Apr 2015 13:14:55: 5000000 INFO @ Tue, 21 Apr 2015 13:14:57: 5000000 INFO @ Tue, 21 Apr 2015 13:14:57: 5000000 INFO @ Tue, 21 Apr 2015 13:15:01: 6000000 INFO @ Tue, 21 Apr 2015 13:15:04: 6000000 INFO @ Tue, 21 Apr 2015 13:15:04: 6000000 INFO @ Tue, 21 Apr 2015 13:15:07: 7000000 INFO @ Tue, 21 Apr 2015 13:15:08: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:15:08: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:15:08: #1 total tags in treatment: 7006604 INFO @ Tue, 21 Apr 2015 13:15:08: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:15:08: #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 13:15:09: #1 tags after filtering in treatment: 6999946 INFO @ Tue, 21 Apr 2015 13:15:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:15:09: #1 finished! INFO @ Tue, 21 Apr 2015 13:15:09: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:15:10: 7000000 INFO @ Tue, 21 Apr 2015 13:15:10: 7000000 INFO @ Tue, 21 Apr 2015 13:15:10: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:15:10: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:15:10: #1 total tags in treatment: 7006604 INFO @ Tue, 21 Apr 2015 13:15:10: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:15:10: #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 13:15:10: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:15:10: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:15:10: #1 total tags in treatment: 7006604 INFO @ Tue, 21 Apr 2015 13:15:10: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:15:10: #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 13:15:11: #1 tags after filtering in treatment: 6999946 INFO @ Tue, 21 Apr 2015 13:15:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:15:11: #1 finished! INFO @ Tue, 21 Apr 2015 13:15:11: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:15:11: #1 tags after filtering in treatment: 6999946 INFO @ Tue, 21 Apr 2015 13:15:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:15:11: #1 finished! INFO @ Tue, 21 Apr 2015 13:15:11: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:15:11: #2 number of paired peaks: 11920 INFO @ Tue, 21 Apr 2015 13:15:11: start model_add_line... INFO @ Tue, 21 Apr 2015 13:15:14: #2 number of paired peaks: 11920 INFO @ Tue, 21 Apr 2015 13:15:14: start model_add_line... INFO @ Tue, 21 Apr 2015 13:15:14: #2 number of paired peaks: 11920 INFO @ Tue, 21 Apr 2015 13:15:14: start model_add_line... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 21 Apr 2015 13:16:44: start X-correlation... INFO @ Tue, 21 Apr 2015 13:16:44: end of X-cor INFO @ Tue, 21 Apr 2015 13:16:44: #2 finished! INFO @ Tue, 21 Apr 2015 13:16:44: #2 predicted fragment length is 209 bps INFO @ Tue, 21 Apr 2015 13:16:44: #2 alternative fragment length(s) may be 209 bps INFO @ Tue, 21 Apr 2015 13:16:44: #2.2 Generate R script for model : SRX040609.10_model.r INFO @ Tue, 21 Apr 2015 13:16:44: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:16:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:16:49: start X-correlation... INFO @ Tue, 21 Apr 2015 13:16:49: end of X-cor INFO @ Tue, 21 Apr 2015 13:16:49: #2 finished! INFO @ Tue, 21 Apr 2015 13:16:49: #2 predicted fragment length is 209 bps INFO @ Tue, 21 Apr 2015 13:16:49: #2 alternative fragment length(s) may be 209 bps INFO @ Tue, 21 Apr 2015 13:16:49: #2.2 Generate R script for model : SRX040609.05_model.r INFO @ Tue, 21 Apr 2015 13:16:49: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:16:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:16:49: start X-correlation... INFO @ Tue, 21 Apr 2015 13:16:49: end of X-cor INFO @ Tue, 21 Apr 2015 13:16:49: #2 finished! INFO @ Tue, 21 Apr 2015 13:16:49: #2 predicted fragment length is 209 bps INFO @ Tue, 21 Apr 2015 13:16:49: #2 alternative fragment length(s) may be 209 bps INFO @ Tue, 21 Apr 2015 13:16:49: #2.2 Generate R script for model : SRX040609.20_model.r INFO @ Tue, 21 Apr 2015 13:16:49: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:16:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:17:36: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:17:42: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:17:42: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:18:18: #4 Write output xls file... SRX040609.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:18:18: #4 Write peak in narrowPeak format file... SRX040609.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:18:19: #4 Write summits bed file... SRX040609.10_summits.bed INFO @ Tue, 21 Apr 2015 13:18:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7524 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:18:21: #4 Write output xls file... SRX040609.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:18:21: #4 Write peak in narrowPeak format file... SRX040609.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:18:21: #4 Write summits bed file... SRX040609.20_summits.bed INFO @ Tue, 21 Apr 2015 13:18:21: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6841 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:18:27: #4 Write output xls file... SRX040609.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:18:28: #4 Write peak in narrowPeak format file... SRX040609.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:18:28: #4 Write summits bed file... SRX040609.05_summits.bed INFO @ Tue, 21 Apr 2015 13:18:28: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8023 records, 4 fields): 12 millis CompletedMACS2peakCalling