Job ID = 2161909 sra ファイルのダウンロード中... Completed: 772964K bytes transferred in 9 seconds (693474K 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 19265 0 19265 0 0 22655 0 --:--:-- --:--:-- --:--:-- 29189 100 36260 0 36260 0 0 42595 0 --:--:-- --:--:-- --:--:-- 54856 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 32201005 spots for /home/okishinya/chipatlas/results/dm3/SRX040613/SRR097982.sra Written 32201005 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: 00:06:28 32201005 reads; of these: 32201005 (100.00%) were unpaired; of these: 809977 (2.52%) aligned 0 times 29995620 (93.15%) aligned exactly 1 time 1395408 (4.33%) aligned >1 times 97.48% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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] 22728980 / 31391028 = 0.7241 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 13:23:47: # Command line: callpeak -t SRX040613.bam -f BAM -g dm -n SRX040613.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX040613.05 # format = BAM # ChIP-seq file = ['SRX040613.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 13:23:47: # Command line: callpeak -t SRX040613.bam -f BAM -g dm -n SRX040613.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX040613.10 # format = BAM # ChIP-seq file = ['SRX040613.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 13:23:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:23:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:23:47: # Command line: callpeak -t SRX040613.bam -f BAM -g dm -n SRX040613.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX040613.20 # format = BAM # ChIP-seq file = ['SRX040613.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 13:23:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:23:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:23:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:23:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:23:52: 1000000 INFO @ Tue, 21 Apr 2015 13:23:52: 1000000 INFO @ Tue, 21 Apr 2015 13:23:52: 1000000 INFO @ Tue, 21 Apr 2015 13:23:57: 2000000 INFO @ Tue, 21 Apr 2015 13:23:57: 2000000 INFO @ Tue, 21 Apr 2015 13:23:57: 2000000 INFO @ Tue, 21 Apr 2015 13:24:02: 3000000 INFO @ Tue, 21 Apr 2015 13:24:02: 3000000 INFO @ Tue, 21 Apr 2015 13:24:02: 3000000 INFO @ Tue, 21 Apr 2015 13:24:06: 4000000 INFO @ Tue, 21 Apr 2015 13:24:06: 4000000 INFO @ Tue, 21 Apr 2015 13:24:06: 4000000 INFO @ Tue, 21 Apr 2015 13:24:11: 5000000 INFO @ Tue, 21 Apr 2015 13:24:11: 5000000 INFO @ Tue, 21 Apr 2015 13:24:11: 5000000 INFO @ Tue, 21 Apr 2015 13:24:16: 6000000 INFO @ Tue, 21 Apr 2015 13:24:16: 6000000 INFO @ Tue, 21 Apr 2015 13:24:16: 6000000 INFO @ Tue, 21 Apr 2015 13:24:21: 7000000 INFO @ Tue, 21 Apr 2015 13:24:21: 7000000 INFO @ Tue, 21 Apr 2015 13:24:21: 7000000 INFO @ Tue, 21 Apr 2015 13:24:26: 8000000 INFO @ Tue, 21 Apr 2015 13:24:26: 8000000 INFO @ Tue, 21 Apr 2015 13:24:27: 8000000 INFO @ Tue, 21 Apr 2015 13:24:30: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:24:30: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:24:30: #1 total tags in treatment: 8662048 INFO @ Tue, 21 Apr 2015 13:24:30: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:24:30: #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 13:24:30: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:24:30: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:24:30: #1 total tags in treatment: 8662048 INFO @ Tue, 21 Apr 2015 13:24:30: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:24:30: #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 13:24:31: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:24:31: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:24:31: #1 total tags in treatment: 8662048 INFO @ Tue, 21 Apr 2015 13:24:31: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:24:31: #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 13:24:31: #1 tags after filtering in treatment: 8658275 INFO @ Tue, 21 Apr 2015 13:24:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:24:31: #1 finished! INFO @ Tue, 21 Apr 2015 13:24:31: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:24:31: #1 tags after filtering in treatment: 8658275 INFO @ Tue, 21 Apr 2015 13:24:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:24:31: #1 finished! INFO @ Tue, 21 Apr 2015 13:24:31: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:24:33: #1 tags after filtering in treatment: 8658275 INFO @ Tue, 21 Apr 2015 13:24:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:24:33: #1 finished! INFO @ Tue, 21 Apr 2015 13:24:33: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:24:34: #2 number of paired peaks: 11776 INFO @ Tue, 21 Apr 2015 13:24:34: start model_add_line... INFO @ Tue, 21 Apr 2015 13:24:34: #2 number of paired peaks: 11776 INFO @ Tue, 21 Apr 2015 13:24:34: start model_add_line... INFO @ Tue, 21 Apr 2015 13:24:36: #2 number of paired peaks: 11776 INFO @ Tue, 21 Apr 2015 13:24:36: 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 13:26:31: start X-correlation... INFO @ Tue, 21 Apr 2015 13:26:31: end of X-cor INFO @ Tue, 21 Apr 2015 13:26:31: #2 finished! INFO @ Tue, 21 Apr 2015 13:26:31: #2 predicted fragment length is 215 bps INFO @ Tue, 21 Apr 2015 13:26:31: #2 alternative fragment length(s) may be 215 bps INFO @ Tue, 21 Apr 2015 13:26:31: #2.2 Generate R script for model : SRX040613.05_model.r INFO @ Tue, 21 Apr 2015 13:26:31: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:26:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:26:32: start X-correlation... INFO @ Tue, 21 Apr 2015 13:26:32: end of X-cor INFO @ Tue, 21 Apr 2015 13:26:32: #2 finished! INFO @ Tue, 21 Apr 2015 13:26:32: #2 predicted fragment length is 215 bps INFO @ Tue, 21 Apr 2015 13:26:32: #2 alternative fragment length(s) may be 215 bps INFO @ Tue, 21 Apr 2015 13:26:32: #2.2 Generate R script for model : SRX040613.10_model.r INFO @ Tue, 21 Apr 2015 13:26:32: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:26:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:26:40: start X-correlation... INFO @ Tue, 21 Apr 2015 13:26:40: end of X-cor INFO @ Tue, 21 Apr 2015 13:26:40: #2 finished! INFO @ Tue, 21 Apr 2015 13:26:40: #2 predicted fragment length is 215 bps INFO @ Tue, 21 Apr 2015 13:26:40: #2 alternative fragment length(s) may be 215 bps INFO @ Tue, 21 Apr 2015 13:26:40: #2.2 Generate R script for model : SRX040613.20_model.r INFO @ Tue, 21 Apr 2015 13:26:40: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:26:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:27:42: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:27:44: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:27:50: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:28:29: #4 Write output xls file... SRX040613.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:28:29: #4 Write peak in narrowPeak format file... SRX040613.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:28:29: #4 Write summits bed file... SRX040613.10_summits.bed INFO @ Tue, 21 Apr 2015 13:28:29: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8066 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:28:34: #4 Write output xls file... SRX040613.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:28:34: #4 Write peak in narrowPeak format file... SRX040613.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:28:34: #4 Write summits bed file... SRX040613.05_summits.bed INFO @ Tue, 21 Apr 2015 13:28:34: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8861 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:28:36: #4 Write output xls file... SRX040613.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:28:36: #4 Write peak in narrowPeak format file... SRX040613.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:28:36: #4 Write summits bed file... SRX040613.20_summits.bed INFO @ Tue, 21 Apr 2015 13:28:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7193 records, 4 fields): 11 millis CompletedMACS2peakCalling