Job ID = 2162395 sra ファイルのダウンロード中... Completed: 454940K bytes transferred in 7 seconds (520843K 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 37925 0 37925 0 0 50363 0 --:--:-- --:--:-- --:--:-- 67602 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 22822197 spots for /home/okishinya/chipatlas/results/dm3/SRX084385/SRR314831.sra Written 22822197 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: 00:05:50 22822197 reads; of these: 22822197 (100.00%) were unpaired; of these: 2031438 (8.90%) aligned 0 times 17575890 (77.01%) aligned exactly 1 time 3214869 (14.09%) aligned >1 times 91.10% overall alignment rate Time searching: 00:05:50 Overall time: 00:05:50 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] 11494807 / 20790759 = 0.5529 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 13:53:47: # Command line: callpeak -t SRX084385.bam -f BAM -g dm -n SRX084385.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX084385.10 # format = BAM # ChIP-seq file = ['SRX084385.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 13:53:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:53:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:53:47: # Command line: callpeak -t SRX084385.bam -f BAM -g dm -n SRX084385.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX084385.20 # format = BAM # ChIP-seq file = ['SRX084385.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 13:53:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:53:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:53:47: # Command line: callpeak -t SRX084385.bam -f BAM -g dm -n SRX084385.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX084385.05 # format = BAM # ChIP-seq file = ['SRX084385.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 13:53:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:53:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:53:53: 1000000 INFO @ Tue, 21 Apr 2015 13:53:53: 1000000 INFO @ Tue, 21 Apr 2015 13:53:53: 1000000 INFO @ Tue, 21 Apr 2015 13:53:59: 2000000 INFO @ Tue, 21 Apr 2015 13:53:59: 2000000 INFO @ Tue, 21 Apr 2015 13:53:59: 2000000 INFO @ Tue, 21 Apr 2015 13:54:05: 3000000 INFO @ Tue, 21 Apr 2015 13:54:05: 3000000 INFO @ Tue, 21 Apr 2015 13:54:05: 3000000 INFO @ Tue, 21 Apr 2015 13:54:10: 4000000 INFO @ Tue, 21 Apr 2015 13:54:11: 4000000 INFO @ Tue, 21 Apr 2015 13:54:11: 4000000 INFO @ Tue, 21 Apr 2015 13:54:16: 5000000 INFO @ Tue, 21 Apr 2015 13:54:17: 5000000 INFO @ Tue, 21 Apr 2015 13:54:17: 5000000 INFO @ Tue, 21 Apr 2015 13:54:22: 6000000 INFO @ Tue, 21 Apr 2015 13:54:23: 6000000 INFO @ Tue, 21 Apr 2015 13:54:23: 6000000 INFO @ Tue, 21 Apr 2015 13:54:27: 7000000 INFO @ Tue, 21 Apr 2015 13:54:29: 7000000 INFO @ Tue, 21 Apr 2015 13:54:29: 7000000 INFO @ Tue, 21 Apr 2015 13:54:33: 8000000 INFO @ Tue, 21 Apr 2015 13:54:35: 8000000 INFO @ Tue, 21 Apr 2015 13:54:35: 8000000 INFO @ Tue, 21 Apr 2015 13:54:39: 9000000 INFO @ Tue, 21 Apr 2015 13:54:41: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:54:41: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:54:41: #1 total tags in treatment: 9295952 INFO @ Tue, 21 Apr 2015 13:54:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:54:41: #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 13:54:41: 9000000 INFO @ Tue, 21 Apr 2015 13:54:41: 9000000 INFO @ Tue, 21 Apr 2015 13:54:42: #1 tags after filtering in treatment: 9290848 INFO @ Tue, 21 Apr 2015 13:54:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:54:42: #1 finished! INFO @ Tue, 21 Apr 2015 13:54:42: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:54:42: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:54:42: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:54:42: #1 total tags in treatment: 9295952 INFO @ Tue, 21 Apr 2015 13:54:42: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:54:42: #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 13:54:43: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:54:43: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:54:43: #1 total tags in treatment: 9295952 INFO @ Tue, 21 Apr 2015 13:54:43: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:54:43: #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 13:54:44: #1 tags after filtering in treatment: 9290848 INFO @ Tue, 21 Apr 2015 13:54:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:54:44: #1 finished! INFO @ Tue, 21 Apr 2015 13:54:44: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:54:45: #1 tags after filtering in treatment: 9290848 INFO @ Tue, 21 Apr 2015 13:54:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:54:45: #1 finished! INFO @ Tue, 21 Apr 2015 13:54:45: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:54:45: #2 number of paired peaks: 5200 INFO @ Tue, 21 Apr 2015 13:54:45: start model_add_line... INFO @ Tue, 21 Apr 2015 13:54:46: #2 number of paired peaks: 5200 INFO @ Tue, 21 Apr 2015 13:54:46: start model_add_line... INFO @ Tue, 21 Apr 2015 13:54:47: #2 number of paired peaks: 5200 INFO @ Tue, 21 Apr 2015 13:54:47: start model_add_line... INFO @ Tue, 21 Apr 2015 13:55:21: start X-correlation... INFO @ Tue, 21 Apr 2015 13:55:21: end of X-cor INFO @ Tue, 21 Apr 2015 13:55:21: #2 finished! INFO @ Tue, 21 Apr 2015 13:55:21: #2 predicted fragment length is 152 bps INFO @ Tue, 21 Apr 2015 13:55:21: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 21 Apr 2015 13:55:21: #2.2 Generate R script for model : SRX084385.05_model.r INFO @ Tue, 21 Apr 2015 13:55:21: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:55:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:55:21: start X-correlation... INFO @ Tue, 21 Apr 2015 13:55:21: end of X-cor INFO @ Tue, 21 Apr 2015 13:55:21: #2 finished! INFO @ Tue, 21 Apr 2015 13:55:21: #2 predicted fragment length is 152 bps INFO @ Tue, 21 Apr 2015 13:55:21: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 21 Apr 2015 13:55:21: #2.2 Generate R script for model : SRX084385.10_model.r INFO @ Tue, 21 Apr 2015 13:55:21: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:55:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:55:22: start X-correlation... INFO @ Tue, 21 Apr 2015 13:55:22: end of X-cor INFO @ Tue, 21 Apr 2015 13:55:22: #2 finished! INFO @ Tue, 21 Apr 2015 13:55:22: #2 predicted fragment length is 152 bps INFO @ Tue, 21 Apr 2015 13:55:22: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 21 Apr 2015 13:55:22: #2.2 Generate R script for model : SRX084385.20_model.r INFO @ Tue, 21 Apr 2015 13:55:22: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:55:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:56:18: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:56:18: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:56:20: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 21 Apr 2015 13:57:03: #4 Write output xls file... SRX084385.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:57:04: #4 Write peak in narrowPeak format file... SRX084385.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:57:04: #4 Write summits bed file... SRX084385.20_summits.bed INFO @ Tue, 21 Apr 2015 13:57:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7339 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:57:07: #4 Write output xls file... SRX084385.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:57:08: #4 Write peak in narrowPeak format file... SRX084385.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:57:08: #4 Write summits bed file... SRX084385.10_summits.bed INFO @ Tue, 21 Apr 2015 13:57:08: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10519 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:57:15: #4 Write output xls file... SRX084385.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:57:15: #4 Write peak in narrowPeak format file... SRX084385.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:57:15: #4 Write summits bed file... SRX084385.05_summits.bed INFO @ Tue, 21 Apr 2015 13:57:16: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (13689 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。