Job ID = 8696823 sra ファイルのダウンロード中... Completed: 860981K bytes transferred in 49 seconds (142464K 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 --:--:-- 0:00:06 --:--:-- 0 100 12695 0 12695 0 0 1707 0 --:--:-- 0:00:07 --:--:-- 13101 100 31486 0 31486 0 0 3789 0 --:--:-- 0:00:08 --:--:-- 17121 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 31457054 spots for /home/okishinya/chipatlas/results/dm3/SRX110761/SRR388343.sra Written 31457054 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: 00:13:56 31457054 reads; of these: 31457054 (100.00%) were unpaired; of these: 15094262 (47.98%) aligned 0 times 14674051 (46.65%) aligned exactly 1 time 1688741 (5.37%) aligned >1 times 52.02% overall alignment rate Time searching: 00:13:56 Overall time: 00:13:56 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] 4409776 / 16362792 = 0.2695 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 @ Fri, 10 Mar 2017 12:20:59: # Command line: callpeak -t SRX110761.bam -f BAM -g dm -n SRX110761.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110761.10 # format = BAM # ChIP-seq file = ['SRX110761.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 @ Fri, 10 Mar 2017 12:20:59: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:20:59: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:20:59: # Command line: callpeak -t SRX110761.bam -f BAM -g dm -n SRX110761.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110761.05 # format = BAM # ChIP-seq file = ['SRX110761.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 @ Fri, 10 Mar 2017 12:20:59: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:20:59: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:21:00: # Command line: callpeak -t SRX110761.bam -f BAM -g dm -n SRX110761.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110761.20 # format = BAM # ChIP-seq file = ['SRX110761.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 @ Fri, 10 Mar 2017 12:21:00: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:21:00: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:21:08: 1000000 INFO @ Fri, 10 Mar 2017 12:21:17: 2000000 INFO @ Fri, 10 Mar 2017 12:21:25: 3000000 INFO @ Fri, 10 Mar 2017 12:21:29: 1000000 INFO @ Fri, 10 Mar 2017 12:21:31: 1000000 INFO @ Fri, 10 Mar 2017 12:21:33: 4000000 INFO @ Fri, 10 Mar 2017 12:21:43: 5000000 INFO @ Fri, 10 Mar 2017 12:21:59: 2000000 INFO @ Fri, 10 Mar 2017 12:21:59: 6000000 INFO @ Fri, 10 Mar 2017 12:22:01: 2000000 INFO @ Fri, 10 Mar 2017 12:22:09: 7000000 INFO @ Fri, 10 Mar 2017 12:22:17: 8000000 INFO @ Fri, 10 Mar 2017 12:22:24: 9000000 INFO @ Fri, 10 Mar 2017 12:22:32: 10000000 INFO @ Fri, 10 Mar 2017 12:22:40: 11000000 INFO @ Fri, 10 Mar 2017 12:22:41: 3000000 INFO @ Fri, 10 Mar 2017 12:22:43: 3000000 INFO @ Fri, 10 Mar 2017 12:22:49: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:22:49: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:22:49: #1 total tags in treatment: 11953016 INFO @ Fri, 10 Mar 2017 12:22:49: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:22:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:22:52: #1 tags after filtering in treatment: 11951124 INFO @ Fri, 10 Mar 2017 12:22:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:22:52: #1 finished! INFO @ Fri, 10 Mar 2017 12:22:52: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:22:56: #2 number of paired peaks: 5070 INFO @ Fri, 10 Mar 2017 12:22:56: start model_add_line... INFO @ Fri, 10 Mar 2017 12:23:11: 4000000 INFO @ Fri, 10 Mar 2017 12:23:13: 4000000 INFO @ Fri, 10 Mar 2017 12:23:42: 5000000 INFO @ Fri, 10 Mar 2017 12:23:45: 5000000 INFO @ Fri, 10 Mar 2017 12:24:05: start X-correlation... INFO @ Fri, 10 Mar 2017 12:24:05: end of X-cor INFO @ Fri, 10 Mar 2017 12:24:05: #2 finished! INFO @ Fri, 10 Mar 2017 12:24:05: #2 predicted fragment length is 81 bps INFO @ Fri, 10 Mar 2017 12:24:05: #2 alternative fragment length(s) may be 81 bps INFO @ Fri, 10 Mar 2017 12:24:05: #2.2 Generate R script for model : SRX110761.20_model.r INFO @ Fri, 10 Mar 2017 12:24:05: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:24:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:24:09: 6000000 INFO @ Fri, 10 Mar 2017 12:24:11: 6000000 INFO @ Fri, 10 Mar 2017 12:24:21: 7000000 INFO @ Fri, 10 Mar 2017 12:24:34: 8000000 INFO @ Fri, 10 Mar 2017 12:24:42: 9000000 INFO @ Fri, 10 Mar 2017 12:24:45: 7000000 INFO @ Fri, 10 Mar 2017 12:24:49: 10000000 INFO @ Fri, 10 Mar 2017 12:24:57: 11000000 INFO @ Fri, 10 Mar 2017 12:25:04: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:25:04: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:25:04: #1 total tags in treatment: 11953016 INFO @ Fri, 10 Mar 2017 12:25:04: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:25:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:25:05: 8000000 INFO @ Fri, 10 Mar 2017 12:25:07: #1 tags after filtering in treatment: 11951124 INFO @ Fri, 10 Mar 2017 12:25:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:25:07: #1 finished! INFO @ Fri, 10 Mar 2017 12:25:07: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:25:11: #2 number of paired peaks: 5070 INFO @ Fri, 10 Mar 2017 12:25:11: start model_add_line... INFO @ Fri, 10 Mar 2017 12:25:13: 9000000 INFO @ Fri, 10 Mar 2017 12:25:19: 10000000 INFO @ Fri, 10 Mar 2017 12:25:26: 11000000 INFO @ Fri, 10 Mar 2017 12:25:33: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:25:33: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:25:33: #1 total tags in treatment: 11953016 INFO @ Fri, 10 Mar 2017 12:25:33: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:25:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:25:35: #1 tags after filtering in treatment: 11951124 INFO @ Fri, 10 Mar 2017 12:25:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:25:35: #1 finished! INFO @ Fri, 10 Mar 2017 12:25:35: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:25:39: #2 number of paired peaks: 5070 INFO @ Fri, 10 Mar 2017 12:25:39: start model_add_line... INFO @ Fri, 10 Mar 2017 12:25:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:25:59: start X-correlation... INFO @ Fri, 10 Mar 2017 12:25:59: end of X-cor INFO @ Fri, 10 Mar 2017 12:25:59: #2 finished! INFO @ Fri, 10 Mar 2017 12:25:59: #2 predicted fragment length is 81 bps INFO @ Fri, 10 Mar 2017 12:25:59: #2 alternative fragment length(s) may be 81 bps INFO @ Fri, 10 Mar 2017 12:25:59: #2.2 Generate R script for model : SRX110761.05_model.r INFO @ Fri, 10 Mar 2017 12:25:59: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:25:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:26:28: start X-correlation... INFO @ Fri, 10 Mar 2017 12:26:28: end of X-cor INFO @ Fri, 10 Mar 2017 12:26:28: #2 finished! INFO @ Fri, 10 Mar 2017 12:26:28: #2 predicted fragment length is 81 bps INFO @ Fri, 10 Mar 2017 12:26:28: #2 alternative fragment length(s) may be 81 bps INFO @ Fri, 10 Mar 2017 12:26:28: #2.2 Generate R script for model : SRX110761.10_model.r INFO @ Fri, 10 Mar 2017 12:26:28: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:26:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:26:44: #4 Write output xls file... SRX110761.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:26:44: #4 Write peak in narrowPeak format file... SRX110761.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:26:44: #4 Write summits bed file... SRX110761.20_summits.bed INFO @ Fri, 10 Mar 2017 12:26:44: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (4777 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:27:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:28:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:28:33: #4 Write output xls file... SRX110761.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:28:33: #4 Write peak in narrowPeak format file... SRX110761.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:28:33: #4 Write summits bed file... SRX110761.05_summits.bed INFO @ Fri, 10 Mar 2017 12:28:33: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (12770 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:29:29: #4 Write output xls file... SRX110761.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:29:29: #4 Write peak in narrowPeak format file... SRX110761.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:29:29: #4 Write summits bed file... SRX110761.10_summits.bed INFO @ Fri, 10 Mar 2017 12:29:29: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (8167 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。