Job ID = 8696819 sra ファイルのダウンロード中... Completed: 900007K bytes transferred in 47 seconds (153698K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 22575 0 22575 0 0 2800 0 --:--:-- 0:00:08 --:--:-- 14424 100 31482 0 31482 0 0 3743 0 --:--:-- 0:00:08 --:--:-- 16448 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 33722807 spots for /home/okishinya/chipatlas/results/dm3/SRX110757/SRR388339.sra Written 33722807 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:42 33722807 reads; of these: 33722807 (100.00%) were unpaired; of these: 7862768 (23.32%) aligned 0 times 21637328 (64.16%) aligned exactly 1 time 4222711 (12.52%) aligned >1 times 76.68% overall alignment rate Time searching: 00:18:43 Overall time: 00:18:43 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] 12151054 / 25860039 = 0.4699 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 12:27:39: # Command line: callpeak -t SRX110757.bam -f BAM -g dm -n SRX110757.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110757.20 # format = BAM # ChIP-seq file = ['SRX110757.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 12:27:39: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:27:39: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:27:39: # Command line: callpeak -t SRX110757.bam -f BAM -g dm -n SRX110757.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110757.05 # format = BAM # ChIP-seq file = ['SRX110757.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 12:27:39: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:27:39: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:27:39: # Command line: callpeak -t SRX110757.bam -f BAM -g dm -n SRX110757.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110757.10 # format = BAM # ChIP-seq file = ['SRX110757.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 12:27:39: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:27:39: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:27:50: 1000000 INFO @ Fri, 10 Mar 2017 12:27:55: 1000000 INFO @ Fri, 10 Mar 2017 12:28:01: 2000000 INFO @ Fri, 10 Mar 2017 12:28:04: 1000000 INFO @ Fri, 10 Mar 2017 12:28:11: 2000000 INFO @ Fri, 10 Mar 2017 12:28:12: 3000000 INFO @ Fri, 10 Mar 2017 12:28:20: 2000000 INFO @ Fri, 10 Mar 2017 12:28:23: 4000000 INFO @ Fri, 10 Mar 2017 12:28:27: 3000000 INFO @ Fri, 10 Mar 2017 12:28:32: 3000000 INFO @ Fri, 10 Mar 2017 12:28:33: 5000000 INFO @ Fri, 10 Mar 2017 12:28:34: 4000000 INFO @ Fri, 10 Mar 2017 12:28:40: 4000000 INFO @ Fri, 10 Mar 2017 12:28:42: 5000000 INFO @ Fri, 10 Mar 2017 12:28:43: 6000000 INFO @ Fri, 10 Mar 2017 12:28:48: 5000000 INFO @ Fri, 10 Mar 2017 12:28:49: 6000000 INFO @ Fri, 10 Mar 2017 12:28:55: 7000000 INFO @ Fri, 10 Mar 2017 12:28:56: 6000000 INFO @ Fri, 10 Mar 2017 12:28:57: 7000000 INFO @ Fri, 10 Mar 2017 12:29:04: 7000000 INFO @ Fri, 10 Mar 2017 12:29:05: 8000000 INFO @ Fri, 10 Mar 2017 12:29:09: 8000000 INFO @ Fri, 10 Mar 2017 12:29:13: 9000000 INFO @ Fri, 10 Mar 2017 12:29:13: 8000000 INFO @ Fri, 10 Mar 2017 12:29:17: 9000000 INFO @ Fri, 10 Mar 2017 12:29:21: 10000000 INFO @ Fri, 10 Mar 2017 12:29:25: 10000000 INFO @ Fri, 10 Mar 2017 12:29:26: 9000000 INFO @ Fri, 10 Mar 2017 12:29:28: 11000000 INFO @ Fri, 10 Mar 2017 12:29:33: 11000000 INFO @ Fri, 10 Mar 2017 12:29:36: 12000000 INFO @ Fri, 10 Mar 2017 12:29:41: 10000000 INFO @ Fri, 10 Mar 2017 12:29:41: 12000000 INFO @ Fri, 10 Mar 2017 12:29:44: 13000000 INFO @ Fri, 10 Mar 2017 12:29:49: 13000000 INFO @ Fri, 10 Mar 2017 12:29:49: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:29:49: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:29:49: #1 total tags in treatment: 13708985 INFO @ Fri, 10 Mar 2017 12:29:49: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:29:49: #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 12:29:52: #1 tags after filtering in treatment: 13705472 INFO @ Fri, 10 Mar 2017 12:29:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:29:52: #1 finished! INFO @ Fri, 10 Mar 2017 12:29:52: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:29:55: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:29:55: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:29:55: #1 total tags in treatment: 13708985 INFO @ Fri, 10 Mar 2017 12:29:55: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:29:55: #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 12:29:55: 11000000 INFO @ Fri, 10 Mar 2017 12:29:56: #2 number of paired peaks: 5176 INFO @ Fri, 10 Mar 2017 12:29:56: start model_add_line... INFO @ Fri, 10 Mar 2017 12:29:58: #1 tags after filtering in treatment: 13705472 INFO @ Fri, 10 Mar 2017 12:29:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:29:58: #1 finished! INFO @ Fri, 10 Mar 2017 12:29:58: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:30:02: #2 number of paired peaks: 5176 INFO @ Fri, 10 Mar 2017 12:30:02: start model_add_line... INFO @ Fri, 10 Mar 2017 12:30:10: 12000000 INFO @ Fri, 10 Mar 2017 12:30:24: 13000000 INFO @ Fri, 10 Mar 2017 12:30:34: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:30:34: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:30:34: #1 total tags in treatment: 13708985 INFO @ Fri, 10 Mar 2017 12:30:34: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:30:34: #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 12:30:38: #1 tags after filtering in treatment: 13705472 INFO @ Fri, 10 Mar 2017 12:30:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:30:38: #1 finished! INFO @ Fri, 10 Mar 2017 12:30:38: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:30:41: #2 number of paired peaks: 5176 INFO @ Fri, 10 Mar 2017 12:30:41: start model_add_line... INFO @ Fri, 10 Mar 2017 12:30:52: start X-correlation... INFO @ Fri, 10 Mar 2017 12:30:52: end of X-cor INFO @ Fri, 10 Mar 2017 12:30:52: #2 finished! INFO @ Fri, 10 Mar 2017 12:30:52: #2 predicted fragment length is 85 bps INFO @ Fri, 10 Mar 2017 12:30:52: #2 alternative fragment length(s) may be 85 bps INFO @ Fri, 10 Mar 2017 12:30:52: #2.2 Generate R script for model : SRX110757.20_model.r INFO @ Fri, 10 Mar 2017 12:30:52: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:30:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:30:59: start X-correlation... INFO @ Fri, 10 Mar 2017 12:30:59: end of X-cor INFO @ Fri, 10 Mar 2017 12:30:59: #2 finished! INFO @ Fri, 10 Mar 2017 12:30:59: #2 predicted fragment length is 85 bps INFO @ Fri, 10 Mar 2017 12:30:59: #2 alternative fragment length(s) may be 85 bps INFO @ Fri, 10 Mar 2017 12:30:59: #2.2 Generate R script for model : SRX110757.05_model.r INFO @ Fri, 10 Mar 2017 12:30:59: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:30:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:31:37: start X-correlation... INFO @ Fri, 10 Mar 2017 12:31:37: end of X-cor INFO @ Fri, 10 Mar 2017 12:31:37: #2 finished! INFO @ Fri, 10 Mar 2017 12:31:37: #2 predicted fragment length is 85 bps INFO @ Fri, 10 Mar 2017 12:31:37: #2 alternative fragment length(s) may be 85 bps INFO @ Fri, 10 Mar 2017 12:31:37: #2.2 Generate R script for model : SRX110757.10_model.r INFO @ Fri, 10 Mar 2017 12:31:37: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:31:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:32:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:32:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:33:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:33:32: #4 Write output xls file... SRX110757.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:33:32: #4 Write peak in narrowPeak format file... SRX110757.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:33:32: #4 Write summits bed file... SRX110757.20_summits.bed INFO @ Fri, 10 Mar 2017 12:33:32: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5145 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:33:41: #4 Write output xls file... SRX110757.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:33:41: #4 Write peak in narrowPeak format file... SRX110757.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:33:42: #4 Write summits bed file... SRX110757.05_summits.bed INFO @ Fri, 10 Mar 2017 12:33:42: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (13074 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:34:20: #4 Write output xls file... SRX110757.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:34:20: #4 Write peak in narrowPeak format file... SRX110757.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:34:20: #4 Write summits bed file... SRX110757.10_summits.bed INFO @ Fri, 10 Mar 2017 12:34:20: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (8833 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。