Job ID = 2163361 sra ファイルのダウンロード中... Completed: 1490989K bytes transferred in 13 seconds (921044K 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 4007 0 4007 0 0 4153 0 --:--:-- --:--:-- --:--:-- 5177 100 36096 0 36096 0 0 31261 0 --:--:-- 0:00:01 --:--:-- 37443 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 36531342 spots for /home/okishinya/chipatlas/results/dm3/SRX128169/SRR442090.sra Written 36531342 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: 00:10:02 36531342 reads; of these: 36531342 (100.00%) were unpaired; of these: 1697717 (4.65%) aligned 0 times 29135753 (79.76%) aligned exactly 1 time 5697872 (15.60%) aligned >1 times 95.35% overall alignment rate Time searching: 00:10:02 Overall time: 00:10:02 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 12 files... [bam_rmdupse_core] 12663005 / 34833625 = 0.3635 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 16:26:36: # Command line: callpeak -t SRX128169.bam -f BAM -g dm -n SRX128169.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX128169.20 # format = BAM # ChIP-seq file = ['SRX128169.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 16:26:36: # Command line: callpeak -t SRX128169.bam -f BAM -g dm -n SRX128169.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX128169.10 # format = BAM # ChIP-seq file = ['SRX128169.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 16:26:36: #1 read tag files... INFO @ Tue, 21 Apr 2015 16:26:36: #1 read tag files... INFO @ Tue, 21 Apr 2015 16:26:36: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 16:26:36: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 16:26:36: # Command line: callpeak -t SRX128169.bam -f BAM -g dm -n SRX128169.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX128169.05 # format = BAM # ChIP-seq file = ['SRX128169.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 16:26:36: #1 read tag files... INFO @ Tue, 21 Apr 2015 16:26:36: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 16:26:41: 1000000 INFO @ Tue, 21 Apr 2015 16:26:41: 1000000 INFO @ Tue, 21 Apr 2015 16:26:42: 1000000 INFO @ Tue, 21 Apr 2015 16:26:46: 2000000 INFO @ Tue, 21 Apr 2015 16:26:47: 2000000 INFO @ Tue, 21 Apr 2015 16:26:47: 2000000 INFO @ Tue, 21 Apr 2015 16:26:52: 3000000 INFO @ Tue, 21 Apr 2015 16:26:52: 3000000 INFO @ Tue, 21 Apr 2015 16:26:53: 3000000 INFO @ Tue, 21 Apr 2015 16:26:57: 4000000 INFO @ Tue, 21 Apr 2015 16:26:57: 4000000 INFO @ Tue, 21 Apr 2015 16:26:58: 4000000 INFO @ Tue, 21 Apr 2015 16:27:02: 5000000 INFO @ Tue, 21 Apr 2015 16:27:02: 5000000 INFO @ Tue, 21 Apr 2015 16:27:04: 5000000 INFO @ Tue, 21 Apr 2015 16:27:07: 6000000 INFO @ Tue, 21 Apr 2015 16:27:08: 6000000 INFO @ Tue, 21 Apr 2015 16:27:10: 6000000 INFO @ Tue, 21 Apr 2015 16:27:13: 7000000 INFO @ Tue, 21 Apr 2015 16:27:13: 7000000 INFO @ Tue, 21 Apr 2015 16:27:16: 7000000 INFO @ Tue, 21 Apr 2015 16:27:18: 8000000 INFO @ Tue, 21 Apr 2015 16:27:19: 8000000 INFO @ Tue, 21 Apr 2015 16:27:22: 8000000 INFO @ Tue, 21 Apr 2015 16:27:23: 9000000 INFO @ Tue, 21 Apr 2015 16:27:24: 9000000 INFO @ Tue, 21 Apr 2015 16:27:28: 9000000 INFO @ Tue, 21 Apr 2015 16:27:29: 10000000 INFO @ Tue, 21 Apr 2015 16:27:30: 10000000 INFO @ Tue, 21 Apr 2015 16:27:34: 10000000 INFO @ Tue, 21 Apr 2015 16:27:34: 11000000 INFO @ Tue, 21 Apr 2015 16:27:35: 11000000 INFO @ Tue, 21 Apr 2015 16:27:40: 12000000 INFO @ Tue, 21 Apr 2015 16:27:40: 11000000 INFO @ Tue, 21 Apr 2015 16:27:41: 12000000 INFO @ Tue, 21 Apr 2015 16:27:45: 13000000 INFO @ Tue, 21 Apr 2015 16:27:46: 12000000 INFO @ Tue, 21 Apr 2015 16:27:46: 13000000 INFO @ Tue, 21 Apr 2015 16:27:51: 14000000 INFO @ Tue, 21 Apr 2015 16:27:52: 14000000 INFO @ Tue, 21 Apr 2015 16:27:52: 13000000 INFO @ Tue, 21 Apr 2015 16:27:56: 15000000 INFO @ Tue, 21 Apr 2015 16:27:57: 15000000 INFO @ Tue, 21 Apr 2015 16:27:58: 14000000 INFO @ Tue, 21 Apr 2015 16:28:02: 16000000 INFO @ Tue, 21 Apr 2015 16:28:03: 16000000 INFO @ Tue, 21 Apr 2015 16:28:04: 15000000 INFO @ Tue, 21 Apr 2015 16:28:07: 17000000 INFO @ Tue, 21 Apr 2015 16:28:09: 17000000 INFO @ Tue, 21 Apr 2015 16:28:10: 16000000 INFO @ Tue, 21 Apr 2015 16:28:13: 18000000 INFO @ Tue, 21 Apr 2015 16:28:14: 18000000 INFO @ Tue, 21 Apr 2015 16:28:16: 17000000 INFO @ Tue, 21 Apr 2015 16:28:18: 19000000 INFO @ Tue, 21 Apr 2015 16:28:20: 19000000 INFO @ Tue, 21 Apr 2015 16:28:22: 18000000 INFO @ Tue, 21 Apr 2015 16:28:23: 20000000 INFO @ Tue, 21 Apr 2015 16:28:26: 20000000 INFO @ Tue, 21 Apr 2015 16:28:28: 19000000 INFO @ Tue, 21 Apr 2015 16:28:29: 21000000 INFO @ Tue, 21 Apr 2015 16:28:31: 21000000 INFO @ Tue, 21 Apr 2015 16:28:34: 20000000 INFO @ Tue, 21 Apr 2015 16:28:34: 22000000 INFO @ Tue, 21 Apr 2015 16:28:36: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 16:28:36: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 16:28:36: #1 total tags in treatment: 22170620 INFO @ Tue, 21 Apr 2015 16:28:36: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 16:28:36: #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 16:28:37: 22000000 INFO @ Tue, 21 Apr 2015 16:28:38: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 16:28:38: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 16:28:38: #1 total tags in treatment: 22170620 INFO @ Tue, 21 Apr 2015 16:28:38: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 16:28:38: #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 16:28:39: 21000000 INFO @ Tue, 21 Apr 2015 16:28:40: #1 tags after filtering in treatment: 22158174 INFO @ Tue, 21 Apr 2015 16:28:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 16:28:40: #1 finished! INFO @ Tue, 21 Apr 2015 16:28:40: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 16:28:42: #1 tags after filtering in treatment: 22158174 INFO @ Tue, 21 Apr 2015 16:28:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 16:28:42: #1 finished! INFO @ Tue, 21 Apr 2015 16:28:42: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 16:28:44: #2 number of paired peaks: 1891 INFO @ Tue, 21 Apr 2015 16:28:44: start model_add_line... INFO @ Tue, 21 Apr 2015 16:28:44: 22000000 INFO @ Tue, 21 Apr 2015 16:28:45: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 16:28:45: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 16:28:45: #1 total tags in treatment: 22170620 INFO @ Tue, 21 Apr 2015 16:28:45: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 16:28:45: #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 16:28:46: #2 number of paired peaks: 1891 INFO @ Tue, 21 Apr 2015 16:28:46: start model_add_line... INFO @ Tue, 21 Apr 2015 16:28:49: #1 tags after filtering in treatment: 22158174 INFO @ Tue, 21 Apr 2015 16:28:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 16:28:49: #1 finished! INFO @ Tue, 21 Apr 2015 16:28:49: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 16:28:54: #2 number of paired peaks: 1891 INFO @ Tue, 21 Apr 2015 16:28:54: start model_add_line... INFO @ Tue, 21 Apr 2015 16:29:09: start X-correlation... INFO @ Tue, 21 Apr 2015 16:29:09: end of X-cor INFO @ Tue, 21 Apr 2015 16:29:09: #2 finished! INFO @ Tue, 21 Apr 2015 16:29:09: #2 predicted fragment length is 160 bps INFO @ Tue, 21 Apr 2015 16:29:09: #2 alternative fragment length(s) may be 4,160 bps INFO @ Tue, 21 Apr 2015 16:29:09: #2.2 Generate R script for model : SRX128169.10_model.r INFO @ Tue, 21 Apr 2015 16:29:09: #3 Call peaks... INFO @ Tue, 21 Apr 2015 16:29:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 16:29:10: start X-correlation... INFO @ Tue, 21 Apr 2015 16:29:10: end of X-cor INFO @ Tue, 21 Apr 2015 16:29:10: #2 finished! INFO @ Tue, 21 Apr 2015 16:29:10: #2 predicted fragment length is 160 bps INFO @ Tue, 21 Apr 2015 16:29:10: #2 alternative fragment length(s) may be 4,160 bps INFO @ Tue, 21 Apr 2015 16:29:10: #2.2 Generate R script for model : SRX128169.20_model.r INFO @ Tue, 21 Apr 2015 16:29:10: #3 Call peaks... INFO @ Tue, 21 Apr 2015 16:29:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 16:29:18: start X-correlation... INFO @ Tue, 21 Apr 2015 16:29:18: end of X-cor INFO @ Tue, 21 Apr 2015 16:29:18: #2 finished! INFO @ Tue, 21 Apr 2015 16:29:18: #2 predicted fragment length is 160 bps INFO @ Tue, 21 Apr 2015 16:29:18: #2 alternative fragment length(s) may be 4,160 bps INFO @ Tue, 21 Apr 2015 16:29:18: #2.2 Generate R script for model : SRX128169.05_model.r INFO @ Tue, 21 Apr 2015 16:29:18: #3 Call peaks... INFO @ Tue, 21 Apr 2015 16:29:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 16:31:05: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 16:31:06: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 16:31:16: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 16:32:22: #4 Write output xls file... SRX128169.20_peaks.xls INFO @ Tue, 21 Apr 2015 16:32:22: #4 Write peak in narrowPeak format file... SRX128169.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 16:32:22: #4 Write summits bed file... SRX128169.20_summits.bed INFO @ Tue, 21 Apr 2015 16:32:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4977 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 16:32:35: #4 Write output xls file... SRX128169.10_peaks.xls INFO @ Tue, 21 Apr 2015 16:32:36: #4 Write peak in narrowPeak format file... SRX128169.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 16:32:36: #4 Write summits bed file... SRX128169.10_summits.bed INFO @ Tue, 21 Apr 2015 16:32:36: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11783 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 21 Apr 2015 16:33:07: #4 Write output xls file... SRX128169.05_peaks.xls INFO @ Tue, 21 Apr 2015 16:33:07: #4 Write peak in narrowPeak format file... SRX128169.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 16:33:07: #4 Write summits bed file... SRX128169.05_summits.bed INFO @ Tue, 21 Apr 2015 16:33:07: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (18395 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。