Job ID = 2162405 sra ファイルのダウンロード中... Completed: 1324199K bytes transferred in 12 seconds (836368K 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 --:--:-- --:--:-- --:--:-- 0 101 2540 0 2540 0 0 2285 0 --:--:-- 0:00:01 --:--:-- 2757 100 36148 0 36148 0 0 27780 0 --:--:-- 0:00:01 --:--:-- 32565 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 33553611 spots for /home/okishinya/chipatlas/results/dm3/SRX085401/SRR317179.sra Written 33553611 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: 00:09:36 33553611 reads; of these: 33553611 (100.00%) were unpaired; of these: 3218458 (9.59%) aligned 0 times 24177448 (72.06%) aligned exactly 1 time 6157705 (18.35%) aligned >1 times 90.41% overall alignment rate Time searching: 00:09:36 Overall time: 00:09:36 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] 15929130 / 30335153 = 0.5251 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 14:05:53: # Command line: callpeak -t SRX085401.bam -f BAM -g dm -n SRX085401.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX085401.10 # format = BAM # ChIP-seq file = ['SRX085401.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 14:05:53: # Command line: callpeak -t SRX085401.bam -f BAM -g dm -n SRX085401.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX085401.20 # format = BAM # ChIP-seq file = ['SRX085401.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 14:05:53: # Command line: callpeak -t SRX085401.bam -f BAM -g dm -n SRX085401.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX085401.05 # format = BAM # ChIP-seq file = ['SRX085401.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 14:05:53: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:05:53: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:05:53: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:05:53: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:05:53: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:05:53: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:05:59: 1000000 INFO @ Tue, 21 Apr 2015 14:05:59: 1000000 INFO @ Tue, 21 Apr 2015 14:05:59: 1000000 INFO @ Tue, 21 Apr 2015 14:06:05: 2000000 INFO @ Tue, 21 Apr 2015 14:06:05: 2000000 INFO @ Tue, 21 Apr 2015 14:06:05: 2000000 INFO @ Tue, 21 Apr 2015 14:06:10: 3000000 INFO @ Tue, 21 Apr 2015 14:06:11: 3000000 INFO @ Tue, 21 Apr 2015 14:06:11: 3000000 INFO @ Tue, 21 Apr 2015 14:06:16: 4000000 INFO @ Tue, 21 Apr 2015 14:06:17: 4000000 INFO @ Tue, 21 Apr 2015 14:06:17: 4000000 INFO @ Tue, 21 Apr 2015 14:06:22: 5000000 INFO @ Tue, 21 Apr 2015 14:06:23: 5000000 INFO @ Tue, 21 Apr 2015 14:06:23: 5000000 INFO @ Tue, 21 Apr 2015 14:06:28: 6000000 INFO @ Tue, 21 Apr 2015 14:06:29: 6000000 INFO @ Tue, 21 Apr 2015 14:06:29: 6000000 INFO @ Tue, 21 Apr 2015 14:06:33: 7000000 INFO @ Tue, 21 Apr 2015 14:06:35: 7000000 INFO @ Tue, 21 Apr 2015 14:06:35: 7000000 INFO @ Tue, 21 Apr 2015 14:06:39: 8000000 INFO @ Tue, 21 Apr 2015 14:06:41: 8000000 INFO @ Tue, 21 Apr 2015 14:06:41: 8000000 INFO @ Tue, 21 Apr 2015 14:06:45: 9000000 INFO @ Tue, 21 Apr 2015 14:06:47: 9000000 INFO @ Tue, 21 Apr 2015 14:06:47: 9000000 INFO @ Tue, 21 Apr 2015 14:06:50: 10000000 INFO @ Tue, 21 Apr 2015 14:06:52: 10000000 INFO @ Tue, 21 Apr 2015 14:06:52: 10000000 INFO @ Tue, 21 Apr 2015 14:06:56: 11000000 INFO @ Tue, 21 Apr 2015 14:06:58: 11000000 INFO @ Tue, 21 Apr 2015 14:06:58: 11000000 INFO @ Tue, 21 Apr 2015 14:07:02: 12000000 INFO @ Tue, 21 Apr 2015 14:07:04: 12000000 INFO @ Tue, 21 Apr 2015 14:07:04: 12000000 INFO @ Tue, 21 Apr 2015 14:07:07: 13000000 INFO @ Tue, 21 Apr 2015 14:07:10: 13000000 INFO @ Tue, 21 Apr 2015 14:07:10: 13000000 INFO @ Tue, 21 Apr 2015 14:07:13: 14000000 INFO @ Tue, 21 Apr 2015 14:07:16: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:07:16: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:07:16: #1 total tags in treatment: 14406023 INFO @ Tue, 21 Apr 2015 14:07:16: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:07:16: #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 14:07:17: 14000000 INFO @ Tue, 21 Apr 2015 14:07:17: 14000000 INFO @ Tue, 21 Apr 2015 14:07:19: #1 tags after filtering in treatment: 14402711 INFO @ Tue, 21 Apr 2015 14:07:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:07:19: #1 finished! INFO @ Tue, 21 Apr 2015 14:07:19: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:07:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:07:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:07:20: #1 total tags in treatment: 14406023 INFO @ Tue, 21 Apr 2015 14:07:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:07:20: #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 14:07:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:07:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:07:20: #1 total tags in treatment: 14406023 INFO @ Tue, 21 Apr 2015 14:07:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:07:20: #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 14:07:22: #2 number of paired peaks: 2079 INFO @ Tue, 21 Apr 2015 14:07:22: start model_add_line... INFO @ Tue, 21 Apr 2015 14:07:22: #1 tags after filtering in treatment: 14402711 INFO @ Tue, 21 Apr 2015 14:07:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:07:22: #1 finished! INFO @ Tue, 21 Apr 2015 14:07:22: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:07:22: #1 tags after filtering in treatment: 14402711 INFO @ Tue, 21 Apr 2015 14:07:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:07:22: #1 finished! INFO @ Tue, 21 Apr 2015 14:07:22: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:07:25: #2 number of paired peaks: 2079 INFO @ Tue, 21 Apr 2015 14:07:25: start model_add_line... INFO @ Tue, 21 Apr 2015 14:07:25: #2 number of paired peaks: 2079 INFO @ Tue, 21 Apr 2015 14:07:25: start model_add_line... INFO @ Tue, 21 Apr 2015 14:07:37: start X-correlation... INFO @ Tue, 21 Apr 2015 14:07:37: end of X-cor INFO @ Tue, 21 Apr 2015 14:07:37: #2 finished! INFO @ Tue, 21 Apr 2015 14:07:37: #2 predicted fragment length is 132 bps INFO @ Tue, 21 Apr 2015 14:07:37: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 21 Apr 2015 14:07:37: #2.2 Generate R script for model : SRX085401.05_model.r INFO @ Tue, 21 Apr 2015 14:07:37: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:07:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:07:40: start X-correlation... INFO @ Tue, 21 Apr 2015 14:07:40: end of X-cor INFO @ Tue, 21 Apr 2015 14:07:40: #2 finished! INFO @ Tue, 21 Apr 2015 14:07:40: #2 predicted fragment length is 132 bps INFO @ Tue, 21 Apr 2015 14:07:40: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 21 Apr 2015 14:07:40: #2.2 Generate R script for model : SRX085401.10_model.r INFO @ Tue, 21 Apr 2015 14:07:40: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:07:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:07:41: start X-correlation... INFO @ Tue, 21 Apr 2015 14:07:41: end of X-cor INFO @ Tue, 21 Apr 2015 14:07:41: #2 finished! INFO @ Tue, 21 Apr 2015 14:07:41: #2 predicted fragment length is 132 bps INFO @ Tue, 21 Apr 2015 14:07:41: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 21 Apr 2015 14:07:41: #2.2 Generate R script for model : SRX085401.20_model.r INFO @ Tue, 21 Apr 2015 14:07:41: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:07:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:08:54: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:08:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:09:00: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:10:01: #4 Write output xls file... SRX085401.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:10:01: #4 Write peak in narrowPeak format file... SRX085401.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:10:01: #4 Write summits bed file... SRX085401.10_summits.bed INFO @ Tue, 21 Apr 2015 14:10:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7779 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:10:01: #4 Write output xls file... SRX085401.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:10:01: #4 Write peak in narrowPeak format file... SRX085401.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:10:01: #4 Write summits bed file... SRX085401.05_summits.bed INFO @ Tue, 21 Apr 2015 14:10:01: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10779 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:10:05: #4 Write output xls file... SRX085401.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:10:05: #4 Write peak in narrowPeak format file... SRX085401.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:10:05: #4 Write summits bed file... SRX085401.20_summits.bed INFO @ Tue, 21 Apr 2015 14:10:05: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5695 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。