Job ID = 2162407 sra ファイルのダウンロード中... Completed: 1459713K bytes transferred in 14 seconds (822403K 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 2488 0 --:--:-- 0:00:01 --:--:-- 3063 100 36145 0 36145 0 0 29860 0 --:--:-- 0:00:01 --:--:-- 35505 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 36819897 spots for /home/okishinya/chipatlas/results/dm3/SRX085403/SRR317181.sra Written 36819897 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: 00:00:01 Multiseed full-index search: 00:10:35 36819897 reads; of these: 36819897 (100.00%) were unpaired; of these: 6157560 (16.72%) aligned 0 times 24184428 (65.68%) aligned exactly 1 time 6477909 (17.59%) aligned >1 times 83.28% overall alignment rate Time searching: 00:10:36 Overall time: 00:10:36 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] 15555514 / 30662337 = 0.5073 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 14:11:01: # Command line: callpeak -t SRX085403.bam -f BAM -g dm -n SRX085403.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX085403.05 # format = BAM # ChIP-seq file = ['SRX085403.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 14:11:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:11:01: # Command line: callpeak -t SRX085403.bam -f BAM -g dm -n SRX085403.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX085403.20 # format = BAM # ChIP-seq file = ['SRX085403.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 14:11:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:11:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:11:01: # Command line: callpeak -t SRX085403.bam -f BAM -g dm -n SRX085403.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX085403.10 # format = BAM # ChIP-seq file = ['SRX085403.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 14:11:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:11:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:11:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:11:06: 1000000 INFO @ Tue, 21 Apr 2015 14:11:06: 1000000 INFO @ Tue, 21 Apr 2015 14:11:06: 1000000 INFO @ Tue, 21 Apr 2015 14:11:11: 2000000 INFO @ Tue, 21 Apr 2015 14:11:11: 2000000 INFO @ Tue, 21 Apr 2015 14:11:12: 2000000 INFO @ Tue, 21 Apr 2015 14:11:16: 3000000 INFO @ Tue, 21 Apr 2015 14:11:16: 3000000 INFO @ Tue, 21 Apr 2015 14:11:17: 3000000 INFO @ Tue, 21 Apr 2015 14:11:21: 4000000 INFO @ Tue, 21 Apr 2015 14:11:22: 4000000 INFO @ Tue, 21 Apr 2015 14:11:22: 4000000 INFO @ Tue, 21 Apr 2015 14:11:27: 5000000 INFO @ Tue, 21 Apr 2015 14:11:27: 5000000 INFO @ Tue, 21 Apr 2015 14:11:28: 5000000 INFO @ Tue, 21 Apr 2015 14:11:32: 6000000 INFO @ Tue, 21 Apr 2015 14:11:32: 6000000 INFO @ Tue, 21 Apr 2015 14:11:33: 6000000 INFO @ Tue, 21 Apr 2015 14:11:37: 7000000 INFO @ Tue, 21 Apr 2015 14:11:38: 7000000 INFO @ Tue, 21 Apr 2015 14:11:39: 7000000 INFO @ Tue, 21 Apr 2015 14:11:43: 8000000 INFO @ Tue, 21 Apr 2015 14:11:43: 8000000 INFO @ Tue, 21 Apr 2015 14:11:45: 8000000 INFO @ Tue, 21 Apr 2015 14:11:48: 9000000 INFO @ Tue, 21 Apr 2015 14:11:49: 9000000 INFO @ Tue, 21 Apr 2015 14:11:50: 9000000 INFO @ Tue, 21 Apr 2015 14:11:54: 10000000 INFO @ Tue, 21 Apr 2015 14:11:54: 10000000 INFO @ Tue, 21 Apr 2015 14:11:56: 10000000 INFO @ Tue, 21 Apr 2015 14:11:59: 11000000 INFO @ Tue, 21 Apr 2015 14:12:00: 11000000 INFO @ Tue, 21 Apr 2015 14:12:02: 11000000 INFO @ Tue, 21 Apr 2015 14:12:05: 12000000 INFO @ Tue, 21 Apr 2015 14:12:06: 12000000 INFO @ Tue, 21 Apr 2015 14:12:08: 12000000 INFO @ Tue, 21 Apr 2015 14:12:10: 13000000 INFO @ Tue, 21 Apr 2015 14:12:11: 13000000 INFO @ Tue, 21 Apr 2015 14:12:13: 13000000 INFO @ Tue, 21 Apr 2015 14:12:16: 14000000 INFO @ Tue, 21 Apr 2015 14:12:17: 14000000 INFO @ Tue, 21 Apr 2015 14:12:19: 14000000 INFO @ Tue, 21 Apr 2015 14:12:21: 15000000 INFO @ Tue, 21 Apr 2015 14:12:22: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:12:22: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:12:22: #1 total tags in treatment: 15106823 INFO @ Tue, 21 Apr 2015 14:12:22: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:12:22: #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 14:12:23: 15000000 INFO @ Tue, 21 Apr 2015 14:12:24: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:12:24: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:12:24: #1 total tags in treatment: 15106823 INFO @ Tue, 21 Apr 2015 14:12:24: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:12:24: #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 14:12:25: 15000000 INFO @ Tue, 21 Apr 2015 14:12:25: #1 tags after filtering in treatment: 15103340 INFO @ Tue, 21 Apr 2015 14:12:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:12:25: #1 finished! INFO @ Tue, 21 Apr 2015 14:12:25: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:12:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:12:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:12:25: #1 total tags in treatment: 15106823 INFO @ Tue, 21 Apr 2015 14:12:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:12:25: #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 14:12:26: #1 tags after filtering in treatment: 15103340 INFO @ Tue, 21 Apr 2015 14:12:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:12:26: #1 finished! INFO @ Tue, 21 Apr 2015 14:12:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:12:28: #2 number of paired peaks: 2304 INFO @ Tue, 21 Apr 2015 14:12:28: start model_add_line... INFO @ Tue, 21 Apr 2015 14:12:28: #1 tags after filtering in treatment: 15103340 INFO @ Tue, 21 Apr 2015 14:12:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:12:28: #1 finished! INFO @ Tue, 21 Apr 2015 14:12:28: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:12:29: #2 number of paired peaks: 2304 INFO @ Tue, 21 Apr 2015 14:12:29: start model_add_line... INFO @ Tue, 21 Apr 2015 14:12:31: #2 number of paired peaks: 2304 INFO @ Tue, 21 Apr 2015 14:12:31: start model_add_line... INFO @ Tue, 21 Apr 2015 14:12:45: start X-correlation... INFO @ Tue, 21 Apr 2015 14:12:45: end of X-cor INFO @ Tue, 21 Apr 2015 14:12:45: #2 finished! INFO @ Tue, 21 Apr 2015 14:12:45: #2 predicted fragment length is 127 bps INFO @ Tue, 21 Apr 2015 14:12:45: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 21 Apr 2015 14:12:45: #2.2 Generate R script for model : SRX085403.20_model.r INFO @ Tue, 21 Apr 2015 14:12:45: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:12:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:12:47: start X-correlation... INFO @ Tue, 21 Apr 2015 14:12:47: end of X-cor INFO @ Tue, 21 Apr 2015 14:12:47: #2 finished! INFO @ Tue, 21 Apr 2015 14:12:47: #2 predicted fragment length is 127 bps INFO @ Tue, 21 Apr 2015 14:12:47: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 21 Apr 2015 14:12:47: #2.2 Generate R script for model : SRX085403.10_model.r INFO @ Tue, 21 Apr 2015 14:12:47: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:12:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:12:48: start X-correlation... INFO @ Tue, 21 Apr 2015 14:12:48: end of X-cor INFO @ Tue, 21 Apr 2015 14:12:48: #2 finished! INFO @ Tue, 21 Apr 2015 14:12:48: #2 predicted fragment length is 127 bps INFO @ Tue, 21 Apr 2015 14:12:48: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 21 Apr 2015 14:12:48: #2.2 Generate R script for model : SRX085403.05_model.r INFO @ Tue, 21 Apr 2015 14:12:48: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:12:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:14:09: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:14:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:14:14: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:15:12: #4 Write output xls file... SRX085403.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:15:12: #4 Write peak in narrowPeak format file... SRX085403.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:15:12: #4 Write summits bed file... SRX085403.20_summits.bed INFO @ Tue, 21 Apr 2015 14:15:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6251 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:15:19: #4 Write output xls file... SRX085403.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:15:19: #4 Write peak in narrowPeak format file... SRX085403.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:15:19: #4 Write summits bed file... SRX085403.05_summits.bed INFO @ Tue, 21 Apr 2015 14:15:19: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11862 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:15:21: #4 Write output xls file... SRX085403.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:15:21: #4 Write peak in narrowPeak format file... SRX085403.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:15:21: #4 Write summits bed file... SRX085403.10_summits.bed INFO @ Tue, 21 Apr 2015 14:15:21: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8598 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。