Job ID = 2161548 sra ファイルのダウンロード中... Completed: 7480646K bytes transferred in 72 seconds (843860K 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 12696 0 12696 0 0 22168 0 --:--:-- --:--:-- --:--:-- 33235 100 36303 0 36303 0 0 47640 0 --:--:-- --:--:-- --:--:-- 63577 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 18330928 spots for /home/okishinya/chipatlas/results/dm3/SRX027824/SRR067907.sra Written 18330928 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: 00:05:04 18330928 reads; of these: 18330928 (100.00%) were unpaired; of these: 2345816 (12.80%) aligned 0 times 11985021 (65.38%) aligned exactly 1 time 4000091 (21.82%) aligned >1 times 87.20% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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_rmdupse_core] 4398634 / 15985112 = 0.2752 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 12:55:53: # Command line: callpeak -t SRX027824.bam -f BAM -g dm -n SRX027824.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX027824.10 # format = BAM # ChIP-seq file = ['SRX027824.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 12:55:53: # Command line: callpeak -t SRX027824.bam -f BAM -g dm -n SRX027824.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX027824.20 # format = BAM # ChIP-seq file = ['SRX027824.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 12:55:53: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:55:53: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:55:53: # Command line: callpeak -t SRX027824.bam -f BAM -g dm -n SRX027824.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX027824.05 # format = BAM # ChIP-seq file = ['SRX027824.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 12:55:53: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:55:53: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:55:53: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:55:53: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:55:58: 1000000 INFO @ Tue, 21 Apr 2015 12:55:58: 1000000 INFO @ Tue, 21 Apr 2015 12:55:58: 1000000 INFO @ Tue, 21 Apr 2015 12:56:04: 2000000 INFO @ Tue, 21 Apr 2015 12:56:04: 2000000 INFO @ Tue, 21 Apr 2015 12:56:04: 2000000 INFO @ Tue, 21 Apr 2015 12:56:09: 3000000 INFO @ Tue, 21 Apr 2015 12:56:10: 3000000 INFO @ Tue, 21 Apr 2015 12:56:10: 3000000 INFO @ Tue, 21 Apr 2015 12:56:14: 4000000 INFO @ Tue, 21 Apr 2015 12:56:15: 4000000 INFO @ Tue, 21 Apr 2015 12:56:16: 4000000 INFO @ Tue, 21 Apr 2015 12:56:20: 5000000 INFO @ Tue, 21 Apr 2015 12:56:21: 5000000 INFO @ Tue, 21 Apr 2015 12:56:22: 5000000 INFO @ Tue, 21 Apr 2015 12:56:25: 6000000 INFO @ Tue, 21 Apr 2015 12:56:27: 6000000 INFO @ Tue, 21 Apr 2015 12:56:28: 6000000 INFO @ Tue, 21 Apr 2015 12:56:30: 7000000 INFO @ Tue, 21 Apr 2015 12:56:33: 7000000 INFO @ Tue, 21 Apr 2015 12:56:34: 7000000 INFO @ Tue, 21 Apr 2015 12:56:36: 8000000 INFO @ Tue, 21 Apr 2015 12:56:38: 8000000 INFO @ Tue, 21 Apr 2015 12:56:39: 8000000 INFO @ Tue, 21 Apr 2015 12:56:41: 9000000 INFO @ Tue, 21 Apr 2015 12:56:44: 9000000 INFO @ Tue, 21 Apr 2015 12:56:45: 9000000 INFO @ Tue, 21 Apr 2015 12:56:46: 10000000 INFO @ Tue, 21 Apr 2015 12:56:50: 10000000 INFO @ Tue, 21 Apr 2015 12:56:51: 10000000 INFO @ Tue, 21 Apr 2015 12:56:52: 11000000 INFO @ Tue, 21 Apr 2015 12:56:55: #1 tag size is determined as 38 bps INFO @ Tue, 21 Apr 2015 12:56:55: #1 tag size = 38 INFO @ Tue, 21 Apr 2015 12:56:55: #1 total tags in treatment: 11586478 INFO @ Tue, 21 Apr 2015 12:56:55: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:56:55: #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 12:56:55: 11000000 INFO @ Tue, 21 Apr 2015 12:56:57: 11000000 INFO @ Tue, 21 Apr 2015 12:56:57: #1 tags after filtering in treatment: 11584865 INFO @ Tue, 21 Apr 2015 12:56:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:56:57: #1 finished! INFO @ Tue, 21 Apr 2015 12:56:57: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:56:59: #1 tag size is determined as 38 bps INFO @ Tue, 21 Apr 2015 12:56:59: #1 tag size = 38 INFO @ Tue, 21 Apr 2015 12:56:59: #1 total tags in treatment: 11586478 INFO @ Tue, 21 Apr 2015 12:56:59: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:56:59: #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 12:56:59: #2 number of paired peaks: 1552 INFO @ Tue, 21 Apr 2015 12:56:59: start model_add_line... INFO @ Tue, 21 Apr 2015 12:57:01: #1 tag size is determined as 38 bps INFO @ Tue, 21 Apr 2015 12:57:01: #1 tag size = 38 INFO @ Tue, 21 Apr 2015 12:57:01: #1 total tags in treatment: 11586478 INFO @ Tue, 21 Apr 2015 12:57:01: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:57:01: #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 12:57:01: #1 tags after filtering in treatment: 11584865 INFO @ Tue, 21 Apr 2015 12:57:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:57:01: #1 finished! INFO @ Tue, 21 Apr 2015 12:57:01: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:57:03: #1 tags after filtering in treatment: 11584865 INFO @ Tue, 21 Apr 2015 12:57:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:57:03: #1 finished! INFO @ Tue, 21 Apr 2015 12:57:03: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:57:03: #2 number of paired peaks: 1552 INFO @ Tue, 21 Apr 2015 12:57:03: start model_add_line... INFO @ Tue, 21 Apr 2015 12:57:05: #2 number of paired peaks: 1552 INFO @ Tue, 21 Apr 2015 12:57:05: start model_add_line... INFO @ Tue, 21 Apr 2015 12:57:13: start X-correlation... INFO @ Tue, 21 Apr 2015 12:57:13: end of X-cor INFO @ Tue, 21 Apr 2015 12:57:13: #2 finished! INFO @ Tue, 21 Apr 2015 12:57:13: #2 predicted fragment length is 105 bps INFO @ Tue, 21 Apr 2015 12:57:13: #2 alternative fragment length(s) may be 105 bps INFO @ Tue, 21 Apr 2015 12:57:13: #2.2 Generate R script for model : SRX027824.05_model.r INFO @ Tue, 21 Apr 2015 12:57:13: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:57:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:57:17: start X-correlation... INFO @ Tue, 21 Apr 2015 12:57:17: end of X-cor INFO @ Tue, 21 Apr 2015 12:57:17: #2 finished! INFO @ Tue, 21 Apr 2015 12:57:17: #2 predicted fragment length is 105 bps INFO @ Tue, 21 Apr 2015 12:57:17: #2 alternative fragment length(s) may be 105 bps INFO @ Tue, 21 Apr 2015 12:57:17: #2.2 Generate R script for model : SRX027824.20_model.r INFO @ Tue, 21 Apr 2015 12:57:17: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:57:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:57:20: start X-correlation... INFO @ Tue, 21 Apr 2015 12:57:20: end of X-cor INFO @ Tue, 21 Apr 2015 12:57:20: #2 finished! INFO @ Tue, 21 Apr 2015 12:57:20: #2 predicted fragment length is 105 bps INFO @ Tue, 21 Apr 2015 12:57:20: #2 alternative fragment length(s) may be 105 bps INFO @ Tue, 21 Apr 2015 12:57:20: #2.2 Generate R script for model : SRX027824.10_model.r INFO @ Tue, 21 Apr 2015 12:57:20: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:57:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:58:18: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:58:23: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:58:24: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:59:09: #4 Write output xls file... SRX027824.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:59:09: #4 Write peak in narrowPeak format file... SRX027824.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:59:09: #4 Write summits bed file... SRX027824.20_summits.bed INFO @ Tue, 21 Apr 2015 12:59:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2682 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:59:11: #4 Write output xls file... SRX027824.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:59:11: #4 Write peak in narrowPeak format file... SRX027824.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:59:11: #4 Write summits bed file... SRX027824.05_summits.bed INFO @ Tue, 21 Apr 2015 12:59:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9023 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:59:12: #4 Write output xls file... SRX027824.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:59:12: #4 Write peak in narrowPeak format file... SRX027824.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:59:12: #4 Write summits bed file... SRX027824.10_summits.bed INFO @ Tue, 21 Apr 2015 12:59:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5499 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。