Job ID = 8696842 sra ファイルのダウンロード中... Completed: 279677K bytes transferred in 6 seconds (343505K 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 --:--:-- 0:00:06 --:--:-- 0 100 22575 0 22575 0 0 2833 0 --:--:-- 0:00:07 --:--:-- 15842 100 31440 0 31440 0 0 3702 0 --:--:-- 0:00:08 --:--:-- 16139 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 10901385 spots for /home/okishinya/chipatlas/results/dm3/SRX110780/SRR388362.sra Written 10901385 spots total rm: cannot remove `[DSE]RR*.fastq': No such file or directory 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: 00:06:05 10901385 reads; of these: 10901385 (100.00%) were unpaired; of these: 625936 (5.74%) aligned 0 times 7554357 (69.30%) aligned exactly 1 time 2721092 (24.96%) aligned >1 times 94.26% overall alignment rate Time searching: 00:06:05 Overall time: 00:06:05 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] 611431 / 10275449 = 0.0595 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 12:22:01: # Command line: callpeak -t SRX110780.bam -f BAM -g dm -n SRX110780.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110780.10 # format = BAM # ChIP-seq file = ['SRX110780.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 12:22:01: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:22:01: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:22:01: # Command line: callpeak -t SRX110780.bam -f BAM -g dm -n SRX110780.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110780.05 # format = BAM # ChIP-seq file = ['SRX110780.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 12:22:01: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:22:01: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:22:01: # Command line: callpeak -t SRX110780.bam -f BAM -g dm -n SRX110780.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110780.20 # format = BAM # ChIP-seq file = ['SRX110780.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 12:22:01: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:22:01: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:22:08: 1000000 INFO @ Fri, 10 Mar 2017 12:22:12: 1000000 INFO @ Fri, 10 Mar 2017 12:22:15: 1000000 INFO @ Fri, 10 Mar 2017 12:22:15: 2000000 INFO @ Fri, 10 Mar 2017 12:22:22: 3000000 INFO @ Fri, 10 Mar 2017 12:22:23: 2000000 INFO @ Fri, 10 Mar 2017 12:22:28: 4000000 INFO @ Fri, 10 Mar 2017 12:22:29: 2000000 INFO @ Fri, 10 Mar 2017 12:22:34: 3000000 INFO @ Fri, 10 Mar 2017 12:22:35: 5000000 INFO @ Fri, 10 Mar 2017 12:22:41: 6000000 INFO @ Fri, 10 Mar 2017 12:22:42: 3000000 INFO @ Fri, 10 Mar 2017 12:22:44: 4000000 INFO @ Fri, 10 Mar 2017 12:22:48: 7000000 INFO @ Fri, 10 Mar 2017 12:22:53: 4000000 INFO @ Fri, 10 Mar 2017 12:22:54: 5000000 INFO @ Fri, 10 Mar 2017 12:22:55: 8000000 INFO @ Fri, 10 Mar 2017 12:23:04: 6000000 INFO @ Fri, 10 Mar 2017 12:23:05: 5000000 INFO @ Fri, 10 Mar 2017 12:23:06: 9000000 INFO @ Fri, 10 Mar 2017 12:23:13: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:23:13: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:23:13: #1 total tags in treatment: 9664018 INFO @ Fri, 10 Mar 2017 12:23:13: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:23:13: #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 12:23:14: 7000000 INFO @ Fri, 10 Mar 2017 12:23:15: #1 tags after filtering in treatment: 9662379 INFO @ Fri, 10 Mar 2017 12:23:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:23:15: #1 finished! INFO @ Fri, 10 Mar 2017 12:23:15: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:23:15: 6000000 INFO @ Fri, 10 Mar 2017 12:23:17: #2 number of paired peaks: 1483 INFO @ Fri, 10 Mar 2017 12:23:17: start model_add_line... INFO @ Fri, 10 Mar 2017 12:23:23: 8000000 INFO @ Fri, 10 Mar 2017 12:23:25: 7000000 INFO @ Fri, 10 Mar 2017 12:23:30: 9000000 INFO @ Fri, 10 Mar 2017 12:23:30: start X-correlation... INFO @ Fri, 10 Mar 2017 12:23:30: end of X-cor INFO @ Fri, 10 Mar 2017 12:23:30: #2 finished! INFO @ Fri, 10 Mar 2017 12:23:30: #2 predicted fragment length is 81 bps INFO @ Fri, 10 Mar 2017 12:23:30: #2 alternative fragment length(s) may be 81 bps INFO @ Fri, 10 Mar 2017 12:23:30: #2.2 Generate R script for model : SRX110780.10_model.r INFO @ Fri, 10 Mar 2017 12:23:30: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:23:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:23:33: 8000000 INFO @ Fri, 10 Mar 2017 12:23:34: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:23:34: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:23:34: #1 total tags in treatment: 9664018 INFO @ Fri, 10 Mar 2017 12:23:34: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:23:34: #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 12:23:37: #1 tags after filtering in treatment: 9662379 INFO @ Fri, 10 Mar 2017 12:23:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:23:37: #1 finished! INFO @ Fri, 10 Mar 2017 12:23:37: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:23:39: #2 number of paired peaks: 1483 INFO @ Fri, 10 Mar 2017 12:23:39: start model_add_line... INFO @ Fri, 10 Mar 2017 12:23:41: 9000000 INFO @ Fri, 10 Mar 2017 12:23:46: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:23:46: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:23:46: #1 total tags in treatment: 9664018 INFO @ Fri, 10 Mar 2017 12:23:46: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:23:46: #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 12:23:49: #1 tags after filtering in treatment: 9662379 INFO @ Fri, 10 Mar 2017 12:23:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:23:49: #1 finished! INFO @ Fri, 10 Mar 2017 12:23:49: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:23:51: #2 number of paired peaks: 1483 INFO @ Fri, 10 Mar 2017 12:23:51: start model_add_line... INFO @ Fri, 10 Mar 2017 12:23:52: start X-correlation... INFO @ Fri, 10 Mar 2017 12:23:52: end of X-cor INFO @ Fri, 10 Mar 2017 12:23:52: #2 finished! INFO @ Fri, 10 Mar 2017 12:23:52: #2 predicted fragment length is 81 bps INFO @ Fri, 10 Mar 2017 12:23:52: #2 alternative fragment length(s) may be 81 bps INFO @ Fri, 10 Mar 2017 12:23:52: #2.2 Generate R script for model : SRX110780.05_model.r INFO @ Fri, 10 Mar 2017 12:23:52: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:23:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:24:03: start X-correlation... INFO @ Fri, 10 Mar 2017 12:24:03: end of X-cor INFO @ Fri, 10 Mar 2017 12:24:03: #2 finished! INFO @ Fri, 10 Mar 2017 12:24:03: #2 predicted fragment length is 81 bps INFO @ Fri, 10 Mar 2017 12:24:03: #2 alternative fragment length(s) may be 81 bps INFO @ Fri, 10 Mar 2017 12:24:03: #2.2 Generate R script for model : SRX110780.20_model.r INFO @ Fri, 10 Mar 2017 12:24:03: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:24:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:24:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:24:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:25:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:25:21: #4 Write output xls file... SRX110780.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:25:22: #4 Write peak in narrowPeak format file... SRX110780.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:25:22: #4 Write summits bed file... SRX110780.10_summits.bed INFO @ Fri, 10 Mar 2017 12:25:22: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1546 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:25:47: #4 Write output xls file... SRX110780.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:25:47: #4 Write peak in narrowPeak format file... SRX110780.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:25:47: #4 Write summits bed file... SRX110780.05_summits.bed INFO @ Fri, 10 Mar 2017 12:25:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3694 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:25:49: #4 Write output xls file... SRX110780.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:25:49: #4 Write peak in narrowPeak format file... SRX110780.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:25:49: #4 Write summits bed file... SRX110780.20_summits.bed INFO @ Fri, 10 Mar 2017 12:25:49: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (414 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。