Job ID = 3001494 sra ファイルのダウンロード中... Completed: 134293K bytes transferred in 6 seconds (180391K 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 5467 0 5467 0 0 9208 0 --:--:-- --:--:-- --:--:-- 13565 100 14953 0 14953 0 0 8348 0 --:--:-- 0:00:01 --:--:-- 9345 100 14953 0 14953 0 0 5353 0 --:--:-- 0:00:02 --:--:-- 5746 100 14953 0 14953 0 0 3940 0 --:--:-- 0:00:03 --:--:-- 4149 100 14953 0 14953 0 0 3117 0 --:--:-- 0:00:04 --:--:-- 3246 100 14953 0 14953 0 0 2578 0 --:--:-- 0:00:05 --:--:-- 1822 100 14953 0 14953 0 0 2198 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1916 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1698 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1524 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1383 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1266 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1167 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1082 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1009 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 945 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 889 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 839 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 794 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 754 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 718 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 685 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 655 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 627 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 602 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 578 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 557 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 537 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 518 0 --:--:-- 0:00:28 --:--:-- 0 100 14953 0 14953 0 0 501 0 --:--:-- 0:00:29 --:--:-- 0 100 22247 0 22247 0 0 726 0 --:--:-- 0:00:30 --:--:-- 1516 100 35081 0 35081 0 0 1137 0 --:--:-- 0:00:30 --:--:-- 5034 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 7403385 spots for /home/okishinya/chipatlas/results/ce10/SRX005628/SRR017597.sra Written 7403385 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: 00:01:02 7403385 reads; of these: 7403385 (100.00%) were unpaired; of these: 2028249 (27.40%) aligned 0 times 4586899 (61.96%) aligned exactly 1 time 788237 (10.65%) aligned >1 times 72.60% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1548766 / 5375136 = 0.2881 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 @ Mon, 07 Sep 2015 18:47:20: # Command line: callpeak -t SRX005628.bam -f BAM -g ce -n SRX005628.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005628.10 # format = BAM # ChIP-seq file = ['SRX005628.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 07 Sep 2015 18:47:20: # Command line: callpeak -t SRX005628.bam -f BAM -g ce -n SRX005628.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005628.20 # format = BAM # ChIP-seq file = ['SRX005628.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 07 Sep 2015 18:47:20: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:47:20: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:47:20: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:47:20: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:47:20: # Command line: callpeak -t SRX005628.bam -f BAM -g ce -n SRX005628.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005628.05 # format = BAM # ChIP-seq file = ['SRX005628.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 07 Sep 2015 18:47:20: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:47:20: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:47:25: 1000000 INFO @ Mon, 07 Sep 2015 18:47:25: 1000000 INFO @ Mon, 07 Sep 2015 18:47:25: 1000000 INFO @ Mon, 07 Sep 2015 18:47:30: 2000000 INFO @ Mon, 07 Sep 2015 18:47:31: 2000000 INFO @ Mon, 07 Sep 2015 18:47:31: 2000000 INFO @ Mon, 07 Sep 2015 18:47:36: 3000000 INFO @ Mon, 07 Sep 2015 18:47:36: 3000000 INFO @ Mon, 07 Sep 2015 18:47:36: 3000000 INFO @ Mon, 07 Sep 2015 18:47:40: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:47:40: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:47:40: #1 total tags in treatment: 3826370 INFO @ Mon, 07 Sep 2015 18:47:40: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:47:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:47:40: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:47:40: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:47:40: #1 total tags in treatment: 3826370 INFO @ Mon, 07 Sep 2015 18:47:40: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:47:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:47:41: #1 tags after filtering in treatment: 3826350 INFO @ Mon, 07 Sep 2015 18:47:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:47:41: #1 finished! INFO @ Mon, 07 Sep 2015 18:47:41: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:47:41: #1 tags after filtering in treatment: 3826350 INFO @ Mon, 07 Sep 2015 18:47:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:47:41: #1 finished! INFO @ Mon, 07 Sep 2015 18:47:41: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:47:41: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:47:41: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:47:41: #1 total tags in treatment: 3826370 INFO @ Mon, 07 Sep 2015 18:47:41: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:47:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:47:42: #2 number of paired peaks: 1939 INFO @ Mon, 07 Sep 2015 18:47:42: start model_add_line... INFO @ Mon, 07 Sep 2015 18:47:42: #2 number of paired peaks: 1939 INFO @ Mon, 07 Sep 2015 18:47:42: start model_add_line... INFO @ Mon, 07 Sep 2015 18:47:42: #1 tags after filtering in treatment: 3826350 INFO @ Mon, 07 Sep 2015 18:47:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:47:42: #1 finished! INFO @ Mon, 07 Sep 2015 18:47:42: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:47:43: #2 number of paired peaks: 1939 INFO @ Mon, 07 Sep 2015 18:47:43: start model_add_line... INFO @ Mon, 07 Sep 2015 18:47:51: start X-correlation... INFO @ Mon, 07 Sep 2015 18:47:51: end of X-cor INFO @ Mon, 07 Sep 2015 18:47:51: #2 finished! INFO @ Mon, 07 Sep 2015 18:47:51: #2 predicted fragment length is 129 bps INFO @ Mon, 07 Sep 2015 18:47:51: #2 alternative fragment length(s) may be 4,129 bps INFO @ Mon, 07 Sep 2015 18:47:51: #2.2 Generate R script for model : SRX005628.05_model.r INFO @ Mon, 07 Sep 2015 18:47:51: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:47:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:47:52: start X-correlation... INFO @ Mon, 07 Sep 2015 18:47:52: end of X-cor INFO @ Mon, 07 Sep 2015 18:47:52: #2 finished! INFO @ Mon, 07 Sep 2015 18:47:52: #2 predicted fragment length is 129 bps INFO @ Mon, 07 Sep 2015 18:47:52: #2 alternative fragment length(s) may be 4,129 bps INFO @ Mon, 07 Sep 2015 18:47:52: #2.2 Generate R script for model : SRX005628.10_model.r INFO @ Mon, 07 Sep 2015 18:47:52: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:47:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:47:53: start X-correlation... INFO @ Mon, 07 Sep 2015 18:47:53: end of X-cor INFO @ Mon, 07 Sep 2015 18:47:53: #2 finished! INFO @ Mon, 07 Sep 2015 18:47:53: #2 predicted fragment length is 129 bps INFO @ Mon, 07 Sep 2015 18:47:53: #2 alternative fragment length(s) may be 4,129 bps INFO @ Mon, 07 Sep 2015 18:47:53: #2.2 Generate R script for model : SRX005628.20_model.r INFO @ Mon, 07 Sep 2015 18:47:53: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:47:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:48:15: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:48:16: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:48:19: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:48:33: #4 Write output xls file... SRX005628.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:48:33: #4 Write peak in narrowPeak format file... SRX005628.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:48:33: #4 Write summits bed file... SRX005628.10_summits.bed INFO @ Mon, 07 Sep 2015 18:48:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1268 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:48:34: #4 Write output xls file... SRX005628.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:48:34: #4 Write peak in narrowPeak format file... SRX005628.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:48:34: #4 Write summits bed file... SRX005628.20_summits.bed INFO @ Mon, 07 Sep 2015 18:48:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (355 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:48:34: #4 Write output xls file... SRX005628.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:48:34: #4 Write peak in narrowPeak format file... SRX005628.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:48:34: #4 Write summits bed file... SRX005628.05_summits.bed INFO @ Mon, 07 Sep 2015 18:48:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2987 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。