Job ID = 3001509 sra ファイルのダウンロード中... Completed: 41487K bytes transferred in 4 seconds (74977K 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 14953 0 14953 0 0 8745 0 --:--:-- 0:00:01 --:--:-- 9850 100 14953 0 14953 0 0 5514 0 --:--:-- 0:00:02 --:--:-- 5933 100 14953 0 14953 0 0 4026 0 --:--:-- 0:00:03 --:--:-- 4245 100 14953 0 14953 0 0 3171 0 --:--:-- 0:00:04 --:--:-- 3305 100 14953 0 14953 0 0 2615 0 --:--:-- 0:00:05 --:--:-- 2706 100 14953 0 14953 0 0 2225 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1936 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1714 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1537 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1394 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1274 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1174 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1088 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1014 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 950 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 893 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 842 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 797 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 757 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 720 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 687 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 657 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 629 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 604 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 580 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 558 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 538 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 519 0 --:--:-- 0:00:28 --:--:-- 0 100 14953 0 14953 0 0 502 0 --:--:-- 0:00:29 --:--:-- 0 100 16407 0 16407 0 0 536 0 --:--:-- 0:00:30 --:--:-- 302 100 34815 0 34815 0 0 1131 0 --:--:-- 0:00:30 --:--:-- 4966 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 2855301 spots for /home/okishinya/chipatlas/results/ce10/SRX005650/SRR017619.sra Written 2855301 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: 00:00:26 2855301 reads; of these: 2855301 (100.00%) were unpaired; of these: 819145 (28.69%) aligned 0 times 1716755 (60.13%) aligned exactly 1 time 319401 (11.19%) aligned >1 times 71.31% overall alignment rate Time searching: 00:00:26 Overall time: 00:00:26 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] 134880 / 2036156 = 0.0662 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 18:46:23: # Command line: callpeak -t SRX005650.bam -f BAM -g ce -n SRX005650.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005650.05 # format = BAM # ChIP-seq file = ['SRX005650.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 18:46:23: # Command line: callpeak -t SRX005650.bam -f BAM -g ce -n SRX005650.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005650.20 # format = BAM # ChIP-seq file = ['SRX005650.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 18:46:23: # Command line: callpeak -t SRX005650.bam -f BAM -g ce -n SRX005650.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005650.10 # format = BAM # ChIP-seq file = ['SRX005650.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 18:46:23: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:23: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:23: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:23: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:23: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:23: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:29: 1000000 INFO @ Mon, 07 Sep 2015 18:46:29: 1000000 INFO @ Mon, 07 Sep 2015 18:46:29: 1000000 INFO @ Mon, 07 Sep 2015 18:46:34: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:34: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:34: #1 total tags in treatment: 1901276 INFO @ Mon, 07 Sep 2015 18:46:34: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:34: #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 18:46:34: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:34: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:34: #1 total tags in treatment: 1901276 INFO @ Mon, 07 Sep 2015 18:46:34: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:34: #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 18:46:34: #1 tags after filtering in treatment: 1901275 INFO @ Mon, 07 Sep 2015 18:46:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:34: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:34: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:34: #1 tags after filtering in treatment: 1901275 INFO @ Mon, 07 Sep 2015 18:46:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:34: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:34: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:34: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:34: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:34: #1 total tags in treatment: 1901276 INFO @ Mon, 07 Sep 2015 18:46:34: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:34: #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 18:46:35: #2 number of paired peaks: 1016 INFO @ Mon, 07 Sep 2015 18:46:35: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:35: #2 number of paired peaks: 1016 INFO @ Mon, 07 Sep 2015 18:46:35: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:35: #1 tags after filtering in treatment: 1901275 INFO @ Mon, 07 Sep 2015 18:46:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:35: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:35: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:35: #2 number of paired peaks: 1016 INFO @ Mon, 07 Sep 2015 18:46:35: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:37: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:37: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:37: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:37: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:37: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:37: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:37: #2 predicted fragment length is 118 bps INFO @ Mon, 07 Sep 2015 18:46:37: #2 predicted fragment length is 118 bps INFO @ Mon, 07 Sep 2015 18:46:37: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 07 Sep 2015 18:46:37: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 07 Sep 2015 18:46:37: #2.2 Generate R script for model : SRX005650.05_model.r INFO @ Mon, 07 Sep 2015 18:46:37: #2.2 Generate R script for model : SRX005650.10_model.r INFO @ Mon, 07 Sep 2015 18:46:37: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:37: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:38: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:38: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:38: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:38: #2 predicted fragment length is 118 bps INFO @ Mon, 07 Sep 2015 18:46:38: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 07 Sep 2015 18:46:38: #2.2 Generate R script for model : SRX005650.20_model.r INFO @ Mon, 07 Sep 2015 18:46:38: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:49: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:49: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:50: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:57: #4 Write output xls file... SRX005650.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:57: #4 Write peak in narrowPeak format file... SRX005650.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:57: #4 Write summits bed file... SRX005650.10_summits.bed INFO @ Mon, 07 Sep 2015 18:46:57: Done! INFO @ Mon, 07 Sep 2015 18:46:57: #4 Write output xls file... SRX005650.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:57: #4 Write peak in narrowPeak format file... SRX005650.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:57: #4 Write summits bed file... SRX005650.05_summits.bed INFO @ Mon, 07 Sep 2015 18:46:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1079 records, 4 fields): 70 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (386 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:59: #4 Write output xls file... SRX005650.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:59: #4 Write peak in narrowPeak format file... SRX005650.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:59: #4 Write summits bed file... SRX005650.20_summits.bed INFO @ Mon, 07 Sep 2015 18:46:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (111 records, 4 fields): 39 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。