Job ID = 3001500 sra ファイルのダウンロード中... Completed: 59185K bytes transferred in 5 seconds (91004K 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 8443 0 --:--:-- 0:00:01 --:--:-- 9481 100 14953 0 14953 0 0 5392 0 --:--:-- 0:00:02 --:--:-- 5797 100 14953 0 14953 0 0 3961 0 --:--:-- 0:00:03 --:--:-- 4175 100 14953 0 14953 0 0 3130 0 --:--:-- 0:00:04 --:--:-- 3263 100 14953 0 14953 0 0 2587 0 --:--:-- 0:00:05 --:--:-- 2677 100 14953 0 14953 0 0 2205 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1921 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1702 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1528 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1386 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1268 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1169 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1084 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1010 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 946 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 890 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 840 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 795 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 755 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 0 628 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 602 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 579 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 --:--:-- 1514 100 34295 0 34295 0 0 1112 0 --:--:-- 0:00:30 --:--:-- 4830 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 4418118 spots for /home/okishinya/chipatlas/results/ce10/SRX005634/SRR017603.sra Written 4418118 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: 00:00:27 4418118 reads; of these: 4418118 (100.00%) were unpaired; of these: 2925003 (66.20%) aligned 0 times 1214523 (27.49%) aligned exactly 1 time 278592 (6.31%) aligned >1 times 33.80% overall alignment rate Time searching: 00:00:27 Overall time: 00:00:27 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] 237160 / 1493115 = 0.1588 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 18:46:07: # Command line: callpeak -t SRX005634.bam -f BAM -g ce -n SRX005634.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005634.10 # format = BAM # ChIP-seq file = ['SRX005634.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 18:46:07: # Command line: callpeak -t SRX005634.bam -f BAM -g ce -n SRX005634.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005634.20 # format = BAM # ChIP-seq file = ['SRX005634.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 18:46:07: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:07: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:07: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:07: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:07: # Command line: callpeak -t SRX005634.bam -f BAM -g ce -n SRX005634.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005634.05 # format = BAM # ChIP-seq file = ['SRX005634.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 18:46:07: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:07: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:12: 1000000 INFO @ Mon, 07 Sep 2015 18:46:12: 1000000 INFO @ Mon, 07 Sep 2015 18:46:12: 1000000 INFO @ Mon, 07 Sep 2015 18:46:13: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:13: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:13: #1 total tags in treatment: 1255955 INFO @ Mon, 07 Sep 2015 18:46:13: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:13: #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 18:46:13: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:13: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:13: #1 total tags in treatment: 1255955 INFO @ Mon, 07 Sep 2015 18:46:13: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:13: #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 18:46:13: #1 tags after filtering in treatment: 1255948 INFO @ Mon, 07 Sep 2015 18:46:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:13: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:13: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:13: #1 tags after filtering in treatment: 1255948 INFO @ Mon, 07 Sep 2015 18:46:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:13: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:13: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:13: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:13: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:13: #1 total tags in treatment: 1255955 INFO @ Mon, 07 Sep 2015 18:46:13: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:13: #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 18:46:13: #1 tags after filtering in treatment: 1255948 INFO @ Mon, 07 Sep 2015 18:46:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:13: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:13: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:14: #2 number of paired peaks: 3081 INFO @ Mon, 07 Sep 2015 18:46:14: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:14: #2 number of paired peaks: 3081 INFO @ Mon, 07 Sep 2015 18:46:14: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:14: #2 number of paired peaks: 3081 INFO @ Mon, 07 Sep 2015 18:46:14: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:16: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:16: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:16: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:16: #2 predicted fragment length is 92 bps INFO @ Mon, 07 Sep 2015 18:46:16: #2 alternative fragment length(s) may be 92 bps INFO @ Mon, 07 Sep 2015 18:46:16: #2.2 Generate R script for model : SRX005634.20_model.r INFO @ Mon, 07 Sep 2015 18:46:16: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:17: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:17: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:17: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:17: #2 predicted fragment length is 92 bps INFO @ Mon, 07 Sep 2015 18:46:17: #2 alternative fragment length(s) may be 92 bps INFO @ Mon, 07 Sep 2015 18:46:17: #2.2 Generate R script for model : SRX005634.05_model.r INFO @ Mon, 07 Sep 2015 18:46:17: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:17: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:17: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:17: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:17: #2 predicted fragment length is 92 bps INFO @ Mon, 07 Sep 2015 18:46:17: #2 alternative fragment length(s) may be 92 bps INFO @ Mon, 07 Sep 2015 18:46:17: #2.2 Generate R script for model : SRX005634.10_model.r INFO @ Mon, 07 Sep 2015 18:46:17: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:24: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:24: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:24: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:30: #4 Write output xls file... SRX005634.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:30: #4 Write peak in narrowPeak format file... SRX005634.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:30: #4 Write summits bed file... SRX005634.20_summits.bed INFO @ Mon, 07 Sep 2015 18:46:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (844 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:31: #4 Write output xls file... SRX005634.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:31: #4 Write peak in narrowPeak format file... SRX005634.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:31: #4 Write summits bed file... SRX005634.10_summits.bed INFO @ Mon, 07 Sep 2015 18:46:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2717 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:32: #4 Write output xls file... SRX005634.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:32: #4 Write peak in narrowPeak format file... SRX005634.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:32: #4 Write summits bed file... SRX005634.05_summits.bed INFO @ Mon, 07 Sep 2015 18:46:32: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5620 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。