Job ID = 3001503 sra ファイルのダウンロード中... Completed: 40398K bytes transferred in 4 seconds (74380K 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 --:--:-- --:--:-- --:--:-- 0 108 1087 0 1087 0 0 1855 0 --:--:-- --:--:-- --:--:-- 2751 100 14953 0 14953 0 0 8417 0 --:--:-- 0:00:01 --:--:-- 9428 100 14953 0 14953 0 0 5381 0 --:--:-- 0:00:02 --:--:-- 5777 100 14953 0 14953 0 0 3956 0 --:--:-- 0:00:03 --:--:-- 4166 100 14953 0 14953 0 0 3127 0 --:--:-- 0:00:04 --:--:-- 3257 100 14953 0 14953 0 0 2585 0 --:--:-- 0:00:05 --:--:-- 2668 100 14953 0 14953 0 0 2204 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1920 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1701 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1527 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1385 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1268 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1168 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 0 839 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 19327 0 19327 0 0 630 0 --:--:-- 0:00:30 --:--:-- 907 100 34251 0 34251 0 0 1111 0 --:--:-- 0:00:30 --:--:-- 4814 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 2245066 spots for /home/okishinya/chipatlas/results/ce10/SRX005637/SRR017606.sra Written 2245066 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: 00:00:18 2245066 reads; of these: 2245066 (100.00%) were unpaired; of these: 776048 (34.57%) aligned 0 times 1242230 (55.33%) aligned exactly 1 time 226788 (10.10%) aligned >1 times 65.43% overall alignment rate Time searching: 00:00:18 Overall time: 00:00:18 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] 655286 / 1469018 = 0.4461 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 18:45:52: # Command line: callpeak -t SRX005637.bam -f BAM -g ce -n SRX005637.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005637.10 # format = BAM # ChIP-seq file = ['SRX005637.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 18:45:52: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:52: # Command line: callpeak -t SRX005637.bam -f BAM -g ce -n SRX005637.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005637.20 # format = BAM # ChIP-seq file = ['SRX005637.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 18:45:52: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:52: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:52: # Command line: callpeak -t SRX005637.bam -f BAM -g ce -n SRX005637.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005637.05 # format = BAM # ChIP-seq file = ['SRX005637.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 18:45:52: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:52: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:52: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:56: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:45:56: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:45:56: #1 total tags in treatment: 813732 INFO @ Mon, 07 Sep 2015 18:45:56: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:56: #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 18:45:56: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:45:56: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:45:56: #1 total tags in treatment: 813732 INFO @ Mon, 07 Sep 2015 18:45:56: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:56: #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 18:45:56: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:45:56: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:45:56: #1 total tags in treatment: 813732 INFO @ Mon, 07 Sep 2015 18:45:56: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:56: #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 18:45:56: #1 tags after filtering in treatment: 813730 INFO @ Mon, 07 Sep 2015 18:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:56: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:56: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:56: #1 tags after filtering in treatment: 813730 INFO @ Mon, 07 Sep 2015 18:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:56: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:56: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:56: #1 tags after filtering in treatment: 813730 INFO @ Mon, 07 Sep 2015 18:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:56: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:56: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:56: #2 number of paired peaks: 1150 INFO @ Mon, 07 Sep 2015 18:45:56: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:56: #2 number of paired peaks: 1150 INFO @ Mon, 07 Sep 2015 18:45:56: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:56: #2 number of paired peaks: 1150 INFO @ Mon, 07 Sep 2015 18:45:56: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:57: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:57: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:57: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:57: #2 predicted fragment length is 175 bps INFO @ Mon, 07 Sep 2015 18:45:57: #2 alternative fragment length(s) may be 175 bps INFO @ Mon, 07 Sep 2015 18:45:57: #2.2 Generate R script for model : SRX005637.05_model.r INFO @ Mon, 07 Sep 2015 18:45:57: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:57: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:57: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:57: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:57: #2 predicted fragment length is 175 bps INFO @ Mon, 07 Sep 2015 18:45:57: #2 alternative fragment length(s) may be 175 bps INFO @ Mon, 07 Sep 2015 18:45:57: #2.2 Generate R script for model : SRX005637.10_model.r INFO @ Mon, 07 Sep 2015 18:45:57: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:57: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:58: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:58: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:58: #2 predicted fragment length is 175 bps INFO @ Mon, 07 Sep 2015 18:45:58: #2 alternative fragment length(s) may be 175 bps INFO @ Mon, 07 Sep 2015 18:45:58: #2.2 Generate R script for model : SRX005637.20_model.r INFO @ Mon, 07 Sep 2015 18:45:58: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:03: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:03: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:03: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:06: #4 Write output xls file... SRX005637.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:06: #4 Write peak in narrowPeak format file... SRX005637.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:06: #4 Write summits bed file... SRX005637.20_summits.bed INFO @ Mon, 07 Sep 2015 18:46:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (71 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:07: #4 Write output xls file... SRX005637.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:07: #4 Write peak in narrowPeak format file... SRX005637.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:07: #4 Write summits bed file... SRX005637.05_summits.bed INFO @ Mon, 07 Sep 2015 18:46:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1185 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:07: #4 Write output xls file... SRX005637.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:07: #4 Write peak in narrowPeak format file... SRX005637.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:07: #4 Write summits bed file... SRX005637.10_summits.bed INFO @ Mon, 07 Sep 2015 18:46:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (393 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。