Job ID = 3001479 sra ファイルのダウンロード中... Completed: 2977592K bytes transferred in 39 seconds (612901K 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 9088 0 9088 0 0 18001 0 --:--:-- --:--:-- --:--:-- 28942 100 14953 0 14953 0 0 8822 0 --:--:-- 0:00:01 --:--:-- 9942 100 14953 0 14953 0 0 5544 0 --:--:-- 0:00:02 --:--:-- 5966 100 14953 0 14953 0 0 4042 0 --:--:-- 0:00:03 --:--:-- 4262 100 14953 0 14953 0 0 3181 0 --:--:-- 0:00:04 --:--:-- 3315 100 14953 0 14953 0 0 2622 0 --:--:-- 0:00:05 --:--:-- 1128 100 14953 0 14953 0 0 2230 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1940 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1717 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1540 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1395 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1276 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1175 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1090 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1015 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 951 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 894 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 843 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 798 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 757 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 721 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 688 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 0 559 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 539 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 520 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 --:--:-- 301 100 40602 0 40602 0 0 1320 0 --:--:-- 0:00:30 --:--:-- 6404 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 11975152 spots for /home/okishinya/chipatlas/results/ce10/SRX003822/SRR015062.sra Written 11975152 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: 00:01:13 11975152 reads; of these: 11975152 (100.00%) were unpaired; of these: 8816741 (73.63%) aligned 0 times 2749965 (22.96%) aligned exactly 1 time 408446 (3.41%) aligned >1 times 26.37% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 316033 / 3158411 = 0.1001 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 18:47:50: # Command line: callpeak -t SRX003822.bam -f BAM -g ce -n SRX003822.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX003822.20 # format = BAM # ChIP-seq file = ['SRX003822.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 18:47:50: # Command line: callpeak -t SRX003822.bam -f BAM -g ce -n SRX003822.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX003822.05 # format = BAM # ChIP-seq file = ['SRX003822.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 18:47:50: # Command line: callpeak -t SRX003822.bam -f BAM -g ce -n SRX003822.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX003822.10 # format = BAM # ChIP-seq file = ['SRX003822.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 18:47:50: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:47:50: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:47:50: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:47:50: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:47:50: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:47:50: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:47:56: 1000000 INFO @ Mon, 07 Sep 2015 18:47:56: 1000000 INFO @ Mon, 07 Sep 2015 18:47:56: 1000000 INFO @ Mon, 07 Sep 2015 18:48:01: 2000000 INFO @ Mon, 07 Sep 2015 18:48:01: 2000000 INFO @ Mon, 07 Sep 2015 18:48:01: 2000000 INFO @ Mon, 07 Sep 2015 18:48:06: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:48:06: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:48:06: #1 total tags in treatment: 2842378 INFO @ Mon, 07 Sep 2015 18:48:06: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:48:06: #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 18:48:06: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:48:06: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:48:06: #1 total tags in treatment: 2842378 INFO @ Mon, 07 Sep 2015 18:48:06: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:48:06: #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 18:48:06: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:48:06: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:48:06: #1 total tags in treatment: 2842378 INFO @ Mon, 07 Sep 2015 18:48:06: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:48:06: #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 18:48:06: #1 tags after filtering in treatment: 2842062 INFO @ Mon, 07 Sep 2015 18:48:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:48:06: #1 finished! INFO @ Mon, 07 Sep 2015 18:48:06: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:48:06: #1 tags after filtering in treatment: 2842062 INFO @ Mon, 07 Sep 2015 18:48:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:48:06: #1 finished! INFO @ Mon, 07 Sep 2015 18:48:06: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:48:06: #1 tags after filtering in treatment: 2842062 INFO @ Mon, 07 Sep 2015 18:48:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:48:06: #1 finished! INFO @ Mon, 07 Sep 2015 18:48:06: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:48:07: #2 number of paired peaks: 3040 INFO @ Mon, 07 Sep 2015 18:48:07: start model_add_line... INFO @ Mon, 07 Sep 2015 18:48:07: #2 number of paired peaks: 3040 INFO @ Mon, 07 Sep 2015 18:48:07: start model_add_line... INFO @ Mon, 07 Sep 2015 18:48:07: #2 number of paired peaks: 3040 INFO @ Mon, 07 Sep 2015 18:48:07: start model_add_line... INFO @ Mon, 07 Sep 2015 18:48:17: start X-correlation... INFO @ Mon, 07 Sep 2015 18:48:17: end of X-cor INFO @ Mon, 07 Sep 2015 18:48:17: #2 finished! INFO @ Mon, 07 Sep 2015 18:48:17: #2 predicted fragment length is 76 bps INFO @ Mon, 07 Sep 2015 18:48:17: #2 alternative fragment length(s) may be 76 bps INFO @ Mon, 07 Sep 2015 18:48:17: #2.2 Generate R script for model : SRX003822.05_model.r INFO @ Mon, 07 Sep 2015 18:48:17: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:48:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:48:17: start X-correlation... INFO @ Mon, 07 Sep 2015 18:48:17: end of X-cor INFO @ Mon, 07 Sep 2015 18:48:17: #2 finished! INFO @ Mon, 07 Sep 2015 18:48:17: #2 predicted fragment length is 76 bps INFO @ Mon, 07 Sep 2015 18:48:17: #2 alternative fragment length(s) may be 76 bps INFO @ Mon, 07 Sep 2015 18:48:17: #2.2 Generate R script for model : SRX003822.20_model.r INFO @ Mon, 07 Sep 2015 18:48:17: start X-correlation... INFO @ Mon, 07 Sep 2015 18:48:17: end of X-cor INFO @ Mon, 07 Sep 2015 18:48:17: #2 finished! INFO @ Mon, 07 Sep 2015 18:48:17: #2 predicted fragment length is 76 bps INFO @ Mon, 07 Sep 2015 18:48:17: #2 alternative fragment length(s) may be 76 bps INFO @ Mon, 07 Sep 2015 18:48:17: #2.2 Generate R script for model : SRX003822.10_model.r INFO @ Mon, 07 Sep 2015 18:48:17: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:48:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:48:17: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:48:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:48:34: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:48:35: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:48:35: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:48:48: #4 Write output xls file... SRX003822.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:48:48: #4 Write peak in narrowPeak format file... SRX003822.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:48:48: #4 Write summits bed file... SRX003822.20_summits.bed INFO @ Mon, 07 Sep 2015 18:48:48: Done! INFO @ Mon, 07 Sep 2015 18:48:48: #4 Write output xls file... SRX003822.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:48:48: #4 Write output xls file... SRX003822.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:48:48: #4 Write peak in narrowPeak format file... SRX003822.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:48:48: #4 Write summits bed file... SRX003822.10_summits.bed pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (999 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:48:48: #4 Write peak in narrowPeak format file... SRX003822.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:48:48: Done! INFO @ Mon, 07 Sep 2015 18:48:48: #4 Write summits bed file... SRX003822.05_summits.bed INFO @ Mon, 07 Sep 2015 18:48:48: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6093 records, 4 fields): 8 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2718 records, 4 fields): 180 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。