Job ID = 3001481 sra ファイルのダウンロード中... Completed: 3409325K bytes transferred in 40 seconds (681232K 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 8813 0 --:--:-- 0:00:01 --:--:-- 9935 100 14953 0 14953 0 0 5541 0 --:--:-- 0:00:02 --:--:-- 5964 100 14953 0 14953 0 0 4040 0 --:--:-- 0:00:03 --:--:-- 4261 100 14953 0 14953 0 0 3179 0 --:--:-- 0:00:04 --:--:-- 3314 100 14953 0 14953 0 0 2621 0 --:--:-- 0:00:05 --:--:-- 2712 100 14953 0 14953 0 0 2229 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 1396 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1276 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1176 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 0 758 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 0 630 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 604 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 581 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 40608 0 40608 0 0 1320 0 --:--:-- 0:00:30 --:--:-- 6400 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 14069076 spots for /home/okishinya/chipatlas/results/ce10/SRX003824/SRR015064.sra Written 14069076 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: 00:01:49 14069076 reads; of these: 14069076 (100.00%) were unpaired; of these: 7706519 (54.78%) aligned 0 times 5266968 (37.44%) aligned exactly 1 time 1095589 (7.79%) aligned >1 times 45.22% overall alignment rate Time searching: 00:01:49 Overall time: 00:01:49 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] 874090 / 6362557 = 0.1374 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 18:49:18: # Command line: callpeak -t SRX003824.bam -f BAM -g ce -n SRX003824.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX003824.20 # format = BAM # ChIP-seq file = ['SRX003824.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 18:49:18: # Command line: callpeak -t SRX003824.bam -f BAM -g ce -n SRX003824.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX003824.10 # format = BAM # ChIP-seq file = ['SRX003824.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 18:49:18: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:49:18: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:49:18: # Command line: callpeak -t SRX003824.bam -f BAM -g ce -n SRX003824.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX003824.05 # format = BAM # ChIP-seq file = ['SRX003824.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 18:49:18: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:49:18: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:49:18: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:49:18: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:49:23: 1000000 INFO @ Mon, 07 Sep 2015 18:49:23: 1000000 INFO @ Mon, 07 Sep 2015 18:49:24: 1000000 INFO @ Mon, 07 Sep 2015 18:49:29: 2000000 INFO @ Mon, 07 Sep 2015 18:49:29: 2000000 INFO @ Mon, 07 Sep 2015 18:49:29: 2000000 INFO @ Mon, 07 Sep 2015 18:49:34: 3000000 INFO @ Mon, 07 Sep 2015 18:49:34: 3000000 INFO @ Mon, 07 Sep 2015 18:49:34: 3000000 INFO @ Mon, 07 Sep 2015 18:49:39: 4000000 INFO @ Mon, 07 Sep 2015 18:49:40: 4000000 INFO @ Mon, 07 Sep 2015 18:49:40: 4000000 INFO @ Mon, 07 Sep 2015 18:49:45: 5000000 INFO @ Mon, 07 Sep 2015 18:49:45: 5000000 INFO @ Mon, 07 Sep 2015 18:49:45: 5000000 INFO @ Mon, 07 Sep 2015 18:49:48: #1 tag size is determined as 37 bps INFO @ Mon, 07 Sep 2015 18:49:48: #1 tag size = 37 INFO @ Mon, 07 Sep 2015 18:49:48: #1 total tags in treatment: 5488467 INFO @ Mon, 07 Sep 2015 18:49:48: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:49:48: #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 18:49:48: #1 tag size is determined as 37 bps INFO @ Mon, 07 Sep 2015 18:49:48: #1 tag size = 37 INFO @ Mon, 07 Sep 2015 18:49:48: #1 total tags in treatment: 5488467 INFO @ Mon, 07 Sep 2015 18:49:48: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:49:48: #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 18:49:48: #1 tag size is determined as 37 bps INFO @ Mon, 07 Sep 2015 18:49:48: #1 tag size = 37 INFO @ Mon, 07 Sep 2015 18:49:48: #1 total tags in treatment: 5488467 INFO @ Mon, 07 Sep 2015 18:49:48: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:49:48: #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 18:49:49: #1 tags after filtering in treatment: 5487600 INFO @ Mon, 07 Sep 2015 18:49:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:49:49: #1 finished! INFO @ Mon, 07 Sep 2015 18:49:49: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:49:49: #1 tags after filtering in treatment: 5487600 INFO @ Mon, 07 Sep 2015 18:49:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:49:49: #1 finished! INFO @ Mon, 07 Sep 2015 18:49:49: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:49:49: #1 tags after filtering in treatment: 5487600 INFO @ Mon, 07 Sep 2015 18:49:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:49:49: #1 finished! INFO @ Mon, 07 Sep 2015 18:49:49: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:49:50: #2 number of paired peaks: 1859 INFO @ Mon, 07 Sep 2015 18:49:50: start model_add_line... INFO @ Mon, 07 Sep 2015 18:49:50: #2 number of paired peaks: 1859 INFO @ Mon, 07 Sep 2015 18:49:50: start model_add_line... INFO @ Mon, 07 Sep 2015 18:49:50: #2 number of paired peaks: 1859 INFO @ Mon, 07 Sep 2015 18:49:50: start model_add_line... INFO @ Mon, 07 Sep 2015 18:50:00: start X-correlation... INFO @ Mon, 07 Sep 2015 18:50:00: end of X-cor INFO @ Mon, 07 Sep 2015 18:50:00: #2 finished! INFO @ Mon, 07 Sep 2015 18:50:00: #2 predicted fragment length is 78 bps INFO @ Mon, 07 Sep 2015 18:50:00: #2 alternative fragment length(s) may be 78 bps INFO @ Mon, 07 Sep 2015 18:50:00: #2.2 Generate R script for model : SRX003824.20_model.r INFO @ Mon, 07 Sep 2015 18:50:00: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:50:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:50:00: start X-correlation... INFO @ Mon, 07 Sep 2015 18:50:00: end of X-cor INFO @ Mon, 07 Sep 2015 18:50:00: #2 finished! INFO @ Mon, 07 Sep 2015 18:50:00: #2 predicted fragment length is 78 bps INFO @ Mon, 07 Sep 2015 18:50:00: #2 alternative fragment length(s) may be 78 bps INFO @ Mon, 07 Sep 2015 18:50:00: #2.2 Generate R script for model : SRX003824.10_model.r INFO @ Mon, 07 Sep 2015 18:50:00: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:50:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:50:00: start X-correlation... INFO @ Mon, 07 Sep 2015 18:50:00: end of X-cor INFO @ Mon, 07 Sep 2015 18:50:00: #2 finished! INFO @ Mon, 07 Sep 2015 18:50:00: #2 predicted fragment length is 78 bps INFO @ Mon, 07 Sep 2015 18:50:00: #2 alternative fragment length(s) may be 78 bps INFO @ Mon, 07 Sep 2015 18:50:00: #2.2 Generate R script for model : SRX003824.05_model.r INFO @ Mon, 07 Sep 2015 18:50:00: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:50:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:50:30: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:50:31: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:50:32: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:50:53: #4 Write output xls file... SRX003824.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:50:53: #4 Write peak in narrowPeak format file... SRX003824.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:50:53: #4 Write summits bed file... SRX003824.20_summits.bed INFO @ Mon, 07 Sep 2015 18:50:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1849 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:50:56: #4 Write output xls file... SRX003824.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:50:56: #4 Write peak in narrowPeak format file... SRX003824.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:50:56: #4 Write summits bed file... SRX003824.10_summits.bed INFO @ Mon, 07 Sep 2015 18:50:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5190 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:51:01: #4 Write output xls file... SRX003824.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:51:01: #4 Write peak in narrowPeak format file... SRX003824.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:51:02: #4 Write summits bed file... SRX003824.05_summits.bed INFO @ Mon, 07 Sep 2015 18:51:02: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (12729 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。