Job ID = 3001495 sra ファイルのダウンロード中... Completed: 65968K bytes transferred in 5 seconds (104598K 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 8495 0 --:--:-- 0:00:01 --:--:-- 9530 100 14953 0 14953 0 0 5415 0 --:--:-- 0:00:02 --:--:-- 5818 100 14953 0 14953 0 0 3973 0 --:--:-- 0:00:03 --:--:-- 4186 100 14953 0 14953 0 0 3138 0 --:--:-- 0:00:04 --:--:-- 3269 100 14953 0 14953 0 0 2592 0 --:--:-- 0:00:05 --:--:-- 2681 100 14953 0 14953 0 0 2209 0 --:--:-- 0:00:06 --:--:-- 0 100 17860 0 17860 0 0 2352 0 --:--:-- 0:00:07 --:--:-- 601 100 35062 0 35062 0 0 4505 0 --:--:-- 0:00:07 --:--:-- 5003 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 4040048 spots for /home/okishinya/chipatlas/results/ce10/SRX005629/SRR017598.sra Written 4040048 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: 00:00:33 4040048 reads; of these: 4040048 (100.00%) were unpaired; of these: 1162915 (28.78%) aligned 0 times 2444873 (60.52%) aligned exactly 1 time 432260 (10.70%) aligned >1 times 71.22% overall alignment rate Time searching: 00:00:33 Overall time: 00:00:33 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] 662339 / 2877133 = 0.2302 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 SRX005629.bam -f BAM -g ce -n SRX005629.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005629.10 # format = BAM # ChIP-seq file = ['SRX005629.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: # Command line: callpeak -t SRX005629.bam -f BAM -g ce -n SRX005629.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005629.05 # format = BAM # ChIP-seq file = ['SRX005629.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 tag files... 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 18:45:52: # Command line: callpeak -t SRX005629.bam -f BAM -g ce -n SRX005629.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005629.20 # format = BAM # ChIP-seq file = ['SRX005629.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: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:57: 1000000 INFO @ Mon, 07 Sep 2015 18:45:57: 1000000 INFO @ Mon, 07 Sep 2015 18:45:57: 1000000 INFO @ Mon, 07 Sep 2015 18:46:03: 2000000 INFO @ Mon, 07 Sep 2015 18:46:03: 2000000 INFO @ Mon, 07 Sep 2015 18:46:03: 2000000 INFO @ Mon, 07 Sep 2015 18:46:04: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:04: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:04: #1 total tags in treatment: 2214794 INFO @ Mon, 07 Sep 2015 18:46:04: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:04: #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 18:46:04: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:04: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:04: #1 total tags in treatment: 2214794 INFO @ Mon, 07 Sep 2015 18:46:04: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:04: #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 18:46:04: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:04: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:04: #1 total tags in treatment: 2214794 INFO @ Mon, 07 Sep 2015 18:46:04: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:04: #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 18:46:04: #1 tags after filtering in treatment: 2214778 INFO @ Mon, 07 Sep 2015 18:46:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:04: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:04: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:04: #1 tags after filtering in treatment: 2214778 INFO @ Mon, 07 Sep 2015 18:46:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:04: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:04: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:04: #1 tags after filtering in treatment: 2214778 INFO @ Mon, 07 Sep 2015 18:46:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:04: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:04: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:05: #2 number of paired peaks: 2882 INFO @ Mon, 07 Sep 2015 18:46:05: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:05: #2 number of paired peaks: 2882 INFO @ Mon, 07 Sep 2015 18:46:05: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:05: #2 number of paired peaks: 2882 INFO @ Mon, 07 Sep 2015 18:46:05: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:13: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:13: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:13: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:13: #2 predicted fragment length is 111 bps INFO @ Mon, 07 Sep 2015 18:46:13: #2 alternative fragment length(s) may be 111 bps INFO @ Mon, 07 Sep 2015 18:46:13: #2.2 Generate R script for model : SRX005629.10_model.r INFO @ Mon, 07 Sep 2015 18:46:13: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:13: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:13: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:13: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:13: #2 predicted fragment length is 111 bps INFO @ Mon, 07 Sep 2015 18:46:13: #2 alternative fragment length(s) may be 111 bps INFO @ Mon, 07 Sep 2015 18:46:13: #2.2 Generate R script for model : SRX005629.20_model.r INFO @ Mon, 07 Sep 2015 18:46:13: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:13: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:13: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:13: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:13: #2 predicted fragment length is 111 bps INFO @ Mon, 07 Sep 2015 18:46:13: #2 alternative fragment length(s) may be 111 bps INFO @ Mon, 07 Sep 2015 18:46:13: #2.2 Generate R script for model : SRX005629.05_model.r INFO @ Mon, 07 Sep 2015 18:46:13: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:27: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:28: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:29: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:37: #4 Write output xls file... SRX005629.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:37: #4 Write peak in narrowPeak format file... SRX005629.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:37: #4 Write summits bed file... SRX005629.10_summits.bed INFO @ Mon, 07 Sep 2015 18:46:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (839 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:38: #4 Write output xls file... SRX005629.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:38: #4 Write peak in narrowPeak format file... SRX005629.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:38: #4 Write summits bed file... SRX005629.20_summits.bed INFO @ Mon, 07 Sep 2015 18:46:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (239 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:38: #4 Write output xls file... SRX005629.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:38: #4 Write peak in narrowPeak format file... SRX005629.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:38: #4 Write summits bed file... SRX005629.05_summits.bed INFO @ Mon, 07 Sep 2015 18:46:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2407 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。