Job ID = 2236687 sra ファイルのダウンロード中... Completed: 116341K bytes transferred in 4 seconds (204779K bits/sec), in 2 files, 3 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 6912 0 6912 0 0 13997 0 --:--:-- --:--:-- --:--:-- 22811 100 34349 0 34349 0 0 50268 0 --:--:-- --:--:-- --:--:-- 69815 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 1978701 spots for /home/okishinya/chipatlas/results/ce10/SRX015096/SRR032441.sra Written 1978701 spots total Written 3099942 spots for /home/okishinya/chipatlas/results/ce10/SRX015096/SRR032440.sra Written 3099942 spots total 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: 00:00:29 5078643 reads; of these: 5078643 (100.00%) were unpaired; of these: 4251372 (83.71%) aligned 0 times 730609 (14.39%) aligned exactly 1 time 96662 (1.90%) aligned >1 times 16.29% overall alignment rate Time searching: 00:00:29 Overall time: 00:00:29 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] 55195 / 827271 = 0.0667 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 @ Thu, 30 Apr 2015 10:54:36: # Command line: callpeak -t SRX015096.bam -f BAM -g ce -n SRX015096.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX015096.20 # format = BAM # ChIP-seq file = ['SRX015096.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 @ Thu, 30 Apr 2015 10:54:36: # Command line: callpeak -t SRX015096.bam -f BAM -g ce -n SRX015096.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX015096.05 # format = BAM # ChIP-seq file = ['SRX015096.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 @ Thu, 30 Apr 2015 10:54:36: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:54:36: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:54:36: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:54:36: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:54:36: # Command line: callpeak -t SRX015096.bam -f BAM -g ce -n SRX015096.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX015096.10 # format = BAM # ChIP-seq file = ['SRX015096.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 @ Thu, 30 Apr 2015 10:54:36: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:54:36: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:54:41: #1 tag size is determined as 34 bps INFO @ Thu, 30 Apr 2015 10:54:41: #1 tag size is determined as 34 bps INFO @ Thu, 30 Apr 2015 10:54:41: #1 tag size is determined as 34 bps INFO @ Thu, 30 Apr 2015 10:54:41: #1 tag size = 34 INFO @ Thu, 30 Apr 2015 10:54:41: #1 tag size = 34 INFO @ Thu, 30 Apr 2015 10:54:41: #1 tag size = 34 INFO @ Thu, 30 Apr 2015 10:54:41: #1 total tags in treatment: 772076 INFO @ Thu, 30 Apr 2015 10:54:41: #1 total tags in treatment: 772076 INFO @ Thu, 30 Apr 2015 10:54:41: #1 total tags in treatment: 772076 INFO @ Thu, 30 Apr 2015 10:54:41: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:54:41: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:54:41: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:54:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 10:54:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 10:54:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 10:54:42: #1 tags after filtering in treatment: 770889 INFO @ Thu, 30 Apr 2015 10:54:42: #1 tags after filtering in treatment: 770889 INFO @ Thu, 30 Apr 2015 10:54:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:54:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:54:42: #1 finished! INFO @ Thu, 30 Apr 2015 10:54:42: #1 finished! INFO @ Thu, 30 Apr 2015 10:54:42: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:54:42: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:54:42: #1 tags after filtering in treatment: 770889 INFO @ Thu, 30 Apr 2015 10:54:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:54:42: #1 finished! INFO @ Thu, 30 Apr 2015 10:54:42: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:54:42: #2 number of paired peaks: 2022 INFO @ Thu, 30 Apr 2015 10:54:42: start model_add_line... INFO @ Thu, 30 Apr 2015 10:54:42: #2 number of paired peaks: 2022 INFO @ Thu, 30 Apr 2015 10:54:42: start model_add_line... INFO @ Thu, 30 Apr 2015 10:54:42: #2 number of paired peaks: 2022 INFO @ Thu, 30 Apr 2015 10:54:42: start model_add_line... INFO @ Thu, 30 Apr 2015 10:54:43: start X-correlation... INFO @ Thu, 30 Apr 2015 10:54:43: end of X-cor INFO @ Thu, 30 Apr 2015 10:54:43: #2 finished! INFO @ Thu, 30 Apr 2015 10:54:43: #2 predicted fragment length is 190 bps INFO @ Thu, 30 Apr 2015 10:54:43: #2 alternative fragment length(s) may be 190 bps INFO @ Thu, 30 Apr 2015 10:54:43: #2.2 Generate R script for model : SRX015096.05_model.r INFO @ Thu, 30 Apr 2015 10:54:43: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:54:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:54:43: start X-correlation... INFO @ Thu, 30 Apr 2015 10:54:43: end of X-cor INFO @ Thu, 30 Apr 2015 10:54:43: #2 finished! INFO @ Thu, 30 Apr 2015 10:54:43: #2 predicted fragment length is 190 bps INFO @ Thu, 30 Apr 2015 10:54:43: #2 alternative fragment length(s) may be 190 bps INFO @ Thu, 30 Apr 2015 10:54:43: #2.2 Generate R script for model : SRX015096.20_model.r INFO @ Thu, 30 Apr 2015 10:54:43: start X-correlation... INFO @ Thu, 30 Apr 2015 10:54:43: end of X-cor INFO @ Thu, 30 Apr 2015 10:54:43: #2 finished! INFO @ Thu, 30 Apr 2015 10:54:43: #2 predicted fragment length is 190 bps INFO @ Thu, 30 Apr 2015 10:54:43: #2 alternative fragment length(s) may be 190 bps INFO @ Thu, 30 Apr 2015 10:54:43: #2.2 Generate R script for model : SRX015096.10_model.r INFO @ Thu, 30 Apr 2015 10:54:43: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:54:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:54:43: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:54:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:54:48: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:54:48: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:54:49: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:54:52: #4 Write output xls file... SRX015096.20_peaks.xls INFO @ Thu, 30 Apr 2015 10:54:52: #4 Write peak in narrowPeak format file... SRX015096.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 10:54:52: #4 Write summits bed file... SRX015096.20_summits.bed INFO @ Thu, 30 Apr 2015 10:54:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (117 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 10:54:52: #4 Write output xls file... SRX015096.05_peaks.xls INFO @ Thu, 30 Apr 2015 10:54:52: #4 Write peak in narrowPeak format file... SRX015096.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 10:54:52: #4 Write summits bed file... SRX015096.05_summits.bed INFO @ Thu, 30 Apr 2015 10:54:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1442 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 10:54:52: #4 Write output xls file... SRX015096.10_peaks.xls INFO @ Thu, 30 Apr 2015 10:54:52: #4 Write peak in narrowPeak format file... SRX015096.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 10:54:52: #4 Write summits bed file... SRX015096.10_summits.bed INFO @ Thu, 30 Apr 2015 10:54:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (547 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。