Job ID = 2237054 sra ファイルのダウンロード中... Completed: 339714K bytes transferred in 7 seconds (359842K 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 4007 0 4007 0 0 7497 0 --:--:-- --:--:-- --:--:-- 11648 100 36265 0 36265 0 0 50059 0 --:--:-- --:--:-- --:--:-- 67911 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 12796605 spots for /home/okishinya/chipatlas/results/ce10/SRX094475/SRR340087.sra Written 12796605 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: 00:02:05 12796605 reads; of these: 12796605 (100.00%) were unpaired; of these: 2950001 (23.05%) aligned 0 times 8728684 (68.21%) aligned exactly 1 time 1117920 (8.74%) aligned >1 times 76.95% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 1039086 / 9846604 = 0.1055 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 11:30:11: # Command line: callpeak -t SRX094475.bam -f BAM -g ce -n SRX094475.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX094475.20 # format = BAM # ChIP-seq file = ['SRX094475.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 11:30:11: # Command line: callpeak -t SRX094475.bam -f BAM -g ce -n SRX094475.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX094475.05 # format = BAM # ChIP-seq file = ['SRX094475.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 11:30:11: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:30:11: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:30:11: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:30:11: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:30:11: # Command line: callpeak -t SRX094475.bam -f BAM -g ce -n SRX094475.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX094475.10 # format = BAM # ChIP-seq file = ['SRX094475.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 11:30:11: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:30:11: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:30:16: 1000000 INFO @ Thu, 30 Apr 2015 11:30:16: 1000000 INFO @ Thu, 30 Apr 2015 11:30:16: 1000000 INFO @ Thu, 30 Apr 2015 11:30:22: 2000000 INFO @ Thu, 30 Apr 2015 11:30:22: 2000000 INFO @ Thu, 30 Apr 2015 11:30:22: 2000000 INFO @ Thu, 30 Apr 2015 11:30:27: 3000000 INFO @ Thu, 30 Apr 2015 11:30:27: 3000000 INFO @ Thu, 30 Apr 2015 11:30:27: 3000000 INFO @ Thu, 30 Apr 2015 11:30:32: 4000000 INFO @ Thu, 30 Apr 2015 11:30:33: 4000000 INFO @ Thu, 30 Apr 2015 11:30:33: 4000000 INFO @ Thu, 30 Apr 2015 11:30:38: 5000000 INFO @ Thu, 30 Apr 2015 11:30:38: 5000000 INFO @ Thu, 30 Apr 2015 11:30:38: 5000000 INFO @ Thu, 30 Apr 2015 11:30:43: 6000000 INFO @ Thu, 30 Apr 2015 11:30:44: 6000000 INFO @ Thu, 30 Apr 2015 11:30:44: 6000000 INFO @ Thu, 30 Apr 2015 11:30:48: 7000000 INFO @ Thu, 30 Apr 2015 11:30:50: 7000000 INFO @ Thu, 30 Apr 2015 11:30:50: 7000000 INFO @ Thu, 30 Apr 2015 11:30:54: 8000000 INFO @ Thu, 30 Apr 2015 11:30:56: 8000000 INFO @ Thu, 30 Apr 2015 11:30:56: 8000000 INFO @ Thu, 30 Apr 2015 11:30:58: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:30:58: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:30:58: #1 total tags in treatment: 8807518 INFO @ Thu, 30 Apr 2015 11:30:58: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:30:58: #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 11:31:00: #1 tags after filtering in treatment: 8807055 INFO @ Thu, 30 Apr 2015 11:31:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:31:00: #1 finished! INFO @ Thu, 30 Apr 2015 11:31:00: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:31:00: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:31:00: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:31:00: #1 total tags in treatment: 8807518 INFO @ Thu, 30 Apr 2015 11:31:00: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:31:00: #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 11:31:01: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:31:01: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:31:01: #1 total tags in treatment: 8807518 INFO @ Thu, 30 Apr 2015 11:31:01: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:31:01: #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 11:31:02: #1 tags after filtering in treatment: 8807055 INFO @ Thu, 30 Apr 2015 11:31:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:31:02: #1 finished! INFO @ Thu, 30 Apr 2015 11:31:02: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:31:02: #1 tags after filtering in treatment: 8807055 INFO @ Thu, 30 Apr 2015 11:31:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:31:02: #1 finished! INFO @ Thu, 30 Apr 2015 11:31:02: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:31:02: #2 number of paired peaks: 2841 INFO @ Thu, 30 Apr 2015 11:31:02: start model_add_line... INFO @ Thu, 30 Apr 2015 11:31:04: #2 number of paired peaks: 2841 INFO @ Thu, 30 Apr 2015 11:31:04: start model_add_line... INFO @ Thu, 30 Apr 2015 11:31:04: #2 number of paired peaks: 2841 INFO @ Thu, 30 Apr 2015 11:31:04: start model_add_line... INFO @ Thu, 30 Apr 2015 11:31:23: start X-correlation... INFO @ Thu, 30 Apr 2015 11:31:23: end of X-cor INFO @ Thu, 30 Apr 2015 11:31:23: #2 finished! INFO @ Thu, 30 Apr 2015 11:31:23: #2 predicted fragment length is 117 bps INFO @ Thu, 30 Apr 2015 11:31:23: #2 alternative fragment length(s) may be 4,117 bps INFO @ Thu, 30 Apr 2015 11:31:23: #2.2 Generate R script for model : SRX094475.10_model.r INFO @ Thu, 30 Apr 2015 11:31:23: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:31:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:31:23: start X-correlation... INFO @ Thu, 30 Apr 2015 11:31:23: end of X-cor INFO @ Thu, 30 Apr 2015 11:31:23: #2 finished! INFO @ Thu, 30 Apr 2015 11:31:23: #2 predicted fragment length is 117 bps INFO @ Thu, 30 Apr 2015 11:31:23: #2 alternative fragment length(s) may be 4,117 bps INFO @ Thu, 30 Apr 2015 11:31:23: #2.2 Generate R script for model : SRX094475.05_model.r INFO @ Thu, 30 Apr 2015 11:31:23: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:31:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:31:24: start X-correlation... INFO @ Thu, 30 Apr 2015 11:31:24: end of X-cor INFO @ Thu, 30 Apr 2015 11:31:24: #2 finished! INFO @ Thu, 30 Apr 2015 11:31:24: #2 predicted fragment length is 117 bps INFO @ Thu, 30 Apr 2015 11:31:24: #2 alternative fragment length(s) may be 4,117 bps INFO @ Thu, 30 Apr 2015 11:31:24: #2.2 Generate R script for model : SRX094475.20_model.r INFO @ Thu, 30 Apr 2015 11:31:24: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:31:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:32:13: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:32:14: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:32:18: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:32:48: #4 Write output xls file... SRX094475.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:32:48: #4 Write peak in narrowPeak format file... SRX094475.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:32:48: #4 Write summits bed file... SRX094475.20_summits.bed INFO @ Thu, 30 Apr 2015 11:32:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1603 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:33:01: #4 Write output xls file... SRX094475.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:33:01: #4 Write peak in narrowPeak format file... SRX094475.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:33:01: #4 Write summits bed file... SRX094475.05_summits.bed INFO @ Thu, 30 Apr 2015 11:33:01: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (12264 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:33:05: #4 Write output xls file... SRX094475.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:33:05: #4 Write peak in narrowPeak format file... SRX094475.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:33:05: #4 Write summits bed file... SRX094475.10_summits.bed INFO @ Thu, 30 Apr 2015 11:33:05: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6516 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。