Job ID = 2237023 sra ファイルのダウンロード中... Completed: 98913K bytes transferred in 4 seconds (184915K 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 37995 0 37995 0 0 55628 0 --:--:-- --:--:-- --:--:-- 77382 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 5303031 spots for /home/okishinya/chipatlas/results/ce10/SRX080078/SRR298898.sra Written 5303031 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: 00:00:42 5303031 reads; of these: 5303031 (100.00%) were unpaired; of these: 2257904 (42.58%) aligned 0 times 2664239 (50.24%) aligned exactly 1 time 380888 (7.18%) aligned >1 times 57.42% overall alignment rate Time searching: 00:00:42 Overall time: 00:00:42 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] 1064855 / 3045127 = 0.3497 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 11:25:06: # Command line: callpeak -t SRX080078.bam -f BAM -g ce -n SRX080078.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080078.05 # format = BAM # ChIP-seq file = ['SRX080078.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 11:25:06: # Command line: callpeak -t SRX080078.bam -f BAM -g ce -n SRX080078.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080078.20 # format = BAM # ChIP-seq file = ['SRX080078.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 11:25:06: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:06: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:06: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:06: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:06: # Command line: callpeak -t SRX080078.bam -f BAM -g ce -n SRX080078.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080078.10 # format = BAM # ChIP-seq file = ['SRX080078.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 11:25:06: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:06: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:11: 1000000 INFO @ Thu, 30 Apr 2015 11:25:12: 1000000 INFO @ Thu, 30 Apr 2015 11:25:12: 1000000 INFO @ Thu, 30 Apr 2015 11:25:17: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:17: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:17: #1 total tags in treatment: 1980272 INFO @ Thu, 30 Apr 2015 11:25:17: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:17: #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 11:25:17: #1 tags after filtering in treatment: 1980145 INFO @ Thu, 30 Apr 2015 11:25:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:17: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:17: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:18: #2 number of paired peaks: 4057 INFO @ Thu, 30 Apr 2015 11:25:18: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:18: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:18: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:18: #1 total tags in treatment: 1980272 INFO @ Thu, 30 Apr 2015 11:25:18: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:18: #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 11:25:18: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:18: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:18: #1 total tags in treatment: 1980272 INFO @ Thu, 30 Apr 2015 11:25:18: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:18: #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 11:25:19: #1 tags after filtering in treatment: 1980145 INFO @ Thu, 30 Apr 2015 11:25:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:19: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:19: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:19: #1 tags after filtering in treatment: 1980145 INFO @ Thu, 30 Apr 2015 11:25:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:19: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:19: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:19: #2 number of paired peaks: 4057 INFO @ Thu, 30 Apr 2015 11:25:19: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:19: #2 number of paired peaks: 4057 INFO @ Thu, 30 Apr 2015 11:25:19: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:27: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:27: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:27: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:27: #2 predicted fragment length is 135 bps INFO @ Thu, 30 Apr 2015 11:25:27: #2 alternative fragment length(s) may be 135 bps INFO @ Thu, 30 Apr 2015 11:25:27: #2.2 Generate R script for model : SRX080078.10_model.r INFO @ Thu, 30 Apr 2015 11:25:27: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:28: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:28: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:28: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:28: #2 predicted fragment length is 135 bps INFO @ Thu, 30 Apr 2015 11:25:28: #2 alternative fragment length(s) may be 135 bps INFO @ Thu, 30 Apr 2015 11:25:28: #2.2 Generate R script for model : SRX080078.20_model.r INFO @ Thu, 30 Apr 2015 11:25:28: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:29: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:29: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:29: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:29: #2 predicted fragment length is 135 bps INFO @ Thu, 30 Apr 2015 11:25:29: #2 alternative fragment length(s) may be 135 bps INFO @ Thu, 30 Apr 2015 11:25:29: #2.2 Generate R script for model : SRX080078.05_model.r INFO @ Thu, 30 Apr 2015 11:25:29: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:39: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:41: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:42: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Thu, 30 Apr 2015 11:25:51: #4 Write output xls file... SRX080078.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:51: #4 Write peak in narrowPeak format file... SRX080078.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:51: #4 Write summits bed file... SRX080078.10_summits.bed INFO @ Thu, 30 Apr 2015 11:25:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4132 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:52: #4 Write output xls file... SRX080078.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:52: #4 Write peak in narrowPeak format file... SRX080078.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:52: #4 Write summits bed file... SRX080078.20_summits.bed INFO @ Thu, 30 Apr 2015 11:25:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2915 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:55: #4 Write output xls file... SRX080078.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:56: #4 Write peak in narrowPeak format file... SRX080078.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:56: #4 Write summits bed file... SRX080078.05_summits.bed INFO @ Thu, 30 Apr 2015 11:25:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5769 records, 4 fields): 8 millis CompletedMACS2peakCalling