Job ID = 2237039 sra ファイルのダウンロード中... Completed: 110400K bytes transferred in 5 seconds (162781K 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 11996 0 11996 0 0 21929 0 --:--:-- --:--:-- --:--:-- 33696 100 38013 0 38013 0 0 51601 0 --:--:-- --:--:-- --:--:-- 69748 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 6016478 spots for /home/okishinya/chipatlas/results/ce10/SRX080094/SRR298914.sra Written 6016478 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: 00:00:59 6016478 reads; of these: 6016478 (100.00%) were unpaired; of these: 1073430 (17.84%) aligned 0 times 4237198 (70.43%) aligned exactly 1 time 705850 (11.73%) aligned >1 times 82.16% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 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] 1120187 / 4943048 = 0.2266 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 11:26:33: # Command line: callpeak -t SRX080094.bam -f BAM -g ce -n SRX080094.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080094.05 # format = BAM # ChIP-seq file = ['SRX080094.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 11:26:33: # Command line: callpeak -t SRX080094.bam -f BAM -g ce -n SRX080094.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080094.20 # format = BAM # ChIP-seq file = ['SRX080094.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 11:26:33: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:26:33: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:26:33: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:26:33: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:26:33: # Command line: callpeak -t SRX080094.bam -f BAM -g ce -n SRX080094.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080094.10 # format = BAM # ChIP-seq file = ['SRX080094.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 11:26:33: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:26:33: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:26:38: 1000000 INFO @ Thu, 30 Apr 2015 11:26:38: 1000000 INFO @ Thu, 30 Apr 2015 11:26:38: 1000000 INFO @ Thu, 30 Apr 2015 11:26:44: 2000000 INFO @ Thu, 30 Apr 2015 11:26:44: 2000000 INFO @ Thu, 30 Apr 2015 11:26:44: 2000000 INFO @ Thu, 30 Apr 2015 11:26:49: 3000000 INFO @ Thu, 30 Apr 2015 11:26:50: 3000000 INFO @ Thu, 30 Apr 2015 11:26:50: 3000000 INFO @ Thu, 30 Apr 2015 11:26:54: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:26:54: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:26:54: #1 total tags in treatment: 3822861 INFO @ Thu, 30 Apr 2015 11:26:54: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:26:54: #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 11:26:54: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:26:54: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:26:54: #1 total tags in treatment: 3822861 INFO @ Thu, 30 Apr 2015 11:26:54: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:26:54: #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 11:26:54: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:26:54: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:26:54: #1 total tags in treatment: 3822861 INFO @ Thu, 30 Apr 2015 11:26:54: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:26:54: #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 11:26:55: #1 tags after filtering in treatment: 3822711 INFO @ Thu, 30 Apr 2015 11:26:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:26:55: #1 finished! INFO @ Thu, 30 Apr 2015 11:26:55: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:26:55: #1 tags after filtering in treatment: 3822711 INFO @ Thu, 30 Apr 2015 11:26:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:26:55: #1 finished! INFO @ Thu, 30 Apr 2015 11:26:55: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:26:55: #1 tags after filtering in treatment: 3822711 INFO @ Thu, 30 Apr 2015 11:26:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:26:55: #1 finished! INFO @ Thu, 30 Apr 2015 11:26:55: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:26:55: #2 number of paired peaks: 1930 INFO @ Thu, 30 Apr 2015 11:26:55: start model_add_line... INFO @ Thu, 30 Apr 2015 11:26:56: #2 number of paired peaks: 1930 INFO @ Thu, 30 Apr 2015 11:26:56: start model_add_line... INFO @ Thu, 30 Apr 2015 11:26:56: #2 number of paired peaks: 1930 INFO @ Thu, 30 Apr 2015 11:26:56: start model_add_line... INFO @ Thu, 30 Apr 2015 11:27:03: start X-correlation... INFO @ Thu, 30 Apr 2015 11:27:03: end of X-cor INFO @ Thu, 30 Apr 2015 11:27:03: #2 finished! INFO @ Thu, 30 Apr 2015 11:27:03: #2 predicted fragment length is 152 bps INFO @ Thu, 30 Apr 2015 11:27:03: #2 alternative fragment length(s) may be 152 bps INFO @ Thu, 30 Apr 2015 11:27:03: #2.2 Generate R script for model : SRX080094.10_model.r INFO @ Thu, 30 Apr 2015 11:27:03: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:27:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:27:03: start X-correlation... INFO @ Thu, 30 Apr 2015 11:27:03: end of X-cor INFO @ Thu, 30 Apr 2015 11:27:03: #2 finished! INFO @ Thu, 30 Apr 2015 11:27:03: #2 predicted fragment length is 152 bps INFO @ Thu, 30 Apr 2015 11:27:03: #2 alternative fragment length(s) may be 152 bps INFO @ Thu, 30 Apr 2015 11:27:03: #2.2 Generate R script for model : SRX080094.20_model.r INFO @ Thu, 30 Apr 2015 11:27:03: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:27:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:27:03: start X-correlation... INFO @ Thu, 30 Apr 2015 11:27:03: end of X-cor INFO @ Thu, 30 Apr 2015 11:27:03: #2 finished! INFO @ Thu, 30 Apr 2015 11:27:03: #2 predicted fragment length is 152 bps INFO @ Thu, 30 Apr 2015 11:27:03: #2 alternative fragment length(s) may be 152 bps INFO @ Thu, 30 Apr 2015 11:27:03: #2.2 Generate R script for model : SRX080094.05_model.r INFO @ Thu, 30 Apr 2015 11:27:03: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:27:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:27:26: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:27:26: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:27:28: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:27:43: #4 Write output xls file... SRX080094.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:27:43: #4 Write peak in narrowPeak format file... SRX080094.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:27:43: #4 Write summits bed file... SRX080094.20_summits.bed INFO @ Thu, 30 Apr 2015 11:27:43: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1964 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:27:45: #4 Write output xls file... SRX080094.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:27:46: #4 Write peak in narrowPeak format file... SRX080094.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:27:46: #4 Write summits bed file... SRX080094.10_summits.bed INFO @ Thu, 30 Apr 2015 11:27:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2974 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:27:48: #4 Write output xls file... SRX080094.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:27:48: #4 Write peak in narrowPeak format file... SRX080094.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:27:48: #4 Write summits bed file... SRX080094.05_summits.bed INFO @ Thu, 30 Apr 2015 11:27:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4239 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。