Job ID = 9036524 sra ファイルのダウンロード中... Completed: 193869K bytes transferred in 4 seconds (327264K 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 --:--:-- 0:00:06 --:--:-- 0 100 6903 0 6903 0 0 961 0 --:--:-- 0:00:07 --:--:-- 8575 100 24454 0 24454 0 0 3052 0 --:--:-- 0:00:08 --:--:-- 14965 100 64380 0 64380 0 0 7280 0 --:--:-- 0:00:08 --:--:-- 26128 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 7971910 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2557350/SRR5251632.sra Written 7971910 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: 00:01:14 7971910 reads; of these: 7971910 (100.00%) were unpaired; of these: 840114 (10.54%) aligned 0 times 4791316 (60.10%) aligned exactly 1 time 2340480 (29.36%) aligned >1 times 89.46% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 4692805 / 7131796 = 0.6580 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 @ Sun, 04 Jun 2017 03:21:20: # Command line: callpeak -t SRX2557350.bam -f BAM -g 12100000 -n SRX2557350.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2557350.05 # format = BAM # ChIP-seq file = ['SRX2557350.bam'] # control file = None # effective genome size = 1.21e+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 @ Sun, 04 Jun 2017 03:21:20: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:21:20: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:21:20: # Command line: callpeak -t SRX2557350.bam -f BAM -g 12100000 -n SRX2557350.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2557350.20 # format = BAM # ChIP-seq file = ['SRX2557350.bam'] # control file = None # effective genome size = 1.21e+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 @ Sun, 04 Jun 2017 03:21:20: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:21:20: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:21:20: # Command line: callpeak -t SRX2557350.bam -f BAM -g 12100000 -n SRX2557350.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2557350.10 # format = BAM # ChIP-seq file = ['SRX2557350.bam'] # control file = None # effective genome size = 1.21e+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 @ Sun, 04 Jun 2017 03:21:20: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:21:20: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:21:26: 1000000 INFO @ Sun, 04 Jun 2017 03:21:26: 1000000 INFO @ Sun, 04 Jun 2017 03:21:26: 1000000 INFO @ Sun, 04 Jun 2017 03:21:31: 2000000 INFO @ Sun, 04 Jun 2017 03:21:31: 2000000 INFO @ Sun, 04 Jun 2017 03:21:32: 2000000 INFO @ Sun, 04 Jun 2017 03:21:34: #1 tag size is determined as 39 bps INFO @ Sun, 04 Jun 2017 03:21:34: #1 tag size = 39 INFO @ Sun, 04 Jun 2017 03:21:34: #1 total tags in treatment: 2438991 INFO @ Sun, 04 Jun 2017 03:21:34: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:21:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 03:21:34: #1 tag size is determined as 39 bps INFO @ Sun, 04 Jun 2017 03:21:34: #1 tag size = 39 INFO @ Sun, 04 Jun 2017 03:21:34: #1 total tags in treatment: 2438991 INFO @ Sun, 04 Jun 2017 03:21:34: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:21:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 03:21:34: #1 tag size is determined as 39 bps INFO @ Sun, 04 Jun 2017 03:21:34: #1 tag size = 39 INFO @ Sun, 04 Jun 2017 03:21:34: #1 total tags in treatment: 2438991 INFO @ Sun, 04 Jun 2017 03:21:34: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:21:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 03:21:34: #1 tags after filtering in treatment: 2438228 INFO @ Sun, 04 Jun 2017 03:21:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:21:34: #1 finished! INFO @ Sun, 04 Jun 2017 03:21:34: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:21:34: #1 tags after filtering in treatment: 2438228 INFO @ Sun, 04 Jun 2017 03:21:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:21:34: #1 finished! INFO @ Sun, 04 Jun 2017 03:21:34: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:21:34: #1 tags after filtering in treatment: 2438228 INFO @ Sun, 04 Jun 2017 03:21:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:21:34: #1 finished! INFO @ Sun, 04 Jun 2017 03:21:34: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:21:35: #2 number of paired peaks: 114 WARNING @ Sun, 04 Jun 2017 03:21:35: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Sun, 04 Jun 2017 03:21:35: start model_add_line... INFO @ Sun, 04 Jun 2017 03:21:35: #2 number of paired peaks: 114 WARNING @ Sun, 04 Jun 2017 03:21:35: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Sun, 04 Jun 2017 03:21:35: start model_add_line... INFO @ Sun, 04 Jun 2017 03:21:35: #2 number of paired peaks: 114 WARNING @ Sun, 04 Jun 2017 03:21:35: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Sun, 04 Jun 2017 03:21:35: start model_add_line... INFO @ Sun, 04 Jun 2017 03:21:36: start X-correlation... INFO @ Sun, 04 Jun 2017 03:21:36: end of X-cor INFO @ Sun, 04 Jun 2017 03:21:36: #2 finished! INFO @ Sun, 04 Jun 2017 03:21:36: #2 predicted fragment length is 153 bps INFO @ Sun, 04 Jun 2017 03:21:36: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 04 Jun 2017 03:21:36: #2.2 Generate R script for model : SRX2557350.20_model.r INFO @ Sun, 04 Jun 2017 03:21:36: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:21:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:21:36: start X-correlation... INFO @ Sun, 04 Jun 2017 03:21:36: end of X-cor INFO @ Sun, 04 Jun 2017 03:21:36: #2 finished! INFO @ Sun, 04 Jun 2017 03:21:36: #2 predicted fragment length is 153 bps INFO @ Sun, 04 Jun 2017 03:21:36: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 04 Jun 2017 03:21:36: #2.2 Generate R script for model : SRX2557350.10_model.r INFO @ Sun, 04 Jun 2017 03:21:36: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:21:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:21:37: start X-correlation... INFO @ Sun, 04 Jun 2017 03:21:37: end of X-cor INFO @ Sun, 04 Jun 2017 03:21:37: #2 finished! INFO @ Sun, 04 Jun 2017 03:21:37: #2 predicted fragment length is 153 bps INFO @ Sun, 04 Jun 2017 03:21:37: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 04 Jun 2017 03:21:37: #2.2 Generate R script for model : SRX2557350.05_model.r INFO @ Sun, 04 Jun 2017 03:21:37: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:21:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:21:50: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:21:50: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:21:50: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:21:59: #4 Write output xls file... SRX2557350.20_peaks.xls INFO @ Sun, 04 Jun 2017 03:21:59: #4 Write peak in narrowPeak format file... SRX2557350.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:21:59: #4 Write summits bed file... SRX2557350.20_summits.bed INFO @ Sun, 04 Jun 2017 03:21:59: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (678 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:22:00: #4 Write output xls file... SRX2557350.10_peaks.xls INFO @ Sun, 04 Jun 2017 03:22:00: #4 Write peak in narrowPeak format file... SRX2557350.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:22:00: #4 Write summits bed file... SRX2557350.10_summits.bed INFO @ Sun, 04 Jun 2017 03:22:00: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1011 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:22:01: #4 Write output xls file... SRX2557350.05_peaks.xls INFO @ Sun, 04 Jun 2017 03:22:01: #4 Write peak in narrowPeak format file... SRX2557350.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:22:01: #4 Write summits bed file... SRX2557350.05_summits.bed INFO @ Sun, 04 Jun 2017 03:22:01: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1489 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。