Job ID = 9036421 sra ファイルのダウンロード中... Completed: 308385K bytes transferred in 6 seconds (415331K 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 7663 0 7663 0 0 1051 0 --:--:-- 0:00:07 --:--:-- 8639 100 38317 0 38317 0 0 4626 0 --:--:-- 0:00:08 --:--:-- 20338 100 46051 0 46051 0 0 5451 0 --:--:-- 0:00:08 --:--:-- 22474 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 10250674 spots for /home/okishinya/chipatlas/results/sacCer3/SRX211432/SRR636683.sra Written 10250674 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: 00:01:50 10250674 reads; of these: 10250674 (100.00%) were unpaired; of these: 1780903 (17.37%) aligned 0 times 7512689 (73.29%) aligned exactly 1 time 957082 (9.34%) aligned >1 times 82.63% overall alignment rate Time searching: 00:01:50 Overall time: 00:01:50 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] 5702505 / 8469771 = 0.6733 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 03:08:15: # Command line: callpeak -t SRX211432.bam -f BAM -g 12100000 -n SRX211432.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX211432.10 # format = BAM # ChIP-seq file = ['SRX211432.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 03:08:15: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:08:15: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:08:15: # Command line: callpeak -t SRX211432.bam -f BAM -g 12100000 -n SRX211432.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX211432.05 # format = BAM # ChIP-seq file = ['SRX211432.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 03:08:15: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:08:15: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:08:15: # Command line: callpeak -t SRX211432.bam -f BAM -g 12100000 -n SRX211432.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX211432.20 # format = BAM # ChIP-seq file = ['SRX211432.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 03:08:15: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:08:15: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:08:20: 1000000 INFO @ Sun, 04 Jun 2017 03:08:20: 1000000 INFO @ Sun, 04 Jun 2017 03:08:20: 1000000 INFO @ Sun, 04 Jun 2017 03:08:25: 2000000 INFO @ Sun, 04 Jun 2017 03:08:25: 2000000 INFO @ Sun, 04 Jun 2017 03:08:25: 2000000 INFO @ Sun, 04 Jun 2017 03:08:28: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:08:28: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:08:28: #1 total tags in treatment: 2767266 INFO @ Sun, 04 Jun 2017 03:08:28: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:08:28: #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 03:08:29: #1 tags after filtering in treatment: 2765952 INFO @ Sun, 04 Jun 2017 03:08:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:08:29: #1 finished! INFO @ Sun, 04 Jun 2017 03:08:29: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:08:29: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:08:29: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:08:29: #1 total tags in treatment: 2767266 INFO @ Sun, 04 Jun 2017 03:08:29: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:08:29: #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 03:08:29: #2 number of paired peaks: 184 WARNING @ Sun, 04 Jun 2017 03:08:29: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Sun, 04 Jun 2017 03:08:29: start model_add_line... INFO @ Sun, 04 Jun 2017 03:08:30: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:08:30: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:08:30: #1 total tags in treatment: 2767266 INFO @ Sun, 04 Jun 2017 03:08:30: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:08:30: #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 03:08:30: #1 tags after filtering in treatment: 2765952 INFO @ Sun, 04 Jun 2017 03:08:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:08:30: #1 finished! INFO @ Sun, 04 Jun 2017 03:08:30: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:08:30: #1 tags after filtering in treatment: 2765952 INFO @ Sun, 04 Jun 2017 03:08:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:08:30: #1 finished! INFO @ Sun, 04 Jun 2017 03:08:30: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:08:30: #2 number of paired peaks: 184 WARNING @ Sun, 04 Jun 2017 03:08:30: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Sun, 04 Jun 2017 03:08:30: start model_add_line... INFO @ Sun, 04 Jun 2017 03:08:31: #2 number of paired peaks: 184 WARNING @ Sun, 04 Jun 2017 03:08:31: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Sun, 04 Jun 2017 03:08:31: start model_add_line... INFO @ Sun, 04 Jun 2017 03:08:32: start X-correlation... INFO @ Sun, 04 Jun 2017 03:08:32: end of X-cor INFO @ Sun, 04 Jun 2017 03:08:32: #2 finished! INFO @ Sun, 04 Jun 2017 03:08:32: #2 predicted fragment length is 134 bps INFO @ Sun, 04 Jun 2017 03:08:32: #2 alternative fragment length(s) may be 1,85,134,148,172,211,274,338,374,398,482,496,535,553,568 bps INFO @ Sun, 04 Jun 2017 03:08:32: #2.2 Generate R script for model : SRX211432.10_model.r INFO @ Sun, 04 Jun 2017 03:08:32: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:08:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:08:33: start X-correlation... INFO @ Sun, 04 Jun 2017 03:08:33: end of X-cor INFO @ Sun, 04 Jun 2017 03:08:33: #2 finished! INFO @ Sun, 04 Jun 2017 03:08:33: #2 predicted fragment length is 134 bps INFO @ Sun, 04 Jun 2017 03:08:33: #2 alternative fragment length(s) may be 1,85,134,148,172,211,274,338,374,398,482,496,535,553,568 bps INFO @ Sun, 04 Jun 2017 03:08:33: #2.2 Generate R script for model : SRX211432.05_model.r INFO @ Sun, 04 Jun 2017 03:08:33: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:08:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:08:34: start X-correlation... INFO @ Sun, 04 Jun 2017 03:08:34: end of X-cor INFO @ Sun, 04 Jun 2017 03:08:34: #2 finished! INFO @ Sun, 04 Jun 2017 03:08:34: #2 predicted fragment length is 134 bps INFO @ Sun, 04 Jun 2017 03:08:34: #2 alternative fragment length(s) may be 1,85,134,148,172,211,274,338,374,398,482,496,535,553,568 bps INFO @ Sun, 04 Jun 2017 03:08:34: #2.2 Generate R script for model : SRX211432.20_model.r INFO @ Sun, 04 Jun 2017 03:08:34: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:08:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:08:45: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:08:47: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:08:48: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:08:54: #4 Write output xls file... SRX211432.10_peaks.xls INFO @ Sun, 04 Jun 2017 03:08:54: #4 Write peak in narrowPeak format file... SRX211432.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:08:54: #4 Write summits bed file... SRX211432.10_summits.bed INFO @ Sun, 04 Jun 2017 03:08:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:08:55: #4 Write output xls file... SRX211432.05_peaks.xls INFO @ Sun, 04 Jun 2017 03:08:55: #4 Write peak in narrowPeak format file... SRX211432.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:08:55: #4 Write summits bed file... SRX211432.05_summits.bed INFO @ Sun, 04 Jun 2017 03:08:55: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (66 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:08:56: #4 Write output xls file... SRX211432.20_peaks.xls INFO @ Sun, 04 Jun 2017 03:08:56: #4 Write peak in narrowPeak format file... SRX211432.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:08:56: #4 Write summits bed file... SRX211432.20_summits.bed INFO @ Sun, 04 Jun 2017 03:08:56: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (8 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。