Job ID = 9037532 sra ファイルのダウンロード中... Completed: 280284K bytes transferred in 6 seconds (328561K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 22318 0 22318 0 0 2887 0 --:--:-- 0:00:07 --:--:-- 15349 100 54318 0 54318 0 0 6225 0 --:--:-- 0:00:08 --:--:-- 22170 100 61070 0 61070 0 0 6998 0 --:--:-- 0:00:08 --:--:-- 24916 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 8744657 spots for /home/okishinya/chipatlas/results/sacCer3/SRX826026/SRR1261247.sra Written 8744657 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: 00:01:36 8744657 reads; of these: 8744657 (100.00%) were unpaired; of these: 2458254 (28.11%) aligned 0 times 4012609 (45.89%) aligned exactly 1 time 2273794 (26.00%) aligned >1 times 71.89% overall alignment rate Time searching: 00:01:36 Overall time: 00:01:36 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] 4851720 / 6286403 = 0.7718 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 04:52:05: # Command line: callpeak -t SRX826026.bam -f BAM -g 12100000 -n SRX826026.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX826026.20 # format = BAM # ChIP-seq file = ['SRX826026.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 04:52:05: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:52:05: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:52:05: # Command line: callpeak -t SRX826026.bam -f BAM -g 12100000 -n SRX826026.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX826026.10 # format = BAM # ChIP-seq file = ['SRX826026.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 04:52:05: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:52:05: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:52:05: # Command line: callpeak -t SRX826026.bam -f BAM -g 12100000 -n SRX826026.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX826026.05 # format = BAM # ChIP-seq file = ['SRX826026.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 04:52:05: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:52:05: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:52:12: 1000000 INFO @ Sun, 04 Jun 2017 04:52:12: 1000000 INFO @ Sun, 04 Jun 2017 04:52:13: 1000000 INFO @ Sun, 04 Jun 2017 04:52:15: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 04:52:15: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 04:52:15: #1 total tags in treatment: 1434683 INFO @ Sun, 04 Jun 2017 04:52:15: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:52:15: #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 04:52:15: #1 tags after filtering in treatment: 1432562 INFO @ Sun, 04 Jun 2017 04:52:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:52:15: #1 finished! INFO @ Sun, 04 Jun 2017 04:52:15: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:52:15: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 04:52:15: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 04:52:15: #1 total tags in treatment: 1434683 INFO @ Sun, 04 Jun 2017 04:52:15: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:52:15: #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 04:52:16: #2 number of paired peaks: 116 WARNING @ Sun, 04 Jun 2017 04:52:16: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sun, 04 Jun 2017 04:52:16: start model_add_line... INFO @ Sun, 04 Jun 2017 04:52:16: #1 tags after filtering in treatment: 1432562 INFO @ Sun, 04 Jun 2017 04:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:52:16: #1 finished! INFO @ Sun, 04 Jun 2017 04:52:16: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:52:16: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 04:52:16: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 04:52:16: #1 total tags in treatment: 1434683 INFO @ Sun, 04 Jun 2017 04:52:16: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:52:16: #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 04:52:16: #2 number of paired peaks: 116 WARNING @ Sun, 04 Jun 2017 04:52:16: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sun, 04 Jun 2017 04:52:16: start model_add_line... INFO @ Sun, 04 Jun 2017 04:52:16: #1 tags after filtering in treatment: 1432562 INFO @ Sun, 04 Jun 2017 04:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:52:16: #1 finished! INFO @ Sun, 04 Jun 2017 04:52:16: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:52:17: #2 number of paired peaks: 116 WARNING @ Sun, 04 Jun 2017 04:52:17: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sun, 04 Jun 2017 04:52:17: start model_add_line... INFO @ Sun, 04 Jun 2017 04:52:17: start X-correlation... INFO @ Sun, 04 Jun 2017 04:52:17: end of X-cor INFO @ Sun, 04 Jun 2017 04:52:17: #2 finished! INFO @ Sun, 04 Jun 2017 04:52:17: #2 predicted fragment length is 120 bps INFO @ Sun, 04 Jun 2017 04:52:17: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sun, 04 Jun 2017 04:52:17: #2.2 Generate R script for model : SRX826026.10_model.r INFO @ Sun, 04 Jun 2017 04:52:17: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:52:18: start X-correlation... INFO @ Sun, 04 Jun 2017 04:52:18: end of X-cor INFO @ Sun, 04 Jun 2017 04:52:18: #2 finished! INFO @ Sun, 04 Jun 2017 04:52:18: #2 predicted fragment length is 120 bps INFO @ Sun, 04 Jun 2017 04:52:18: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sun, 04 Jun 2017 04:52:18: #2.2 Generate R script for model : SRX826026.05_model.r INFO @ Sun, 04 Jun 2017 04:52:18: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:52:18: start X-correlation... INFO @ Sun, 04 Jun 2017 04:52:18: end of X-cor INFO @ Sun, 04 Jun 2017 04:52:18: #2 finished! INFO @ Sun, 04 Jun 2017 04:52:18: #2 predicted fragment length is 120 bps INFO @ Sun, 04 Jun 2017 04:52:18: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sun, 04 Jun 2017 04:52:18: #2.2 Generate R script for model : SRX826026.20_model.r INFO @ Sun, 04 Jun 2017 04:52:18: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:52:26: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:52:26: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:52:27: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:52:32: #4 Write output xls file... SRX826026.10_peaks.xls INFO @ Sun, 04 Jun 2017 04:52:32: #4 Write peak in narrowPeak format file... SRX826026.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:52:32: #4 Write summits bed file... SRX826026.10_summits.bed INFO @ Sun, 04 Jun 2017 04:52:32: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (339 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 04:52:32: #4 Write output xls file... SRX826026.05_peaks.xls INFO @ Sun, 04 Jun 2017 04:52:32: #4 Write peak in narrowPeak format file... SRX826026.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:52:32: #4 Write summits bed file... SRX826026.05_summits.bed INFO @ Sun, 04 Jun 2017 04:52:32: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (613 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 04:52:33: #4 Write output xls file... SRX826026.20_peaks.xls INFO @ Sun, 04 Jun 2017 04:52:33: #4 Write peak in narrowPeak format file... SRX826026.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:52:33: #4 Write summits bed file... SRX826026.20_summits.bed INFO @ Sun, 04 Jun 2017 04:52:33: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (172 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。