Job ID = 9037533 sra ファイルのダウンロード中... Completed: 176752K bytes transferred in 6 seconds (236590K 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 18662 0 18662 0 0 2439 0 --:--:-- 0:00:07 --:--:-- 14858 100 44038 0 44038 0 0 5092 0 --:--:-- 0:00:08 --:--:-- 19546 100 75050 0 75050 0 0 8204 0 --:--:-- 0:00:09 --:--:-- 27271 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 5608885 spots for /home/okishinya/chipatlas/results/sacCer3/SRX826027/SRR1261334.sra Written 5608885 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: 00:00:49 5608885 reads; of these: 5608885 (100.00%) were unpaired; of these: 1592628 (28.39%) aligned 0 times 1985552 (35.40%) aligned exactly 1 time 2030705 (36.21%) aligned >1 times 71.61% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 2462402 / 4016257 = 0.6131 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 04:50:43: # Command line: callpeak -t SRX826027.bam -f BAM -g 12100000 -n SRX826027.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX826027.20 # format = BAM # ChIP-seq file = ['SRX826027.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 04:50:43: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:50:43: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:50:43: # Command line: callpeak -t SRX826027.bam -f BAM -g 12100000 -n SRX826027.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX826027.05 # format = BAM # ChIP-seq file = ['SRX826027.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 04:50:43: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:50:43: # Command line: callpeak -t SRX826027.bam -f BAM -g 12100000 -n SRX826027.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX826027.10 # format = BAM # ChIP-seq file = ['SRX826027.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 04:50:43: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:50:43: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:50:43: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:50:49: 1000000 INFO @ Sun, 04 Jun 2017 04:50:49: 1000000 INFO @ Sun, 04 Jun 2017 04:50:49: 1000000 INFO @ Sun, 04 Jun 2017 04:50:52: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 04:50:52: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 04:50:52: #1 total tags in treatment: 1553855 INFO @ Sun, 04 Jun 2017 04:50:52: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:50:52: #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 04:50:52: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 04:50:52: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 04:50:52: #1 total tags in treatment: 1553855 INFO @ Sun, 04 Jun 2017 04:50:52: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:50:52: #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 04:50:52: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 04:50:52: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 04:50:52: #1 total tags in treatment: 1553855 INFO @ Sun, 04 Jun 2017 04:50:52: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:50:52: #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 04:50:52: #1 tags after filtering in treatment: 1552808 INFO @ Sun, 04 Jun 2017 04:50:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:50:52: #1 finished! INFO @ Sun, 04 Jun 2017 04:50:52: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:50:52: #1 tags after filtering in treatment: 1552808 INFO @ Sun, 04 Jun 2017 04:50:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:50:52: #1 finished! INFO @ Sun, 04 Jun 2017 04:50:52: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:50:52: #1 tags after filtering in treatment: 1552808 INFO @ Sun, 04 Jun 2017 04:50:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:50:52: #1 finished! INFO @ Sun, 04 Jun 2017 04:50:52: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:50:52: #2 number of paired peaks: 251 WARNING @ Sun, 04 Jun 2017 04:50:52: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Sun, 04 Jun 2017 04:50:52: start model_add_line... INFO @ Sun, 04 Jun 2017 04:50:52: #2 number of paired peaks: 251 WARNING @ Sun, 04 Jun 2017 04:50:52: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Sun, 04 Jun 2017 04:50:52: start model_add_line... INFO @ Sun, 04 Jun 2017 04:50:52: #2 number of paired peaks: 251 WARNING @ Sun, 04 Jun 2017 04:50:52: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Sun, 04 Jun 2017 04:50:52: start model_add_line... INFO @ Sun, 04 Jun 2017 04:50:55: start X-correlation... INFO @ Sun, 04 Jun 2017 04:50:55: end of X-cor INFO @ Sun, 04 Jun 2017 04:50:55: #2 finished! INFO @ Sun, 04 Jun 2017 04:50:55: #2 predicted fragment length is 214 bps INFO @ Sun, 04 Jun 2017 04:50:55: #2 alternative fragment length(s) may be 214 bps INFO @ Sun, 04 Jun 2017 04:50:55: #2.2 Generate R script for model : SRX826027.10_model.r INFO @ Sun, 04 Jun 2017 04:50:55: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:50:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:50:55: start X-correlation... INFO @ Sun, 04 Jun 2017 04:50:55: end of X-cor INFO @ Sun, 04 Jun 2017 04:50:55: #2 finished! INFO @ Sun, 04 Jun 2017 04:50:55: #2 predicted fragment length is 214 bps INFO @ Sun, 04 Jun 2017 04:50:55: #2 alternative fragment length(s) may be 214 bps INFO @ Sun, 04 Jun 2017 04:50:55: #2.2 Generate R script for model : SRX826027.05_model.r INFO @ Sun, 04 Jun 2017 04:50:55: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:50:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:50:55: start X-correlation... INFO @ Sun, 04 Jun 2017 04:50:55: end of X-cor INFO @ Sun, 04 Jun 2017 04:50:55: #2 finished! INFO @ Sun, 04 Jun 2017 04:50:55: #2 predicted fragment length is 214 bps INFO @ Sun, 04 Jun 2017 04:50:55: #2 alternative fragment length(s) may be 214 bps INFO @ Sun, 04 Jun 2017 04:50:55: #2.2 Generate R script for model : SRX826027.20_model.r INFO @ Sun, 04 Jun 2017 04:50:55: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:50:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:51:05: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:51:05: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:51:06: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:51:12: #4 Write output xls file... SRX826027.10_peaks.xls INFO @ Sun, 04 Jun 2017 04:51:12: #4 Write peak in narrowPeak format file... SRX826027.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:51:12: #4 Write summits bed file... SRX826027.10_summits.bed INFO @ Sun, 04 Jun 2017 04:51:12: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (514 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 04:51:12: #4 Write output xls file... SRX826027.20_peaks.xls INFO @ Sun, 04 Jun 2017 04:51:12: #4 Write peak in narrowPeak format file... SRX826027.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:51:12: #4 Write summits bed file... SRX826027.20_summits.bed INFO @ Sun, 04 Jun 2017 04:51:12: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (395 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 04:51:12: #4 Write output xls file... SRX826027.05_peaks.xls INFO @ Sun, 04 Jun 2017 04:51:12: #4 Write peak in narrowPeak format file... SRX826027.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:51:12: #4 Write summits bed file... SRX826027.05_summits.bed INFO @ Sun, 04 Jun 2017 04:51:12: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (677 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。