Job ID = 9037534 sra ファイルのダウンロード中... Completed: 163959K bytes transferred in 4 seconds (271664K 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 1087 0 --:--:-- 0:00:07 --:--:-- 10978 100 30318 0 30318 0 0 3848 0 --:--:-- 0:00:07 --:--:-- 19828 100 62274 0 62274 0 0 7434 0 --:--:-- 0:00:08 --:--:-- 30737 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 4870180 spots for /home/okishinya/chipatlas/results/sacCer3/SRX826028/SRR1261339.sra Written 4870180 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: 00:00:45 4870180 reads; of these: 4870180 (100.00%) were unpaired; of these: 1321573 (27.14%) aligned 0 times 3005531 (61.71%) aligned exactly 1 time 543076 (11.15%) aligned >1 times 72.86% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 2078799 / 3548607 = 0.5858 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 04:50:44: # Command line: callpeak -t SRX826028.bam -f BAM -g 12100000 -n SRX826028.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX826028.05 # format = BAM # ChIP-seq file = ['SRX826028.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 04:50:44: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:50:44: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:50:44: # Command line: callpeak -t SRX826028.bam -f BAM -g 12100000 -n SRX826028.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX826028.20 # format = BAM # ChIP-seq file = ['SRX826028.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 04:50:44: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:50:44: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:50:44: # Command line: callpeak -t SRX826028.bam -f BAM -g 12100000 -n SRX826028.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX826028.10 # format = BAM # ChIP-seq file = ['SRX826028.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 04:50:44: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:50:44: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:50:51: 1000000 INFO @ Sun, 04 Jun 2017 04:50:52: 1000000 INFO @ Sun, 04 Jun 2017 04:50:52: 1000000 INFO @ Sun, 04 Jun 2017 04:50:54: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 04:50:54: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 04:50:54: #1 total tags in treatment: 1469808 INFO @ Sun, 04 Jun 2017 04:50:54: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:50:54: #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 04:50:54: #1 tags after filtering in treatment: 1468680 INFO @ Sun, 04 Jun 2017 04:50:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:50:54: #1 finished! INFO @ Sun, 04 Jun 2017 04:50:54: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:50:55: #2 number of paired peaks: 703 WARNING @ Sun, 04 Jun 2017 04:50:55: Fewer paired peaks (703) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 703 pairs to build model! INFO @ Sun, 04 Jun 2017 04:50:55: start model_add_line... INFO @ Sun, 04 Jun 2017 04:50:55: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 04:50:55: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 04:50:55: #1 total tags in treatment: 1469808 INFO @ Sun, 04 Jun 2017 04:50:55: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:50:55: #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 04:50:55: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 04:50:55: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 04:50:55: #1 total tags in treatment: 1469808 INFO @ Sun, 04 Jun 2017 04:50:55: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:50:55: #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 04:50:56: #1 tags after filtering in treatment: 1468680 INFO @ Sun, 04 Jun 2017 04:50:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:50:56: #1 finished! INFO @ Sun, 04 Jun 2017 04:50:56: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:50:56: #1 tags after filtering in treatment: 1468680 INFO @ Sun, 04 Jun 2017 04:50:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:50:56: #1 finished! INFO @ Sun, 04 Jun 2017 04:50:56: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:50:56: #2 number of paired peaks: 703 WARNING @ Sun, 04 Jun 2017 04:50:56: Fewer paired peaks (703) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 703 pairs to build model! INFO @ Sun, 04 Jun 2017 04:50:56: start model_add_line... INFO @ Sun, 04 Jun 2017 04:50:56: #2 number of paired peaks: 703 WARNING @ Sun, 04 Jun 2017 04:50:56: Fewer paired peaks (703) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 703 pairs to build model! INFO @ Sun, 04 Jun 2017 04:50:56: start model_add_line... INFO @ Sun, 04 Jun 2017 04:51:02: start X-correlation... INFO @ Sun, 04 Jun 2017 04:51:02: end of X-cor INFO @ Sun, 04 Jun 2017 04:51:02: #2 finished! INFO @ Sun, 04 Jun 2017 04:51:02: #2 predicted fragment length is 253 bps INFO @ Sun, 04 Jun 2017 04:51:02: #2 alternative fragment length(s) may be 3,253 bps INFO @ Sun, 04 Jun 2017 04:51:02: #2.2 Generate R script for model : SRX826028.05_model.r INFO @ Sun, 04 Jun 2017 04:51:02: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:51:03: start X-correlation... INFO @ Sun, 04 Jun 2017 04:51:03: end of X-cor INFO @ Sun, 04 Jun 2017 04:51:03: #2 finished! INFO @ Sun, 04 Jun 2017 04:51:03: #2 predicted fragment length is 253 bps INFO @ Sun, 04 Jun 2017 04:51:03: #2 alternative fragment length(s) may be 3,253 bps INFO @ Sun, 04 Jun 2017 04:51:03: #2.2 Generate R script for model : SRX826028.20_model.r INFO @ Sun, 04 Jun 2017 04:51:03: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:51:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:51:03: start X-correlation... INFO @ Sun, 04 Jun 2017 04:51:03: end of X-cor INFO @ Sun, 04 Jun 2017 04:51:03: #2 finished! INFO @ Sun, 04 Jun 2017 04:51:03: #2 predicted fragment length is 253 bps INFO @ Sun, 04 Jun 2017 04:51:03: #2 alternative fragment length(s) may be 3,253 bps INFO @ Sun, 04 Jun 2017 04:51:03: #2.2 Generate R script for model : SRX826028.10_model.r INFO @ Sun, 04 Jun 2017 04:51:03: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:51:03: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 04 Jun 2017 04:51:18: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:51:19: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:51:20: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:51:23: #4 Write output xls file... SRX826028.20_peaks.xls INFO @ Sun, 04 Jun 2017 04:51:23: #4 Write peak in narrowPeak format file... SRX826028.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:51:23: #4 Write summits bed file... SRX826028.20_summits.bed INFO @ Sun, 04 Jun 2017 04:51:23: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (31 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 04:51:24: #4 Write output xls file... SRX826028.10_peaks.xls INFO @ Sun, 04 Jun 2017 04:51:24: #4 Write peak in narrowPeak format file... SRX826028.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:51:24: #4 Write summits bed file... SRX826028.10_summits.bed INFO @ Sun, 04 Jun 2017 04:51:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 04:51:24: #4 Write output xls file... SRX826028.05_peaks.xls INFO @ Sun, 04 Jun 2017 04:51:24: #4 Write peak in narrowPeak format file... SRX826028.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:51:24: #4 Write summits bed file... SRX826028.05_summits.bed INFO @ Sun, 04 Jun 2017 04:51:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (390 records, 4 fields): 2 millis CompletedMACS2peakCalling