Job ID = 2161251 sra ファイルのダウンロード中... Completed: 125866K bytes transferred in 4 seconds (236735K 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 --:--:-- --:--:-- --:--:-- 0 101 5467 0 5467 0 0 10520 0 --:--:-- --:--:-- --:--:-- 16617 100 34786 0 34786 0 0 49001 0 --:--:-- --:--:-- --:--:-- 67025 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 4509098 spots for /home/okishinya/chipatlas/results/dm3/SRX013095/SRR030361.sra Written 4509098 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: 00:01:21 4509098 reads; of these: 4509098 (100.00%) were unpaired; of these: 1139248 (25.27%) aligned 0 times 1983508 (43.99%) aligned exactly 1 time 1386342 (30.75%) aligned >1 times 74.73% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 203779 / 3369850 = 0.0605 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 @ Tue, 21 Apr 2015 12:09:32: # Command line: callpeak -t SRX013095.bam -f BAM -g dm -n SRX013095.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013095.05 # format = BAM # ChIP-seq file = ['SRX013095.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 12:09:32: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:32: # Command line: callpeak -t SRX013095.bam -f BAM -g dm -n SRX013095.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013095.20 # format = BAM # ChIP-seq file = ['SRX013095.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 12:09:32: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:32: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:32: # Command line: callpeak -t SRX013095.bam -f BAM -g dm -n SRX013095.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013095.10 # format = BAM # ChIP-seq file = ['SRX013095.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 12:09:32: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:32: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:32: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:37: 1000000 INFO @ Tue, 21 Apr 2015 12:09:37: 1000000 INFO @ Tue, 21 Apr 2015 12:09:37: 1000000 INFO @ Tue, 21 Apr 2015 12:09:43: 2000000 INFO @ Tue, 21 Apr 2015 12:09:43: 2000000 INFO @ Tue, 21 Apr 2015 12:09:43: 2000000 INFO @ Tue, 21 Apr 2015 12:09:48: 3000000 INFO @ Tue, 21 Apr 2015 12:09:48: 3000000 INFO @ Tue, 21 Apr 2015 12:09:49: 3000000 INFO @ Tue, 21 Apr 2015 12:09:49: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:49: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:49: #1 total tags in treatment: 3166071 INFO @ Tue, 21 Apr 2015 12:09:49: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:09:49: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:49: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:49: #1 total tags in treatment: 3166071 INFO @ Tue, 21 Apr 2015 12:09:49: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:09:50: #1 tags after filtering in treatment: 3165672 INFO @ Tue, 21 Apr 2015 12:09:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:50: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:50: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:50: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:50: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:50: #1 total tags in treatment: 3166071 INFO @ Tue, 21 Apr 2015 12:09:50: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:09:50: #1 tags after filtering in treatment: 3165672 INFO @ Tue, 21 Apr 2015 12:09:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:50: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:50: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:50: #2 number of paired peaks: 144 WARNING @ Tue, 21 Apr 2015 12:09:50: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 21 Apr 2015 12:09:50: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:50: #1 tags after filtering in treatment: 3165672 INFO @ Tue, 21 Apr 2015 12:09:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:50: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:50: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:50: #2 number of paired peaks: 144 WARNING @ Tue, 21 Apr 2015 12:09:50: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 21 Apr 2015 12:09:50: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:51: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:51: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:51: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:51: #2 predicted fragment length is 79 bps INFO @ Tue, 21 Apr 2015 12:09:51: #2 alternative fragment length(s) may be 79,558 bps INFO @ Tue, 21 Apr 2015 12:09:51: #2.2 Generate R script for model : SRX013095.05_model.r INFO @ Tue, 21 Apr 2015 12:09:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:51: #2 number of paired peaks: 144 WARNING @ Tue, 21 Apr 2015 12:09:51: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 21 Apr 2015 12:09:51: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:51: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:51: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:51: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:51: #2 predicted fragment length is 79 bps INFO @ Tue, 21 Apr 2015 12:09:51: #2 alternative fragment length(s) may be 79,558 bps INFO @ Tue, 21 Apr 2015 12:09:51: #2.2 Generate R script for model : SRX013095.10_model.r INFO @ Tue, 21 Apr 2015 12:09:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:51: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:51: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:51: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:51: #2 predicted fragment length is 79 bps INFO @ Tue, 21 Apr 2015 12:09:51: #2 alternative fragment length(s) may be 79,558 bps INFO @ Tue, 21 Apr 2015 12:09:51: #2.2 Generate R script for model : SRX013095.20_model.r INFO @ Tue, 21 Apr 2015 12:09:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:10:08: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:21: #4 Write output xls file... SRX013095.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:21: #4 Write peak in narrowPeak format file... SRX013095.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:21: #4 Write summits bed file... SRX013095.10_summits.bed INFO @ Tue, 21 Apr 2015 12:10:21: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (471 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:10:24: #4 Write output xls file... SRX013095.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:24: #4 Write peak in narrowPeak format file... SRX013095.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:24: #4 Write summits bed file... SRX013095.05_summits.bed INFO @ Tue, 21 Apr 2015 12:10:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (897 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:10:24: #4 Write output xls file... SRX013095.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:24: #4 Write peak in narrowPeak format file... SRX013095.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:24: #4 Write summits bed file... SRX013095.20_summits.bed INFO @ Tue, 21 Apr 2015 12:10:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (294 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。