Job ID = 2161328 sra ファイルのダウンロード中... Completed: 147690K bytes transferred in 5 seconds (237841K 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 --:--:-- --:--:-- --:--:-- 0 100 14916 0 14916 0 0 20043 0 --:--:-- --:--:-- --:--:-- 27070 100 36881 0 36881 0 0 49493 0 --:--:-- --:--:-- --:--:-- 66934 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 6602045 spots for /home/okishinya/chipatlas/results/dm3/SRX017857/SRR038293.sra Written 6602045 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 6602045 reads; of these: 6602045 (100.00%) were unpaired; of these: 5184585 (78.53%) aligned 0 times 1003131 (15.19%) aligned exactly 1 time 414329 (6.28%) aligned >1 times 21.47% 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: 15 sequences. [bam_rmdupse_core] 66869 / 1417460 = 0.0472 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 12:23:39: # Command line: callpeak -t SRX017857.bam -f BAM -g dm -n SRX017857.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX017857.10 # format = BAM # ChIP-seq file = ['SRX017857.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 12:23:39: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:23:39: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:23:39: # Command line: callpeak -t SRX017857.bam -f BAM -g dm -n SRX017857.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX017857.20 # format = BAM # ChIP-seq file = ['SRX017857.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 12:23:39: # Command line: callpeak -t SRX017857.bam -f BAM -g dm -n SRX017857.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX017857.05 # format = BAM # ChIP-seq file = ['SRX017857.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 12:23:39: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:23:39: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:23:39: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:23:39: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:23:44: 1000000 INFO @ Tue, 21 Apr 2015 12:23:44: 1000000 INFO @ Tue, 21 Apr 2015 12:23:44: 1000000 INFO @ Tue, 21 Apr 2015 12:23:46: #1 tag size is determined as 25 bps INFO @ Tue, 21 Apr 2015 12:23:46: #1 tag size = 25 INFO @ Tue, 21 Apr 2015 12:23:46: #1 total tags in treatment: 1350591 INFO @ Tue, 21 Apr 2015 12:23:46: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:23:46: #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 12:23:46: #1 tag size is determined as 25 bps INFO @ Tue, 21 Apr 2015 12:23:46: #1 tag size = 25 INFO @ Tue, 21 Apr 2015 12:23:46: #1 total tags in treatment: 1350591 INFO @ Tue, 21 Apr 2015 12:23:46: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:23:46: #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 12:23:46: #1 tag size is determined as 25 bps INFO @ Tue, 21 Apr 2015 12:23:46: #1 tag size = 25 INFO @ Tue, 21 Apr 2015 12:23:46: #1 total tags in treatment: 1350591 INFO @ Tue, 21 Apr 2015 12:23:46: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:23:46: #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 12:23:46: #1 tags after filtering in treatment: 1350591 INFO @ Tue, 21 Apr 2015 12:23:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:23:46: #1 finished! INFO @ Tue, 21 Apr 2015 12:23:46: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:23:46: #1 tags after filtering in treatment: 1350591 INFO @ Tue, 21 Apr 2015 12:23:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:23:46: #1 finished! INFO @ Tue, 21 Apr 2015 12:23:46: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:23:46: #1 tags after filtering in treatment: 1350591 INFO @ Tue, 21 Apr 2015 12:23:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:23:46: #1 finished! INFO @ Tue, 21 Apr 2015 12:23:46: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:23:46: #2 number of paired peaks: 735 WARNING @ Tue, 21 Apr 2015 12:23:46: Fewer paired peaks (735) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 735 pairs to build model! INFO @ Tue, 21 Apr 2015 12:23:46: start model_add_line... INFO @ Tue, 21 Apr 2015 12:23:46: #2 number of paired peaks: 735 WARNING @ Tue, 21 Apr 2015 12:23:46: Fewer paired peaks (735) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 735 pairs to build model! INFO @ Tue, 21 Apr 2015 12:23:46: start model_add_line... INFO @ Tue, 21 Apr 2015 12:23:46: #2 number of paired peaks: 735 WARNING @ Tue, 21 Apr 2015 12:23:46: Fewer paired peaks (735) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 735 pairs to build model! INFO @ Tue, 21 Apr 2015 12:23:46: start model_add_line... INFO @ Tue, 21 Apr 2015 12:23:47: start X-correlation... INFO @ Tue, 21 Apr 2015 12:23:47: end of X-cor INFO @ Tue, 21 Apr 2015 12:23:47: #2 finished! INFO @ Tue, 21 Apr 2015 12:23:47: #2 predicted fragment length is 91 bps INFO @ Tue, 21 Apr 2015 12:23:47: #2 alternative fragment length(s) may be 91 bps INFO @ Tue, 21 Apr 2015 12:23:47: #2.2 Generate R script for model : SRX017857.20_model.r INFO @ Tue, 21 Apr 2015 12:23:47: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:23:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:23:47: start X-correlation... INFO @ Tue, 21 Apr 2015 12:23:47: start X-correlation... INFO @ Tue, 21 Apr 2015 12:23:47: end of X-cor INFO @ Tue, 21 Apr 2015 12:23:47: #2 finished! INFO @ Tue, 21 Apr 2015 12:23:47: #2 predicted fragment length is 91 bps INFO @ Tue, 21 Apr 2015 12:23:47: #2 alternative fragment length(s) may be 91 bps INFO @ Tue, 21 Apr 2015 12:23:47: #2.2 Generate R script for model : SRX017857.05_model.r INFO @ Tue, 21 Apr 2015 12:23:47: end of X-cor INFO @ Tue, 21 Apr 2015 12:23:47: #2 finished! INFO @ Tue, 21 Apr 2015 12:23:47: #2 predicted fragment length is 91 bps INFO @ Tue, 21 Apr 2015 12:23:47: #2 alternative fragment length(s) may be 91 bps INFO @ Tue, 21 Apr 2015 12:23:47: #2.2 Generate R script for model : SRX017857.10_model.r INFO @ Tue, 21 Apr 2015 12:23:47: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:23:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:23:47: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:23:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:23:55: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:23:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:23:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:24:01: #4 Write output xls file... SRX017857.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:24:01: #4 Write peak in narrowPeak format file... SRX017857.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:24:01: #4 Write summits bed file... SRX017857.10_summits.bed INFO @ Tue, 21 Apr 2015 12:24:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (152 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:24:02: #4 Write output xls file... SRX017857.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:24:02: #4 Write peak in narrowPeak format file... SRX017857.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:24:02: #4 Write summits bed file... SRX017857.20_summits.bed INFO @ Tue, 21 Apr 2015 12:24:02: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (12 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:24:02: #4 Write output xls file... SRX017857.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:24:02: #4 Write peak in narrowPeak format file... SRX017857.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:24:02: #4 Write summits bed file... SRX017857.05_summits.bed INFO @ Tue, 21 Apr 2015 12:24:02: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (654 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。