Job ID = 2161086 sra ファイルのダウンロード中... Completed: 60620K bytes transferred in 4 seconds (117993K 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 16362 0 16362 0 0 22887 0 --:--:-- --:--:-- --:--:-- 31225 100 34211 0 34211 0 0 47796 0 --:--:-- --:--:-- --:--:-- 65163 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 2841932 spots for /home/okishinya/chipatlas/results/dm3/SRX013016/SRR030282.sra Written 2841932 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: 00:00:26 2841932 reads; of these: 2841932 (100.00%) were unpaired; of these: 2000455 (70.39%) aligned 0 times 645118 (22.70%) aligned exactly 1 time 196359 (6.91%) aligned >1 times 29.61% overall alignment rate Time searching: 00:00:26 Overall time: 00:00:26 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] 123862 / 841477 = 0.1472 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 11:55:23: # Command line: callpeak -t SRX013016.bam -f BAM -g dm -n SRX013016.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013016.10 # format = BAM # ChIP-seq file = ['SRX013016.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 11:55:23: # Command line: callpeak -t SRX013016.bam -f BAM -g dm -n SRX013016.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013016.20 # format = BAM # ChIP-seq file = ['SRX013016.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 11:55:23: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:55:23: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:55:23: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:55:23: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:55:23: # Command line: callpeak -t SRX013016.bam -f BAM -g dm -n SRX013016.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013016.05 # format = BAM # ChIP-seq file = ['SRX013016.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 11:55:23: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:55:23: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:55:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:55:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:55:27: #1 total tags in treatment: 717615 INFO @ Tue, 21 Apr 2015 11:55:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:55:27: #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 11:55:27: #1 tags after filtering in treatment: 717511 INFO @ Tue, 21 Apr 2015 11:55:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:55:27: #1 finished! INFO @ Tue, 21 Apr 2015 11:55:27: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:55:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:55:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:55:27: #1 total tags in treatment: 717615 INFO @ Tue, 21 Apr 2015 11:55:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:55:27: #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 11:55:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:55:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:55:27: #1 total tags in treatment: 717615 INFO @ Tue, 21 Apr 2015 11:55:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:55:27: #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 11:55:27: #1 tags after filtering in treatment: 717511 INFO @ Tue, 21 Apr 2015 11:55:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:55:27: #1 finished! INFO @ Tue, 21 Apr 2015 11:55:27: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:55:27: #1 tags after filtering in treatment: 717511 INFO @ Tue, 21 Apr 2015 11:55:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:55:27: #1 finished! INFO @ Tue, 21 Apr 2015 11:55:27: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:55:27: #2 number of paired peaks: 230 WARNING @ Tue, 21 Apr 2015 11:55:27: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Tue, 21 Apr 2015 11:55:27: start model_add_line... INFO @ Tue, 21 Apr 2015 11:55:27: #2 number of paired peaks: 230 WARNING @ Tue, 21 Apr 2015 11:55:27: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Tue, 21 Apr 2015 11:55:27: start model_add_line... INFO @ Tue, 21 Apr 2015 11:55:27: #2 number of paired peaks: 230 WARNING @ Tue, 21 Apr 2015 11:55:27: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Tue, 21 Apr 2015 11:55:27: start model_add_line... INFO @ Tue, 21 Apr 2015 11:55:27: start X-correlation... INFO @ Tue, 21 Apr 2015 11:55:27: end of X-cor INFO @ Tue, 21 Apr 2015 11:55:27: #2 finished! INFO @ Tue, 21 Apr 2015 11:55:27: #2 predicted fragment length is 93 bps INFO @ Tue, 21 Apr 2015 11:55:27: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 21 Apr 2015 11:55:27: #2.2 Generate R script for model : SRX013016.05_model.r INFO @ Tue, 21 Apr 2015 11:55:27: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:55:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:55:27: start X-correlation... INFO @ Tue, 21 Apr 2015 11:55:27: start X-correlation... INFO @ Tue, 21 Apr 2015 11:55:27: end of X-cor INFO @ Tue, 21 Apr 2015 11:55:27: #2 finished! INFO @ Tue, 21 Apr 2015 11:55:27: #2 predicted fragment length is 93 bps INFO @ Tue, 21 Apr 2015 11:55:27: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 21 Apr 2015 11:55:27: #2.2 Generate R script for model : SRX013016.20_model.r INFO @ Tue, 21 Apr 2015 11:55:27: end of X-cor INFO @ Tue, 21 Apr 2015 11:55:27: #2 finished! INFO @ Tue, 21 Apr 2015 11:55:27: #2 predicted fragment length is 93 bps INFO @ Tue, 21 Apr 2015 11:55:27: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 21 Apr 2015 11:55:27: #2.2 Generate R script for model : SRX013016.10_model.r INFO @ Tue, 21 Apr 2015 11:55:27: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:55:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:55:27: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:55:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:55:31: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:55:32: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:55:32: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:55:35: #4 Write output xls file... SRX013016.05_peaks.xls INFO @ Tue, 21 Apr 2015 11:55:35: #4 Write peak in narrowPeak format file... SRX013016.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:55:35: #4 Write summits bed file... SRX013016.05_summits.bed INFO @ Tue, 21 Apr 2015 11:55:35: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (389 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 11:55:35: #4 Write output xls file... SRX013016.10_peaks.xls INFO @ Tue, 21 Apr 2015 11:55:35: #4 Write peak in narrowPeak format file... SRX013016.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:55:35: #4 Write summits bed file... SRX013016.10_summits.bed INFO @ Tue, 21 Apr 2015 11:55:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (229 records, 4 fields): 1 millis INFO @ Tue, 21 Apr 2015 11:55:35: #4 Write output xls file... SRX013016.20_peaks.xls CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 11:55:35: #4 Write peak in narrowPeak format file... SRX013016.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:55:35: #4 Write summits bed file... SRX013016.20_summits.bed INFO @ Tue, 21 Apr 2015 11:55:35: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (88 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。