Job ID = 2161241 sra ファイルのダウンロード中... Completed: 197192K bytes transferred in 5 seconds (307484K 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 34574 0 34574 0 0 48536 0 --:--:-- --:--:-- --:--:-- 66488 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 8401854 spots for /home/okishinya/chipatlas/results/dm3/SRX013088/SRR030354.sra Written 8401854 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: 00:02:07 8401854 reads; of these: 8401854 (100.00%) were unpaired; of these: 322946 (3.84%) aligned 0 times 6817686 (81.15%) aligned exactly 1 time 1261222 (15.01%) aligned >1 times 96.16% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 916176 / 8078908 = 0.1134 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 12:10:28: # Command line: callpeak -t SRX013088.bam -f BAM -g dm -n SRX013088.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013088.05 # format = BAM # ChIP-seq file = ['SRX013088.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 12:10:28: # Command line: callpeak -t SRX013088.bam -f BAM -g dm -n SRX013088.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013088.20 # format = BAM # ChIP-seq file = ['SRX013088.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 12:10:28: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:10:28: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:10:28: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:10:28: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:10:28: # Command line: callpeak -t SRX013088.bam -f BAM -g dm -n SRX013088.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013088.10 # format = BAM # ChIP-seq file = ['SRX013088.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 12:10:28: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:10:28: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:10:33: 1000000 INFO @ Tue, 21 Apr 2015 12:10:34: 1000000 INFO @ Tue, 21 Apr 2015 12:10:34: 1000000 INFO @ Tue, 21 Apr 2015 12:10:39: 2000000 INFO @ Tue, 21 Apr 2015 12:10:41: 2000000 INFO @ Tue, 21 Apr 2015 12:10:41: 2000000 INFO @ Tue, 21 Apr 2015 12:10:44: 3000000 INFO @ Tue, 21 Apr 2015 12:10:47: 3000000 INFO @ Tue, 21 Apr 2015 12:10:47: 3000000 INFO @ Tue, 21 Apr 2015 12:10:50: 4000000 INFO @ Tue, 21 Apr 2015 12:10:53: 4000000 INFO @ Tue, 21 Apr 2015 12:10:53: 4000000 INFO @ Tue, 21 Apr 2015 12:10:55: 5000000 INFO @ Tue, 21 Apr 2015 12:11:00: 5000000 INFO @ Tue, 21 Apr 2015 12:11:00: 5000000 INFO @ Tue, 21 Apr 2015 12:11:01: 6000000 INFO @ Tue, 21 Apr 2015 12:11:06: 6000000 INFO @ Tue, 21 Apr 2015 12:11:06: 6000000 INFO @ Tue, 21 Apr 2015 12:11:06: 7000000 INFO @ Tue, 21 Apr 2015 12:11:07: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:11:07: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:11:07: #1 total tags in treatment: 7162732 INFO @ Tue, 21 Apr 2015 12:11:07: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:11:07: #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 12:11:09: #1 tags after filtering in treatment: 7162437 INFO @ Tue, 21 Apr 2015 12:11:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:11:09: #1 finished! INFO @ Tue, 21 Apr 2015 12:11:09: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:11:10: #2 number of paired peaks: 333 WARNING @ Tue, 21 Apr 2015 12:11:10: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Tue, 21 Apr 2015 12:11:10: start model_add_line... INFO @ Tue, 21 Apr 2015 12:11:12: start X-correlation... INFO @ Tue, 21 Apr 2015 12:11:12: end of X-cor INFO @ Tue, 21 Apr 2015 12:11:12: #2 finished! INFO @ Tue, 21 Apr 2015 12:11:12: #2 predicted fragment length is 160 bps INFO @ Tue, 21 Apr 2015 12:11:12: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 21 Apr 2015 12:11:12: #2.2 Generate R script for model : SRX013088.10_model.r INFO @ Tue, 21 Apr 2015 12:11:12: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:11:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:11:12: 7000000 INFO @ Tue, 21 Apr 2015 12:11:12: 7000000 INFO @ Tue, 21 Apr 2015 12:11:13: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:11:13: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:11:13: #1 total tags in treatment: 7162732 INFO @ Tue, 21 Apr 2015 12:11:13: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:11:13: #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 12:11:13: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:11:13: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:11:13: #1 total tags in treatment: 7162732 INFO @ Tue, 21 Apr 2015 12:11:13: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:11:13: #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 12:11:15: #1 tags after filtering in treatment: 7162437 INFO @ Tue, 21 Apr 2015 12:11:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:11:15: #1 finished! INFO @ Tue, 21 Apr 2015 12:11:15: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:11:15: #1 tags after filtering in treatment: 7162437 INFO @ Tue, 21 Apr 2015 12:11:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:11:15: #1 finished! INFO @ Tue, 21 Apr 2015 12:11:15: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:11:16: #2 number of paired peaks: 333 WARNING @ Tue, 21 Apr 2015 12:11:16: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Tue, 21 Apr 2015 12:11:16: start model_add_line... INFO @ Tue, 21 Apr 2015 12:11:16: #2 number of paired peaks: 333 WARNING @ Tue, 21 Apr 2015 12:11:16: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Tue, 21 Apr 2015 12:11:16: start model_add_line... INFO @ Tue, 21 Apr 2015 12:11:18: start X-correlation... INFO @ Tue, 21 Apr 2015 12:11:18: end of X-cor INFO @ Tue, 21 Apr 2015 12:11:18: #2 finished! INFO @ Tue, 21 Apr 2015 12:11:18: #2 predicted fragment length is 160 bps INFO @ Tue, 21 Apr 2015 12:11:18: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 21 Apr 2015 12:11:18: #2.2 Generate R script for model : SRX013088.20_model.r INFO @ Tue, 21 Apr 2015 12:11:18: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:11:18: start X-correlation... INFO @ Tue, 21 Apr 2015 12:11:18: end of X-cor INFO @ Tue, 21 Apr 2015 12:11:18: #2 finished! INFO @ Tue, 21 Apr 2015 12:11:18: #2 predicted fragment length is 160 bps INFO @ Tue, 21 Apr 2015 12:11:18: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 21 Apr 2015 12:11:18: #2.2 Generate R script for model : SRX013088.05_model.r INFO @ Tue, 21 Apr 2015 12:11:18: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:11:52: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:11:59: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:12:00: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:12:22: #4 Write output xls file... SRX013088.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:12:22: #4 Write peak in narrowPeak format file... SRX013088.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:12:22: #4 Write summits bed file... SRX013088.10_summits.bed INFO @ Tue, 21 Apr 2015 12:12:22: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (456 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:12:29: #4 Write output xls file... SRX013088.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:12:29: #4 Write peak in narrowPeak format file... SRX013088.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:12:29: #4 Write summits bed file... SRX013088.20_summits.bed INFO @ Tue, 21 Apr 2015 12:12:29: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (156 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:12:32: #4 Write output xls file... SRX013088.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:12:32: #4 Write peak in narrowPeak format file... SRX013088.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:12:32: #4 Write summits bed file... SRX013088.05_summits.bed INFO @ Tue, 21 Apr 2015 12:12:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1946 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。