Job ID = 2161545 sra ファイルのダウンロード中... Completed: 162519K bytes transferred in 4 seconds (276220K 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 35835 0 35835 0 0 50913 0 --:--:-- --:--:-- --:--:-- 69990 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 6616104 spots for /home/okishinya/chipatlas/results/dm3/SRX027390/SRR066835.sra Written 6616104 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: 00:01:15 6616104 reads; of these: 6616104 (100.00%) were unpaired; of these: 712693 (10.77%) aligned 0 times 5387227 (81.43%) aligned exactly 1 time 516184 (7.80%) aligned >1 times 89.23% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 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] 408596 / 5903411 = 0.0692 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 12:47:30: # Command line: callpeak -t SRX027390.bam -f BAM -g dm -n SRX027390.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX027390.05 # format = BAM # ChIP-seq file = ['SRX027390.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 12:47:30: # Command line: callpeak -t SRX027390.bam -f BAM -g dm -n SRX027390.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX027390.20 # format = BAM # ChIP-seq file = ['SRX027390.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 12:47:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:47:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:47:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:47:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:47:30: # Command line: callpeak -t SRX027390.bam -f BAM -g dm -n SRX027390.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX027390.10 # format = BAM # ChIP-seq file = ['SRX027390.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 12:47:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:47:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:47:36: 1000000 INFO @ Tue, 21 Apr 2015 12:47:36: 1000000 INFO @ Tue, 21 Apr 2015 12:47:36: 1000000 INFO @ Tue, 21 Apr 2015 12:47:42: 2000000 INFO @ Tue, 21 Apr 2015 12:47:43: 2000000 INFO @ Tue, 21 Apr 2015 12:47:43: 2000000 INFO @ Tue, 21 Apr 2015 12:47:48: 3000000 INFO @ Tue, 21 Apr 2015 12:47:49: 3000000 INFO @ Tue, 21 Apr 2015 12:47:49: 3000000 INFO @ Tue, 21 Apr 2015 12:47:54: 4000000 INFO @ Tue, 21 Apr 2015 12:47:55: 4000000 INFO @ Tue, 21 Apr 2015 12:47:55: 4000000 INFO @ Tue, 21 Apr 2015 12:47:59: 5000000 INFO @ Tue, 21 Apr 2015 12:48:01: 5000000 INFO @ Tue, 21 Apr 2015 12:48:01: 5000000 INFO @ Tue, 21 Apr 2015 12:48:02: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:48:02: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:48:02: #1 total tags in treatment: 5494815 INFO @ Tue, 21 Apr 2015 12:48:02: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:48:02: #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 12:48:03: #1 tags after filtering in treatment: 5494638 INFO @ Tue, 21 Apr 2015 12:48:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:48:03: #1 finished! INFO @ Tue, 21 Apr 2015 12:48:03: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:48:04: #2 number of paired peaks: 834 WARNING @ Tue, 21 Apr 2015 12:48:04: Fewer paired peaks (834) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 834 pairs to build model! INFO @ Tue, 21 Apr 2015 12:48:04: start model_add_line... INFO @ Tue, 21 Apr 2015 12:48:05: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:48:05: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:48:05: #1 total tags in treatment: 5494815 INFO @ Tue, 21 Apr 2015 12:48:05: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:48:05: #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 12:48:05: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:48:05: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:48:05: #1 total tags in treatment: 5494815 INFO @ Tue, 21 Apr 2015 12:48:05: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:48:05: #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 12:48:05: #1 tags after filtering in treatment: 5494638 INFO @ Tue, 21 Apr 2015 12:48:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:48:05: #1 finished! INFO @ Tue, 21 Apr 2015 12:48:05: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:48:06: #1 tags after filtering in treatment: 5494638 INFO @ Tue, 21 Apr 2015 12:48:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:48:06: #1 finished! INFO @ Tue, 21 Apr 2015 12:48:06: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:48:07: start X-correlation... INFO @ Tue, 21 Apr 2015 12:48:07: end of X-cor INFO @ Tue, 21 Apr 2015 12:48:07: #2 finished! INFO @ Tue, 21 Apr 2015 12:48:07: #2 predicted fragment length is 109 bps INFO @ Tue, 21 Apr 2015 12:48:07: #2 alternative fragment length(s) may be 109 bps INFO @ Tue, 21 Apr 2015 12:48:07: #2.2 Generate R script for model : SRX027390.10_model.r INFO @ Tue, 21 Apr 2015 12:48:07: #2 number of paired peaks: 834 WARNING @ Tue, 21 Apr 2015 12:48:07: Fewer paired peaks (834) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 834 pairs to build model! INFO @ Tue, 21 Apr 2015 12:48:07: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:48:07: start model_add_line... INFO @ Tue, 21 Apr 2015 12:48:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:48:07: #2 number of paired peaks: 834 WARNING @ Tue, 21 Apr 2015 12:48:07: Fewer paired peaks (834) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 834 pairs to build model! INFO @ Tue, 21 Apr 2015 12:48:07: start model_add_line... INFO @ Tue, 21 Apr 2015 12:48:09: start X-correlation... INFO @ Tue, 21 Apr 2015 12:48:09: end of X-cor INFO @ Tue, 21 Apr 2015 12:48:09: #2 finished! INFO @ Tue, 21 Apr 2015 12:48:09: #2 predicted fragment length is 109 bps INFO @ Tue, 21 Apr 2015 12:48:09: #2 alternative fragment length(s) may be 109 bps INFO @ Tue, 21 Apr 2015 12:48:09: #2.2 Generate R script for model : SRX027390.05_model.r INFO @ Tue, 21 Apr 2015 12:48:09: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:48:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:48:09: start X-correlation... INFO @ Tue, 21 Apr 2015 12:48:09: end of X-cor INFO @ Tue, 21 Apr 2015 12:48:09: #2 finished! INFO @ Tue, 21 Apr 2015 12:48:09: #2 predicted fragment length is 109 bps INFO @ Tue, 21 Apr 2015 12:48:09: #2 alternative fragment length(s) may be 109 bps INFO @ Tue, 21 Apr 2015 12:48:09: #2.2 Generate R script for model : SRX027390.20_model.r INFO @ Tue, 21 Apr 2015 12:48:09: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:48:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:48:38: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:48:40: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:48:42: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:49:02: #4 Write output xls file... SRX027390.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:49:02: #4 Write peak in narrowPeak format file... SRX027390.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:49:02: #4 Write summits bed file... SRX027390.10_summits.bed INFO @ Tue, 21 Apr 2015 12:49:02: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (2210 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:49:05: #4 Write output xls file... SRX027390.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:49:05: #4 Write peak in narrowPeak format file... SRX027390.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:49:05: #4 Write summits bed file... SRX027390.20_summits.bed INFO @ Tue, 21 Apr 2015 12:49:05: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:49:08: #4 Write output xls file... SRX027390.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:49:08: #4 Write peak in narrowPeak format file... SRX027390.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:49:08: #4 Write summits bed file... SRX027390.05_summits.bed INFO @ Tue, 21 Apr 2015 12:49:08: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (9311 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。