Job ID = 2161190 sra ファイルのダウンロード中... Completed: 173384K bytes transferred in 4 seconds (287624K 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 2547 0 2547 0 0 5081 0 --:--:-- --:--:-- --:--:-- 8189 100 34738 0 34738 0 0 50257 0 --:--:-- --:--:-- --:--:-- 69337 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 7294497 spots for /home/okishinya/chipatlas/results/dm3/SRX013038/SRR030304.sra Written 7294497 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: 00:01:37 7294497 reads; of these: 7294497 (100.00%) were unpaired; of these: 392352 (5.38%) aligned 0 times 6213123 (85.18%) aligned exactly 1 time 689022 (9.45%) aligned >1 times 94.62% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 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] 542119 / 6902145 = 0.0785 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 12:03:02: # Command line: callpeak -t SRX013038.bam -f BAM -g dm -n SRX013038.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013038.05 # format = BAM # ChIP-seq file = ['SRX013038.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 12:03:02: # Command line: callpeak -t SRX013038.bam -f BAM -g dm -n SRX013038.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013038.20 # format = BAM # ChIP-seq file = ['SRX013038.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 12:03:02: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:03:02: # Command line: callpeak -t SRX013038.bam -f BAM -g dm -n SRX013038.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013038.10 # format = BAM # ChIP-seq file = ['SRX013038.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 12:03:02: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:03:02: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:03:02: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:03:02: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:03:02: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:03:08: 1000000 INFO @ Tue, 21 Apr 2015 12:03:08: 1000000 INFO @ Tue, 21 Apr 2015 12:03:08: 1000000 INFO @ Tue, 21 Apr 2015 12:03:15: 2000000 INFO @ Tue, 21 Apr 2015 12:03:15: 2000000 INFO @ Tue, 21 Apr 2015 12:03:15: 2000000 INFO @ Tue, 21 Apr 2015 12:03:21: 3000000 INFO @ Tue, 21 Apr 2015 12:03:21: 3000000 INFO @ Tue, 21 Apr 2015 12:03:21: 3000000 INFO @ Tue, 21 Apr 2015 12:03:28: 4000000 INFO @ Tue, 21 Apr 2015 12:03:28: 4000000 INFO @ Tue, 21 Apr 2015 12:03:28: 4000000 INFO @ Tue, 21 Apr 2015 12:03:34: 5000000 INFO @ Tue, 21 Apr 2015 12:03:34: 5000000 INFO @ Tue, 21 Apr 2015 12:03:34: 5000000 INFO @ Tue, 21 Apr 2015 12:03:41: 6000000 INFO @ Tue, 21 Apr 2015 12:03:41: 6000000 INFO @ Tue, 21 Apr 2015 12:03:41: 6000000 INFO @ Tue, 21 Apr 2015 12:03:43: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:03:43: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:03:43: #1 total tags in treatment: 6360026 INFO @ Tue, 21 Apr 2015 12:03:43: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:03:43: #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 12:03:43: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:03:43: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:03:43: #1 total tags in treatment: 6360026 INFO @ Tue, 21 Apr 2015 12:03:43: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:03:43: #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 12:03:43: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:03:43: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:03:43: #1 total tags in treatment: 6360026 INFO @ Tue, 21 Apr 2015 12:03:43: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:03:43: #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 12:03:44: #1 tags after filtering in treatment: 6359570 INFO @ Tue, 21 Apr 2015 12:03:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:03:44: #1 finished! INFO @ Tue, 21 Apr 2015 12:03:44: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:03:44: #1 tags after filtering in treatment: 6359570 INFO @ Tue, 21 Apr 2015 12:03:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:03:44: #1 finished! INFO @ Tue, 21 Apr 2015 12:03:44: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:03:45: #1 tags after filtering in treatment: 6359570 INFO @ Tue, 21 Apr 2015 12:03:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:03:45: #1 finished! INFO @ Tue, 21 Apr 2015 12:03:45: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:03:45: #2 number of paired peaks: 235 WARNING @ Tue, 21 Apr 2015 12:03:45: Fewer paired peaks (235) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 235 pairs to build model! INFO @ Tue, 21 Apr 2015 12:03:45: start model_add_line... INFO @ Tue, 21 Apr 2015 12:03:46: #2 number of paired peaks: 235 WARNING @ Tue, 21 Apr 2015 12:03:46: Fewer paired peaks (235) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 235 pairs to build model! INFO @ Tue, 21 Apr 2015 12:03:46: start model_add_line... INFO @ Tue, 21 Apr 2015 12:03:46: #2 number of paired peaks: 235 WARNING @ Tue, 21 Apr 2015 12:03:46: Fewer paired peaks (235) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 235 pairs to build model! INFO @ Tue, 21 Apr 2015 12:03:46: start model_add_line... INFO @ Tue, 21 Apr 2015 12:03:47: start X-correlation... INFO @ Tue, 21 Apr 2015 12:03:47: end of X-cor INFO @ Tue, 21 Apr 2015 12:03:47: #2 finished! INFO @ Tue, 21 Apr 2015 12:03:47: #2 predicted fragment length is 171 bps INFO @ Tue, 21 Apr 2015 12:03:47: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 21 Apr 2015 12:03:47: #2.2 Generate R script for model : SRX013038.20_model.r INFO @ Tue, 21 Apr 2015 12:03:47: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:03:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:03:47: start X-correlation... INFO @ Tue, 21 Apr 2015 12:03:47: end of X-cor INFO @ Tue, 21 Apr 2015 12:03:47: #2 finished! INFO @ Tue, 21 Apr 2015 12:03:47: #2 predicted fragment length is 171 bps INFO @ Tue, 21 Apr 2015 12:03:47: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 21 Apr 2015 12:03:47: #2.2 Generate R script for model : SRX013038.10_model.r INFO @ Tue, 21 Apr 2015 12:03:47: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:03:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:03:47: start X-correlation... INFO @ Tue, 21 Apr 2015 12:03:47: end of X-cor INFO @ Tue, 21 Apr 2015 12:03:47: #2 finished! INFO @ Tue, 21 Apr 2015 12:03:47: #2 predicted fragment length is 171 bps INFO @ Tue, 21 Apr 2015 12:03:47: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 21 Apr 2015 12:03:47: #2.2 Generate R script for model : SRX013038.05_model.r INFO @ Tue, 21 Apr 2015 12:03:47: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:03:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:04:23: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:04:24: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:04:27: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:04:50: #4 Write output xls file... SRX013038.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:04:50: #4 Write peak in narrowPeak format file... SRX013038.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:04:50: #4 Write summits bed file... SRX013038.10_summits.bed INFO @ Tue, 21 Apr 2015 12:04:50: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (806 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:04:54: #4 Write output xls file... SRX013038.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:04:54: #4 Write peak in narrowPeak format file... SRX013038.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:04:54: #4 Write summits bed file... SRX013038.05_summits.bed INFO @ Tue, 21 Apr 2015 12:04:54: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (2807 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:04:57: #4 Write output xls file... SRX013038.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:04:57: #4 Write peak in narrowPeak format file... SRX013038.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:04:57: #4 Write summits bed file... SRX013038.20_summits.bed INFO @ Tue, 21 Apr 2015 12:04:57: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (134 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。