Job ID = 2161419 sra ファイルのダウンロード中... Completed: 753188K bytes transferred in 8 seconds (759987K bits/sec), in 2 files, 3 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 14909 0 14909 0 0 19094 0 --:--:-- --:--:-- --:--:-- 25269 100 36411 0 36411 0 0 46583 0 --:--:-- --:--:-- --:--:-- 61609 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 11259501 spots for /home/okishinya/chipatlas/results/dm3/SRX026302/SRR064986.sra Written 11259501 spots total Written 16346566 spots for /home/okishinya/chipatlas/results/dm3/SRX026302/SRR064987.sra Written 16346566 spots total 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: 00:07:46 27606067 reads; of these: 27606067 (100.00%) were unpaired; of these: 3878701 (14.05%) aligned 0 times 18297222 (66.28%) aligned exactly 1 time 5430144 (19.67%) aligned >1 times 85.95% overall alignment rate Time searching: 00:07:46 Overall time: 00:07:46 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_sort_core] merging from 8 files... [bam_rmdupse_core] 8349647 / 23727366 = 0.3519 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 12:50:19: # Command line: callpeak -t SRX026302.bam -f BAM -g dm -n SRX026302.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX026302.20 # format = BAM # ChIP-seq file = ['SRX026302.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 12:50:19: # Command line: callpeak -t SRX026302.bam -f BAM -g dm -n SRX026302.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX026302.10 # format = BAM # ChIP-seq file = ['SRX026302.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 12:50:19: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:50:19: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:50:19: # Command line: callpeak -t SRX026302.bam -f BAM -g dm -n SRX026302.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX026302.05 # format = BAM # ChIP-seq file = ['SRX026302.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 12:50:19: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:50:19: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:50:19: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:50:19: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:50:24: 1000000 INFO @ Tue, 21 Apr 2015 12:50:24: 1000000 INFO @ Tue, 21 Apr 2015 12:50:24: 1000000 INFO @ Tue, 21 Apr 2015 12:50:29: 2000000 INFO @ Tue, 21 Apr 2015 12:50:29: 2000000 INFO @ Tue, 21 Apr 2015 12:50:29: 2000000 INFO @ Tue, 21 Apr 2015 12:50:34: 3000000 INFO @ Tue, 21 Apr 2015 12:50:34: 3000000 INFO @ Tue, 21 Apr 2015 12:50:34: 3000000 INFO @ Tue, 21 Apr 2015 12:50:39: 4000000 INFO @ Tue, 21 Apr 2015 12:50:39: 4000000 INFO @ Tue, 21 Apr 2015 12:50:39: 4000000 INFO @ Tue, 21 Apr 2015 12:50:44: 5000000 INFO @ Tue, 21 Apr 2015 12:50:44: 5000000 INFO @ Tue, 21 Apr 2015 12:50:44: 5000000 INFO @ Tue, 21 Apr 2015 12:50:49: 6000000 INFO @ Tue, 21 Apr 2015 12:50:50: 6000000 INFO @ Tue, 21 Apr 2015 12:50:50: 6000000 INFO @ Tue, 21 Apr 2015 12:50:54: 7000000 INFO @ Tue, 21 Apr 2015 12:50:55: 7000000 INFO @ Tue, 21 Apr 2015 12:50:55: 7000000 INFO @ Tue, 21 Apr 2015 12:51:00: 8000000 INFO @ Tue, 21 Apr 2015 12:51:00: 8000000 INFO @ Tue, 21 Apr 2015 12:51:00: 8000000 INFO @ Tue, 21 Apr 2015 12:51:05: 9000000 INFO @ Tue, 21 Apr 2015 12:51:05: 9000000 INFO @ Tue, 21 Apr 2015 12:51:05: 9000000 INFO @ Tue, 21 Apr 2015 12:51:10: 10000000 INFO @ Tue, 21 Apr 2015 12:51:10: 10000000 INFO @ Tue, 21 Apr 2015 12:51:11: 10000000 INFO @ Tue, 21 Apr 2015 12:51:15: 11000000 INFO @ Tue, 21 Apr 2015 12:51:15: 11000000 INFO @ Tue, 21 Apr 2015 12:51:16: 11000000 INFO @ Tue, 21 Apr 2015 12:51:20: 12000000 INFO @ Tue, 21 Apr 2015 12:51:20: 12000000 INFO @ Tue, 21 Apr 2015 12:51:21: 12000000 INFO @ Tue, 21 Apr 2015 12:51:25: 13000000 INFO @ Tue, 21 Apr 2015 12:51:25: 13000000 INFO @ Tue, 21 Apr 2015 12:51:26: 13000000 INFO @ Tue, 21 Apr 2015 12:51:30: 14000000 INFO @ Tue, 21 Apr 2015 12:51:30: 14000000 INFO @ Tue, 21 Apr 2015 12:51:31: 14000000 INFO @ Tue, 21 Apr 2015 12:51:35: 15000000 INFO @ Tue, 21 Apr 2015 12:51:35: 15000000 INFO @ Tue, 21 Apr 2015 12:51:37: 15000000 INFO @ Tue, 21 Apr 2015 12:51:37: #1 tag size is determined as 39 bps INFO @ Tue, 21 Apr 2015 12:51:37: #1 tag size = 39 INFO @ Tue, 21 Apr 2015 12:51:37: #1 total tags in treatment: 15377719 INFO @ Tue, 21 Apr 2015 12:51:37: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:51:37: #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 12:51:38: #1 tag size is determined as 39 bps INFO @ Tue, 21 Apr 2015 12:51:38: #1 tag size = 39 INFO @ Tue, 21 Apr 2015 12:51:38: #1 total tags in treatment: 15377719 INFO @ Tue, 21 Apr 2015 12:51:38: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:51:38: #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 12:51:39: #1 tag size is determined as 39 bps INFO @ Tue, 21 Apr 2015 12:51:39: #1 tag size = 39 INFO @ Tue, 21 Apr 2015 12:51:39: #1 total tags in treatment: 15377719 INFO @ Tue, 21 Apr 2015 12:51:39: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:51:39: #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 12:51:40: #1 tags after filtering in treatment: 15375291 INFO @ Tue, 21 Apr 2015 12:51:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:51:40: #1 finished! INFO @ Tue, 21 Apr 2015 12:51:40: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:51:40: #1 tags after filtering in treatment: 15375291 INFO @ Tue, 21 Apr 2015 12:51:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:51:40: #1 finished! INFO @ Tue, 21 Apr 2015 12:51:40: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:51:41: #1 tags after filtering in treatment: 15375291 INFO @ Tue, 21 Apr 2015 12:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:51:41: #1 finished! INFO @ Tue, 21 Apr 2015 12:51:41: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:51:43: #2 number of paired peaks: 690 WARNING @ Tue, 21 Apr 2015 12:51:43: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Tue, 21 Apr 2015 12:51:43: start model_add_line... INFO @ Tue, 21 Apr 2015 12:51:43: #2 number of paired peaks: 690 WARNING @ Tue, 21 Apr 2015 12:51:43: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Tue, 21 Apr 2015 12:51:43: start model_add_line... INFO @ Tue, 21 Apr 2015 12:51:44: #2 number of paired peaks: 690 WARNING @ Tue, 21 Apr 2015 12:51:44: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Tue, 21 Apr 2015 12:51:44: start model_add_line... INFO @ Tue, 21 Apr 2015 12:51:50: start X-correlation... INFO @ Tue, 21 Apr 2015 12:51:50: end of X-cor INFO @ Tue, 21 Apr 2015 12:51:50: #2 finished! INFO @ Tue, 21 Apr 2015 12:51:50: #2 predicted fragment length is 80 bps INFO @ Tue, 21 Apr 2015 12:51:50: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 21 Apr 2015 12:51:50: #2.2 Generate R script for model : SRX026302.05_model.r INFO @ Tue, 21 Apr 2015 12:51:50: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:51:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:51:51: start X-correlation... INFO @ Tue, 21 Apr 2015 12:51:51: end of X-cor INFO @ Tue, 21 Apr 2015 12:51:51: #2 finished! INFO @ Tue, 21 Apr 2015 12:51:51: #2 predicted fragment length is 80 bps INFO @ Tue, 21 Apr 2015 12:51:51: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 21 Apr 2015 12:51:51: #2.2 Generate R script for model : SRX026302.20_model.r INFO @ Tue, 21 Apr 2015 12:51:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:51:51: start X-correlation... INFO @ Tue, 21 Apr 2015 12:51:51: end of X-cor INFO @ Tue, 21 Apr 2015 12:51:51: #2 finished! INFO @ Tue, 21 Apr 2015 12:51:51: #2 predicted fragment length is 80 bps INFO @ Tue, 21 Apr 2015 12:51:51: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 21 Apr 2015 12:51:51: #2.2 Generate R script for model : SRX026302.10_model.r INFO @ Tue, 21 Apr 2015 12:51:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:53:11: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:53:11: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:53:12: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:54:10: #4 Write output xls file... SRX026302.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:54:10: #4 Write peak in narrowPeak format file... SRX026302.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:54:10: #4 Write summits bed file... SRX026302.20_summits.bed INFO @ Tue, 21 Apr 2015 12:54:10: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3541 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:54:16: #4 Write output xls file... SRX026302.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:54:16: #4 Write peak in narrowPeak format file... SRX026302.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:54:16: #4 Write summits bed file... SRX026302.10_summits.bed INFO @ Tue, 21 Apr 2015 12:54:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6293 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:54:20: #4 Write output xls file... SRX026302.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:54:20: #4 Write peak in narrowPeak format file... SRX026302.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:54:20: #4 Write summits bed file... SRX026302.05_summits.bed INFO @ Tue, 21 Apr 2015 12:54:20: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12880 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。