Job ID = 2161564 sra ファイルのダウンロード中... Completed: 884450K bytes transferred in 9 seconds (778966K 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 19288 0 19288 0 0 21882 0 --:--:-- --:--:-- --:--:-- 27913 100 44904 0 44904 0 0 41922 0 --:--:-- 0:00:01 --:--:-- 51027 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 22621725 spots for /home/okishinya/chipatlas/results/dm3/SRX030958/SRR072385.sra Written 22621725 spots total Written 23212771 spots for /home/okishinya/chipatlas/results/dm3/SRX030958/SRR072384.sra Written 23212771 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: 00:12:29 45834496 reads; of these: 45834496 (100.00%) were unpaired; of these: 4309410 (9.40%) aligned 0 times 33578480 (73.26%) aligned exactly 1 time 7946606 (17.34%) aligned >1 times 90.60% overall alignment rate Time searching: 00:12:29 Overall time: 00:12:29 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 12 files... [bam_rmdupse_core] 21394224 / 41525086 = 0.5152 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 13:11:45: # Command line: callpeak -t SRX030958.bam -f BAM -g dm -n SRX030958.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX030958.20 # format = BAM # ChIP-seq file = ['SRX030958.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 13:11:45: # Command line: callpeak -t SRX030958.bam -f BAM -g dm -n SRX030958.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX030958.10 # format = BAM # ChIP-seq file = ['SRX030958.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 13:11:45: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:11:45: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:11:45: # Command line: callpeak -t SRX030958.bam -f BAM -g dm -n SRX030958.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX030958.05 # format = BAM # ChIP-seq file = ['SRX030958.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 13:11:45: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:11:45: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:11:45: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:11:45: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:11:50: 1000000 INFO @ Tue, 21 Apr 2015 13:11:50: 1000000 INFO @ Tue, 21 Apr 2015 13:11:50: 1000000 INFO @ Tue, 21 Apr 2015 13:11:54: 2000000 INFO @ Tue, 21 Apr 2015 13:11:55: 2000000 INFO @ Tue, 21 Apr 2015 13:11:55: 2000000 INFO @ Tue, 21 Apr 2015 13:11:59: 3000000 INFO @ Tue, 21 Apr 2015 13:12:00: 3000000 INFO @ Tue, 21 Apr 2015 13:12:00: 3000000 INFO @ Tue, 21 Apr 2015 13:12:03: 4000000 INFO @ Tue, 21 Apr 2015 13:12:05: 4000000 INFO @ Tue, 21 Apr 2015 13:12:05: 4000000 INFO @ Tue, 21 Apr 2015 13:12:08: 5000000 INFO @ Tue, 21 Apr 2015 13:12:09: 5000000 INFO @ Tue, 21 Apr 2015 13:12:10: 5000000 INFO @ Tue, 21 Apr 2015 13:12:12: 6000000 INFO @ Tue, 21 Apr 2015 13:12:14: 6000000 INFO @ Tue, 21 Apr 2015 13:12:14: 6000000 INFO @ Tue, 21 Apr 2015 13:12:17: 7000000 INFO @ Tue, 21 Apr 2015 13:12:19: 7000000 INFO @ Tue, 21 Apr 2015 13:12:19: 7000000 INFO @ Tue, 21 Apr 2015 13:12:22: 8000000 INFO @ Tue, 21 Apr 2015 13:12:24: 8000000 INFO @ Tue, 21 Apr 2015 13:12:24: 8000000 INFO @ Tue, 21 Apr 2015 13:12:26: 9000000 INFO @ Tue, 21 Apr 2015 13:12:29: 9000000 INFO @ Tue, 21 Apr 2015 13:12:29: 9000000 INFO @ Tue, 21 Apr 2015 13:12:31: 10000000 INFO @ Tue, 21 Apr 2015 13:12:34: 10000000 INFO @ Tue, 21 Apr 2015 13:12:34: 10000000 INFO @ Tue, 21 Apr 2015 13:12:35: 11000000 INFO @ Tue, 21 Apr 2015 13:12:39: 11000000 INFO @ Tue, 21 Apr 2015 13:12:39: 11000000 INFO @ Tue, 21 Apr 2015 13:12:40: 12000000 INFO @ Tue, 21 Apr 2015 13:12:44: 12000000 INFO @ Tue, 21 Apr 2015 13:12:44: 12000000 INFO @ Tue, 21 Apr 2015 13:12:44: 13000000 INFO @ Tue, 21 Apr 2015 13:12:49: 13000000 INFO @ Tue, 21 Apr 2015 13:12:49: 14000000 INFO @ Tue, 21 Apr 2015 13:12:49: 13000000 INFO @ Tue, 21 Apr 2015 13:12:53: 15000000 INFO @ Tue, 21 Apr 2015 13:12:54: 14000000 INFO @ Tue, 21 Apr 2015 13:12:54: 14000000 INFO @ Tue, 21 Apr 2015 13:12:58: 16000000 INFO @ Tue, 21 Apr 2015 13:12:59: 15000000 INFO @ Tue, 21 Apr 2015 13:12:59: 15000000 INFO @ Tue, 21 Apr 2015 13:13:02: 17000000 INFO @ Tue, 21 Apr 2015 13:13:04: 16000000 INFO @ Tue, 21 Apr 2015 13:13:04: 16000000 INFO @ Tue, 21 Apr 2015 13:13:07: 18000000 INFO @ Tue, 21 Apr 2015 13:13:09: 17000000 INFO @ Tue, 21 Apr 2015 13:13:09: 17000000 INFO @ Tue, 21 Apr 2015 13:13:12: 19000000 INFO @ Tue, 21 Apr 2015 13:13:14: 18000000 INFO @ Tue, 21 Apr 2015 13:13:14: 18000000 INFO @ Tue, 21 Apr 2015 13:13:16: 20000000 INFO @ Tue, 21 Apr 2015 13:13:17: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:13:17: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:13:17: #1 total tags in treatment: 20130862 INFO @ Tue, 21 Apr 2015 13:13:17: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:13:17: #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 13:13:19: 19000000 INFO @ Tue, 21 Apr 2015 13:13:19: 19000000 INFO @ Tue, 21 Apr 2015 13:13:21: #1 tags after filtering in treatment: 20128316 INFO @ Tue, 21 Apr 2015 13:13:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:13:21: #1 finished! INFO @ Tue, 21 Apr 2015 13:13:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:13:24: 20000000 INFO @ Tue, 21 Apr 2015 13:13:24: #2 number of paired peaks: 248 WARNING @ Tue, 21 Apr 2015 13:13:24: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 21 Apr 2015 13:13:24: start model_add_line... INFO @ Tue, 21 Apr 2015 13:13:25: 20000000 INFO @ Tue, 21 Apr 2015 13:13:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:13:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:13:25: #1 total tags in treatment: 20130862 INFO @ Tue, 21 Apr 2015 13:13:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:13:25: #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 13:13:26: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:13:26: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:13:26: #1 total tags in treatment: 20130862 INFO @ Tue, 21 Apr 2015 13:13:26: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:13:26: #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 13:13:28: start X-correlation... INFO @ Tue, 21 Apr 2015 13:13:28: end of X-cor INFO @ Tue, 21 Apr 2015 13:13:28: #2 finished! INFO @ Tue, 21 Apr 2015 13:13:28: #2 predicted fragment length is 108 bps INFO @ Tue, 21 Apr 2015 13:13:28: #2 alternative fragment length(s) may be 108 bps INFO @ Tue, 21 Apr 2015 13:13:28: #2.2 Generate R script for model : SRX030958.05_model.r INFO @ Tue, 21 Apr 2015 13:13:28: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:13:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:13:28: #1 tags after filtering in treatment: 20128316 INFO @ Tue, 21 Apr 2015 13:13:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:13:28: #1 finished! INFO @ Tue, 21 Apr 2015 13:13:28: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:13:29: #1 tags after filtering in treatment: 20128316 INFO @ Tue, 21 Apr 2015 13:13:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:13:29: #1 finished! INFO @ Tue, 21 Apr 2015 13:13:29: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:13:32: #2 number of paired peaks: 248 WARNING @ Tue, 21 Apr 2015 13:13:32: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 21 Apr 2015 13:13:32: start model_add_line... INFO @ Tue, 21 Apr 2015 13:13:33: #2 number of paired peaks: 248 WARNING @ Tue, 21 Apr 2015 13:13:33: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 21 Apr 2015 13:13:33: start model_add_line... INFO @ Tue, 21 Apr 2015 13:13:36: start X-correlation... INFO @ Tue, 21 Apr 2015 13:13:36: end of X-cor INFO @ Tue, 21 Apr 2015 13:13:36: #2 finished! INFO @ Tue, 21 Apr 2015 13:13:36: #2 predicted fragment length is 108 bps INFO @ Tue, 21 Apr 2015 13:13:36: #2 alternative fragment length(s) may be 108 bps INFO @ Tue, 21 Apr 2015 13:13:36: #2.2 Generate R script for model : SRX030958.20_model.r INFO @ Tue, 21 Apr 2015 13:13:36: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:13:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:13:37: start X-correlation... INFO @ Tue, 21 Apr 2015 13:13:37: end of X-cor INFO @ Tue, 21 Apr 2015 13:13:37: #2 finished! INFO @ Tue, 21 Apr 2015 13:13:37: #2 predicted fragment length is 108 bps INFO @ Tue, 21 Apr 2015 13:13:37: #2 alternative fragment length(s) may be 108 bps INFO @ Tue, 21 Apr 2015 13:13:37: #2.2 Generate R script for model : SRX030958.10_model.r INFO @ Tue, 21 Apr 2015 13:13:37: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:13:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:15:05: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:15:17: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:15:18: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:16:21: #4 Write output xls file... SRX030958.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:16:21: #4 Write peak in narrowPeak format file... SRX030958.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:16:21: #4 Write summits bed file... SRX030958.05_summits.bed INFO @ Tue, 21 Apr 2015 13:16:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4413 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:16:27: #4 Write output xls file... SRX030958.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:16:27: #4 Write peak in narrowPeak format file... SRX030958.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:16:27: #4 Write summits bed file... SRX030958.10_summits.bed INFO @ Tue, 21 Apr 2015 13:16:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2122 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:16:36: #4 Write output xls file... SRX030958.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:16:36: #4 Write peak in narrowPeak format file... SRX030958.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:16:36: #4 Write summits bed file... SRX030958.20_summits.bed INFO @ Tue, 21 Apr 2015 13:16:36: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (980 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。