Job ID = 2161934 sra ファイルのダウンロード中... Completed: 939947K bytes transferred in 13 seconds (590700K 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 45591 0 45591 0 0 48829 0 --:--:-- --:--:-- --:--:-- 61443 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 19706651 spots for /home/okishinya/chipatlas/results/dm3/SRX041396/SRR099130.sra Written 19706651 spots total Written 19932071 spots for /home/okishinya/chipatlas/results/dm3/SRX041396/SRR099131.sra Written 19932071 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: 00:14:09 39638722 reads; of these: 39638722 (100.00%) were unpaired; of these: 1081580 (2.73%) aligned 0 times 28638828 (72.25%) aligned exactly 1 time 9918314 (25.02%) aligned >1 times 97.27% overall alignment rate Time searching: 00:14:10 Overall time: 00:14:10 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] 13682146 / 38557142 = 0.3549 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 13:42:31: # Command line: callpeak -t SRX041396.bam -f BAM -g dm -n SRX041396.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX041396.10 # format = BAM # ChIP-seq file = ['SRX041396.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 13:42:31: # Command line: callpeak -t SRX041396.bam -f BAM -g dm -n SRX041396.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX041396.20 # format = BAM # ChIP-seq file = ['SRX041396.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 13:42:31: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:42:31: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:42:31: # Command line: callpeak -t SRX041396.bam -f BAM -g dm -n SRX041396.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX041396.05 # format = BAM # ChIP-seq file = ['SRX041396.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 13:42:31: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:42:31: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:42:31: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:42:31: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:42:36: 1000000 INFO @ Tue, 21 Apr 2015 13:42:36: 1000000 INFO @ Tue, 21 Apr 2015 13:42:36: 1000000 INFO @ Tue, 21 Apr 2015 13:42:41: 2000000 INFO @ Tue, 21 Apr 2015 13:42:41: 2000000 INFO @ Tue, 21 Apr 2015 13:42:42: 2000000 INFO @ Tue, 21 Apr 2015 13:42:47: 3000000 INFO @ Tue, 21 Apr 2015 13:42:47: 3000000 INFO @ Tue, 21 Apr 2015 13:42:47: 3000000 INFO @ Tue, 21 Apr 2015 13:42:52: 4000000 INFO @ Tue, 21 Apr 2015 13:42:52: 4000000 INFO @ Tue, 21 Apr 2015 13:42:52: 4000000 INFO @ Tue, 21 Apr 2015 13:42:57: 5000000 INFO @ Tue, 21 Apr 2015 13:42:58: 5000000 INFO @ Tue, 21 Apr 2015 13:42:58: 5000000 INFO @ Tue, 21 Apr 2015 13:43:02: 6000000 INFO @ Tue, 21 Apr 2015 13:43:03: 6000000 INFO @ Tue, 21 Apr 2015 13:43:03: 6000000 INFO @ Tue, 21 Apr 2015 13:43:07: 7000000 INFO @ Tue, 21 Apr 2015 13:43:08: 7000000 INFO @ Tue, 21 Apr 2015 13:43:08: 7000000 INFO @ Tue, 21 Apr 2015 13:43:12: 8000000 INFO @ Tue, 21 Apr 2015 13:43:13: 8000000 INFO @ Tue, 21 Apr 2015 13:43:13: 8000000 INFO @ Tue, 21 Apr 2015 13:43:18: 9000000 INFO @ Tue, 21 Apr 2015 13:43:19: 9000000 INFO @ Tue, 21 Apr 2015 13:43:19: 9000000 INFO @ Tue, 21 Apr 2015 13:43:23: 10000000 INFO @ Tue, 21 Apr 2015 13:43:24: 10000000 INFO @ Tue, 21 Apr 2015 13:43:24: 10000000 INFO @ Tue, 21 Apr 2015 13:43:28: 11000000 INFO @ Tue, 21 Apr 2015 13:43:29: 11000000 INFO @ Tue, 21 Apr 2015 13:43:29: 11000000 INFO @ Tue, 21 Apr 2015 13:43:33: 12000000 INFO @ Tue, 21 Apr 2015 13:43:35: 12000000 INFO @ Tue, 21 Apr 2015 13:43:35: 12000000 INFO @ Tue, 21 Apr 2015 13:43:38: 13000000 INFO @ Tue, 21 Apr 2015 13:43:40: 13000000 INFO @ Tue, 21 Apr 2015 13:43:40: 13000000 INFO @ Tue, 21 Apr 2015 13:43:44: 14000000 INFO @ Tue, 21 Apr 2015 13:43:45: 14000000 INFO @ Tue, 21 Apr 2015 13:43:45: 14000000 INFO @ Tue, 21 Apr 2015 13:43:49: 15000000 INFO @ Tue, 21 Apr 2015 13:43:51: 15000000 INFO @ Tue, 21 Apr 2015 13:43:51: 15000000 INFO @ Tue, 21 Apr 2015 13:43:54: 16000000 INFO @ Tue, 21 Apr 2015 13:43:56: 16000000 INFO @ Tue, 21 Apr 2015 13:43:56: 16000000 INFO @ Tue, 21 Apr 2015 13:43:59: 17000000 INFO @ Tue, 21 Apr 2015 13:44:02: 17000000 INFO @ Tue, 21 Apr 2015 13:44:02: 17000000 INFO @ Tue, 21 Apr 2015 13:44:04: 18000000 INFO @ Tue, 21 Apr 2015 13:44:08: 18000000 INFO @ Tue, 21 Apr 2015 13:44:08: 18000000 INFO @ Tue, 21 Apr 2015 13:44:10: 19000000 INFO @ Tue, 21 Apr 2015 13:44:13: 19000000 INFO @ Tue, 21 Apr 2015 13:44:13: 19000000 INFO @ Tue, 21 Apr 2015 13:44:15: 20000000 INFO @ Tue, 21 Apr 2015 13:44:19: 20000000 INFO @ Tue, 21 Apr 2015 13:44:19: 20000000 INFO @ Tue, 21 Apr 2015 13:44:20: 21000000 INFO @ Tue, 21 Apr 2015 13:44:25: 21000000 INFO @ Tue, 21 Apr 2015 13:44:25: 21000000 INFO @ Tue, 21 Apr 2015 13:44:25: 22000000 INFO @ Tue, 21 Apr 2015 13:44:30: 22000000 INFO @ Tue, 21 Apr 2015 13:44:30: 22000000 INFO @ Tue, 21 Apr 2015 13:44:31: 23000000 INFO @ Tue, 21 Apr 2015 13:44:36: 23000000 INFO @ Tue, 21 Apr 2015 13:44:36: 23000000 INFO @ Tue, 21 Apr 2015 13:44:36: 24000000 INFO @ Tue, 21 Apr 2015 13:44:41: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:44:41: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:44:41: #1 total tags in treatment: 24874996 INFO @ Tue, 21 Apr 2015 13:44:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:44:41: #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 13:44:42: 24000000 INFO @ Tue, 21 Apr 2015 13:44:42: 24000000 INFO @ Tue, 21 Apr 2015 13:44:46: #1 tags after filtering in treatment: 24859216 INFO @ Tue, 21 Apr 2015 13:44:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:44:46: #1 finished! INFO @ Tue, 21 Apr 2015 13:44:46: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:44:47: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:44:47: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:44:47: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:44:47: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:44:47: #1 total tags in treatment: 24874996 INFO @ Tue, 21 Apr 2015 13:44:47: #1 total tags in treatment: 24874996 INFO @ Tue, 21 Apr 2015 13:44:47: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:44:47: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:44:47: #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 13:44:47: #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 13:44:50: #2 number of paired peaks: 422 WARNING @ Tue, 21 Apr 2015 13:44:50: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Tue, 21 Apr 2015 13:44:50: start model_add_line... INFO @ Tue, 21 Apr 2015 13:44:51: #1 tags after filtering in treatment: 24859216 INFO @ Tue, 21 Apr 2015 13:44:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:44:51: #1 finished! INFO @ Tue, 21 Apr 2015 13:44:51: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:44:51: #1 tags after filtering in treatment: 24859216 INFO @ Tue, 21 Apr 2015 13:44:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:44:51: #1 finished! INFO @ Tue, 21 Apr 2015 13:44:51: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:44:55: #2 number of paired peaks: 422 WARNING @ Tue, 21 Apr 2015 13:44:55: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Tue, 21 Apr 2015 13:44:55: start model_add_line... INFO @ Tue, 21 Apr 2015 13:44:56: #2 number of paired peaks: 422 WARNING @ Tue, 21 Apr 2015 13:44:56: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Tue, 21 Apr 2015 13:44:56: start model_add_line... INFO @ Tue, 21 Apr 2015 13:44:57: start X-correlation... INFO @ Tue, 21 Apr 2015 13:44:57: end of X-cor INFO @ Tue, 21 Apr 2015 13:44:57: #2 finished! INFO @ Tue, 21 Apr 2015 13:44:57: #2 predicted fragment length is 233 bps INFO @ Tue, 21 Apr 2015 13:44:57: #2 alternative fragment length(s) may be 233 bps INFO @ Tue, 21 Apr 2015 13:44:57: #2.2 Generate R script for model : SRX041396.20_model.r INFO @ Tue, 21 Apr 2015 13:44:57: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:44:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:45:02: start X-correlation... INFO @ Tue, 21 Apr 2015 13:45:02: end of X-cor INFO @ Tue, 21 Apr 2015 13:45:02: #2 finished! INFO @ Tue, 21 Apr 2015 13:45:02: #2 predicted fragment length is 233 bps INFO @ Tue, 21 Apr 2015 13:45:02: #2 alternative fragment length(s) may be 233 bps INFO @ Tue, 21 Apr 2015 13:45:02: #2.2 Generate R script for model : SRX041396.05_model.r INFO @ Tue, 21 Apr 2015 13:45:02: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:45:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:45:03: start X-correlation... INFO @ Tue, 21 Apr 2015 13:45:03: end of X-cor INFO @ Tue, 21 Apr 2015 13:45:03: #2 finished! INFO @ Tue, 21 Apr 2015 13:45:03: #2 predicted fragment length is 233 bps INFO @ Tue, 21 Apr 2015 13:45:03: #2 alternative fragment length(s) may be 233 bps INFO @ Tue, 21 Apr 2015 13:45:03: #2.2 Generate R script for model : SRX041396.10_model.r INFO @ Tue, 21 Apr 2015 13:45:03: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:45:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:47:12: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:47:20: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:47:20: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:48:53: #4 Write output xls file... SRX041396.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:48:53: #4 Write peak in narrowPeak format file... SRX041396.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:48:53: #4 Write summits bed file... SRX041396.20_summits.bed INFO @ Tue, 21 Apr 2015 13:48:53: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8361 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:49:29: #4 Write output xls file... SRX041396.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:49:29: #4 Write peak in narrowPeak format file... SRX041396.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:49:29: #4 Write summits bed file... SRX041396.10_summits.bed INFO @ Tue, 21 Apr 2015 13:49:29: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (18217 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:49:48: #4 Write output xls file... SRX041396.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:49:48: #4 Write peak in narrowPeak format file... SRX041396.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:49:49: #4 Write summits bed file... SRX041396.05_summits.bed INFO @ Tue, 21 Apr 2015 13:49:49: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (27836 records, 4 fields): 34 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。