Job ID = 9029581 sra ファイルのダウンロード中... Completed: 453850K bytes transferred in 8 seconds (443326K 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 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 14324 0 14324 0 0 1913 0 --:--:-- 0:00:07 --:--:-- 13424 100 57070 0 57070 0 0 6728 0 --:--:-- 0:00:08 --:--:-- 27663 100 61761 0 61761 0 0 7280 0 --:--:-- 0:00:08 --:--:-- 29922 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 13421313 spots for /home/okishinya/chipatlas/results/dm3/SRX1848134/SRR3671297.sra Written 13421313 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: 00:04:04 13421313 reads; of these: 13421313 (100.00%) were unpaired; of these: 1622973 (12.09%) aligned 0 times 9138924 (68.09%) aligned exactly 1 time 2659416 (19.81%) aligned >1 times 87.91% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:04 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] 5740338 / 11798340 = 0.4865 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 @ Sat, 03 Jun 2017 14:20:18: # Command line: callpeak -t SRX1848134.bam -f BAM -g dm -n SRX1848134.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1848134.20 # format = BAM # ChIP-seq file = ['SRX1848134.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 @ Sat, 03 Jun 2017 14:20:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:20:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:20:18: # Command line: callpeak -t SRX1848134.bam -f BAM -g dm -n SRX1848134.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1848134.10 # format = BAM # ChIP-seq file = ['SRX1848134.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 @ Sat, 03 Jun 2017 14:20:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:20:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:20:18: # Command line: callpeak -t SRX1848134.bam -f BAM -g dm -n SRX1848134.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1848134.05 # format = BAM # ChIP-seq file = ['SRX1848134.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 @ Sat, 03 Jun 2017 14:20:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:20:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:20:24: 1000000 INFO @ Sat, 03 Jun 2017 14:20:24: 1000000 INFO @ Sat, 03 Jun 2017 14:20:25: 1000000 INFO @ Sat, 03 Jun 2017 14:20:30: 2000000 INFO @ Sat, 03 Jun 2017 14:20:31: 2000000 INFO @ Sat, 03 Jun 2017 14:20:32: 2000000 INFO @ Sat, 03 Jun 2017 14:20:36: 3000000 INFO @ Sat, 03 Jun 2017 14:20:38: 3000000 INFO @ Sat, 03 Jun 2017 14:20:39: 3000000 INFO @ Sat, 03 Jun 2017 14:20:42: 4000000 INFO @ Sat, 03 Jun 2017 14:20:44: 4000000 INFO @ Sat, 03 Jun 2017 14:20:45: 4000000 INFO @ Sat, 03 Jun 2017 14:20:48: 5000000 INFO @ Sat, 03 Jun 2017 14:20:50: 5000000 INFO @ Sat, 03 Jun 2017 14:20:52: 5000000 INFO @ Sat, 03 Jun 2017 14:20:55: 6000000 INFO @ Sat, 03 Jun 2017 14:20:55: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:20:55: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:20:55: #1 total tags in treatment: 6058002 INFO @ Sat, 03 Jun 2017 14:20:55: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:20:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:20:56: #1 tags after filtering in treatment: 6056160 INFO @ Sat, 03 Jun 2017 14:20:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:20:56: #1 finished! INFO @ Sat, 03 Jun 2017 14:20:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:20:57: 6000000 INFO @ Sat, 03 Jun 2017 14:20:57: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:20:57: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:20:57: #1 total tags in treatment: 6058002 INFO @ Sat, 03 Jun 2017 14:20:57: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:20:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:20:57: #2 number of paired peaks: 499 WARNING @ Sat, 03 Jun 2017 14:20:57: Fewer paired peaks (499) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 499 pairs to build model! INFO @ Sat, 03 Jun 2017 14:20:57: start model_add_line... INFO @ Sat, 03 Jun 2017 14:20:58: 6000000 INFO @ Sat, 03 Jun 2017 14:20:58: #1 tags after filtering in treatment: 6056160 INFO @ Sat, 03 Jun 2017 14:20:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:20:58: #1 finished! INFO @ Sat, 03 Jun 2017 14:20:58: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:20:59: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:20:59: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:20:59: #1 total tags in treatment: 6058002 INFO @ Sat, 03 Jun 2017 14:20:59: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:20:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:20:59: #2 number of paired peaks: 499 WARNING @ Sat, 03 Jun 2017 14:20:59: Fewer paired peaks (499) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 499 pairs to build model! INFO @ Sat, 03 Jun 2017 14:20:59: start model_add_line... INFO @ Sat, 03 Jun 2017 14:21:00: #1 tags after filtering in treatment: 6056160 INFO @ Sat, 03 Jun 2017 14:21:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:21:00: #1 finished! INFO @ Sat, 03 Jun 2017 14:21:00: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:21:00: start X-correlation... INFO @ Sat, 03 Jun 2017 14:21:00: end of X-cor INFO @ Sat, 03 Jun 2017 14:21:00: #2 finished! INFO @ Sat, 03 Jun 2017 14:21:00: #2 predicted fragment length is 151 bps INFO @ Sat, 03 Jun 2017 14:21:00: #2 alternative fragment length(s) may be 1,38,151,512,573 bps INFO @ Sat, 03 Jun 2017 14:21:00: #2.2 Generate R script for model : SRX1848134.20_model.r INFO @ Sat, 03 Jun 2017 14:21:00: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:21:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:21:01: #2 number of paired peaks: 499 WARNING @ Sat, 03 Jun 2017 14:21:01: Fewer paired peaks (499) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 499 pairs to build model! INFO @ Sat, 03 Jun 2017 14:21:01: start model_add_line... INFO @ Sat, 03 Jun 2017 14:21:02: start X-correlation... INFO @ Sat, 03 Jun 2017 14:21:02: end of X-cor INFO @ Sat, 03 Jun 2017 14:21:02: #2 finished! INFO @ Sat, 03 Jun 2017 14:21:02: #2 predicted fragment length is 151 bps INFO @ Sat, 03 Jun 2017 14:21:02: #2 alternative fragment length(s) may be 1,38,151,512,573 bps INFO @ Sat, 03 Jun 2017 14:21:02: #2.2 Generate R script for model : SRX1848134.10_model.r INFO @ Sat, 03 Jun 2017 14:21:02: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:21:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:21:04: start X-correlation... INFO @ Sat, 03 Jun 2017 14:21:04: end of X-cor INFO @ Sat, 03 Jun 2017 14:21:04: #2 finished! INFO @ Sat, 03 Jun 2017 14:21:04: #2 predicted fragment length is 151 bps INFO @ Sat, 03 Jun 2017 14:21:04: #2 alternative fragment length(s) may be 1,38,151,512,573 bps INFO @ Sat, 03 Jun 2017 14:21:04: #2.2 Generate R script for model : SRX1848134.05_model.r INFO @ Sat, 03 Jun 2017 14:21:04: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:21:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:21:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:21:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:22:04: #4 Write output xls file... SRX1848134.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:22:04: #4 Write peak in narrowPeak format file... SRX1848134.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:22:04: #4 Write summits bed file... SRX1848134.20_summits.bed INFO @ Sat, 03 Jun 2017 14:22:04: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (291 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:22:05: #4 Write output xls file... SRX1848134.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:22:05: #4 Write peak in narrowPeak format file... SRX1848134.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:22:05: #4 Write summits bed file... SRX1848134.10_summits.bed INFO @ Sat, 03 Jun 2017 14:22:05: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1006 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:22:10: #4 Write output xls file... SRX1848134.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:22:10: #4 Write peak in narrowPeak format file... SRX1848134.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:22:10: #4 Write summits bed file... SRX1848134.05_summits.bed INFO @ Sat, 03 Jun 2017 14:22:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2825 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。