Job ID = 2236896 sra ファイルのダウンロード中... Completed: 403970K bytes transferred in 10 seconds (302388K 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 --:--:-- --:--:-- --:--:-- 0 100 35213 0 35213 0 0 48309 0 --:--:-- --:--:-- --:--:-- 65451 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 25891064 spots for /home/okishinya/chipatlas/results/ce10/SRX063957/SRR210885.sra Written 25891064 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: 00:04:59 25891064 reads; of these: 25891064 (100.00%) were unpaired; of these: 4473964 (17.28%) aligned 0 times 17611866 (68.02%) aligned exactly 1 time 3805234 (14.70%) aligned >1 times 82.72% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4575860 / 21417100 = 0.2137 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 @ Thu, 30 Apr 2015 11:21:24: # Command line: callpeak -t SRX063957.bam -f BAM -g ce -n SRX063957.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX063957.05 # format = BAM # ChIP-seq file = ['SRX063957.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:21:24: # Command line: callpeak -t SRX063957.bam -f BAM -g ce -n SRX063957.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX063957.20 # format = BAM # ChIP-seq file = ['SRX063957.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:21:24: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:21:24: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:21:24: # Command line: callpeak -t SRX063957.bam -f BAM -g ce -n SRX063957.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX063957.10 # format = BAM # ChIP-seq file = ['SRX063957.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:21:24: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:21:24: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:21:24: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:21:24: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:21:30: 1000000 INFO @ Thu, 30 Apr 2015 11:21:31: 1000000 INFO @ Thu, 30 Apr 2015 11:21:31: 1000000 INFO @ Thu, 30 Apr 2015 11:21:37: 2000000 INFO @ Thu, 30 Apr 2015 11:21:37: 2000000 INFO @ Thu, 30 Apr 2015 11:21:37: 2000000 INFO @ Thu, 30 Apr 2015 11:21:43: 3000000 INFO @ Thu, 30 Apr 2015 11:21:43: 3000000 INFO @ Thu, 30 Apr 2015 11:21:43: 3000000 INFO @ Thu, 30 Apr 2015 11:21:49: 4000000 INFO @ Thu, 30 Apr 2015 11:21:49: 4000000 INFO @ Thu, 30 Apr 2015 11:21:49: 4000000 INFO @ Thu, 30 Apr 2015 11:21:55: 5000000 INFO @ Thu, 30 Apr 2015 11:21:56: 5000000 INFO @ Thu, 30 Apr 2015 11:21:56: 5000000 INFO @ Thu, 30 Apr 2015 11:22:01: 6000000 INFO @ Thu, 30 Apr 2015 11:22:02: 6000000 INFO @ Thu, 30 Apr 2015 11:22:02: 6000000 INFO @ Thu, 30 Apr 2015 11:22:07: 7000000 INFO @ Thu, 30 Apr 2015 11:22:09: 7000000 INFO @ Thu, 30 Apr 2015 11:22:09: 7000000 INFO @ Thu, 30 Apr 2015 11:22:14: 8000000 INFO @ Thu, 30 Apr 2015 11:22:15: 8000000 INFO @ Thu, 30 Apr 2015 11:22:15: 8000000 INFO @ Thu, 30 Apr 2015 11:22:20: 9000000 INFO @ Thu, 30 Apr 2015 11:22:22: 9000000 INFO @ Thu, 30 Apr 2015 11:22:22: 9000000 INFO @ Thu, 30 Apr 2015 11:22:26: 10000000 INFO @ Thu, 30 Apr 2015 11:22:28: 10000000 INFO @ Thu, 30 Apr 2015 11:22:28: 10000000 INFO @ Thu, 30 Apr 2015 11:22:32: 11000000 INFO @ Thu, 30 Apr 2015 11:22:34: 11000000 INFO @ Thu, 30 Apr 2015 11:22:34: 11000000 INFO @ Thu, 30 Apr 2015 11:22:38: 12000000 INFO @ Thu, 30 Apr 2015 11:22:41: 12000000 INFO @ Thu, 30 Apr 2015 11:22:41: 12000000 INFO @ Thu, 30 Apr 2015 11:22:45: 13000000 INFO @ Thu, 30 Apr 2015 11:22:47: 13000000 INFO @ Thu, 30 Apr 2015 11:22:47: 13000000 INFO @ Thu, 30 Apr 2015 11:22:51: 14000000 INFO @ Thu, 30 Apr 2015 11:22:54: 14000000 INFO @ Thu, 30 Apr 2015 11:22:54: 14000000 INFO @ Thu, 30 Apr 2015 11:22:57: 15000000 INFO @ Thu, 30 Apr 2015 11:23:00: 15000000 INFO @ Thu, 30 Apr 2015 11:23:00: 15000000 INFO @ Thu, 30 Apr 2015 11:23:03: 16000000 INFO @ Thu, 30 Apr 2015 11:23:06: 16000000 INFO @ Thu, 30 Apr 2015 11:23:06: 16000000 INFO @ Thu, 30 Apr 2015 11:23:08: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:23:08: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:23:08: #1 total tags in treatment: 16841240 INFO @ Thu, 30 Apr 2015 11:23:08: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:23:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:23:11: #1 tags after filtering in treatment: 16839080 INFO @ Thu, 30 Apr 2015 11:23:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:23:11: #1 finished! INFO @ Thu, 30 Apr 2015 11:23:11: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:23:12: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:23:12: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:23:12: #1 total tags in treatment: 16841240 INFO @ Thu, 30 Apr 2015 11:23:12: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:23:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:23:12: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:23:12: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:23:12: #1 total tags in treatment: 16841240 INFO @ Thu, 30 Apr 2015 11:23:12: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:23:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:23:14: #2 number of paired peaks: 745 WARNING @ Thu, 30 Apr 2015 11:23:14: Fewer paired peaks (745) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 745 pairs to build model! INFO @ Thu, 30 Apr 2015 11:23:14: start model_add_line... INFO @ Thu, 30 Apr 2015 11:23:15: #1 tags after filtering in treatment: 16839080 INFO @ Thu, 30 Apr 2015 11:23:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:23:15: #1 finished! INFO @ Thu, 30 Apr 2015 11:23:15: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:23:15: #1 tags after filtering in treatment: 16839080 INFO @ Thu, 30 Apr 2015 11:23:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:23:15: #1 finished! INFO @ Thu, 30 Apr 2015 11:23:15: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:23:17: #2 number of paired peaks: 745 WARNING @ Thu, 30 Apr 2015 11:23:17: Fewer paired peaks (745) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 745 pairs to build model! INFO @ Thu, 30 Apr 2015 11:23:17: start model_add_line... INFO @ Thu, 30 Apr 2015 11:23:18: #2 number of paired peaks: 745 WARNING @ Thu, 30 Apr 2015 11:23:18: Fewer paired peaks (745) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 745 pairs to build model! INFO @ Thu, 30 Apr 2015 11:23:18: start model_add_line... INFO @ Thu, 30 Apr 2015 11:23:26: start X-correlation... INFO @ Thu, 30 Apr 2015 11:23:26: end of X-cor INFO @ Thu, 30 Apr 2015 11:23:26: #2 finished! INFO @ Thu, 30 Apr 2015 11:23:26: #2 predicted fragment length is 98 bps INFO @ Thu, 30 Apr 2015 11:23:26: #2 alternative fragment length(s) may be 4,98 bps INFO @ Thu, 30 Apr 2015 11:23:26: #2.2 Generate R script for model : SRX063957.10_model.r INFO @ Thu, 30 Apr 2015 11:23:26: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:23:29: start X-correlation... INFO @ Thu, 30 Apr 2015 11:23:29: end of X-cor INFO @ Thu, 30 Apr 2015 11:23:29: #2 finished! INFO @ Thu, 30 Apr 2015 11:23:29: #2 predicted fragment length is 98 bps INFO @ Thu, 30 Apr 2015 11:23:29: #2 alternative fragment length(s) may be 4,98 bps INFO @ Thu, 30 Apr 2015 11:23:29: #2.2 Generate R script for model : SRX063957.20_model.r INFO @ Thu, 30 Apr 2015 11:23:29: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:23:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:23:29: start X-correlation... INFO @ Thu, 30 Apr 2015 11:23:29: end of X-cor INFO @ Thu, 30 Apr 2015 11:23:29: #2 finished! INFO @ Thu, 30 Apr 2015 11:23:29: #2 predicted fragment length is 98 bps INFO @ Thu, 30 Apr 2015 11:23:29: #2 alternative fragment length(s) may be 4,98 bps INFO @ Thu, 30 Apr 2015 11:23:29: #2.2 Generate R script for model : SRX063957.05_model.r INFO @ Thu, 30 Apr 2015 11:23:29: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:23:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:24:48: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:24:49: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:24:51: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:48: #4 Write output xls file... SRX063957.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:48: #4 Write peak in narrowPeak format file... SRX063957.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:48: #4 Write summits bed file... SRX063957.10_summits.bed INFO @ Thu, 30 Apr 2015 11:25:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3708 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:49: #4 Write output xls file... SRX063957.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:49: #4 Write peak in narrowPeak format file... SRX063957.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:49: #4 Write summits bed file... SRX063957.20_summits.bed INFO @ Thu, 30 Apr 2015 11:25:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2422 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:56: #4 Write output xls file... SRX063957.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:56: #4 Write peak in narrowPeak format file... SRX063957.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:56: #4 Write summits bed file... SRX063957.05_summits.bed INFO @ Thu, 30 Apr 2015 11:25:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5382 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。