Job ID = 2236901 sra ファイルのダウンロード中... Completed: 555061K bytes transferred in 8 seconds (525861K 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 --:--:-- --:--:-- --:--:-- 0 101 5467 0 5467 0 0 9630 0 --:--:-- --:--:-- --:--:-- 14501 100 35175 0 35175 0 0 43160 0 --:--:-- --:--:-- --:--:-- 56370 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 19120178 spots for /home/okishinya/chipatlas/results/ce10/SRX063962/SRR210890.sra Written 19120178 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 19120178 reads; of these: 19120178 (100.00%) were unpaired; of these: 305498 (1.60%) aligned 0 times 15530561 (81.23%) aligned exactly 1 time 3284119 (17.18%) aligned >1 times 98.40% 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: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1969677 / 18814680 = 0.1047 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 11:22:42: # Command line: callpeak -t SRX063962.bam -f BAM -g ce -n SRX063962.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX063962.05 # format = BAM # ChIP-seq file = ['SRX063962.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 11:22:42: # Command line: callpeak -t SRX063962.bam -f BAM -g ce -n SRX063962.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX063962.20 # format = BAM # ChIP-seq file = ['SRX063962.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 11:22:42: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:22:42: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:22:42: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:22:42: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:22:42: # Command line: callpeak -t SRX063962.bam -f BAM -g ce -n SRX063962.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX063962.10 # format = BAM # ChIP-seq file = ['SRX063962.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 11:22:42: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:22:42: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:22:47: 1000000 INFO @ Thu, 30 Apr 2015 11:22:47: 1000000 INFO @ Thu, 30 Apr 2015 11:22:47: 1000000 INFO @ Thu, 30 Apr 2015 11:22:53: 2000000 INFO @ Thu, 30 Apr 2015 11:22:53: 2000000 INFO @ Thu, 30 Apr 2015 11:22:53: 2000000 INFO @ Thu, 30 Apr 2015 11:22:58: 3000000 INFO @ Thu, 30 Apr 2015 11:22:58: 3000000 INFO @ Thu, 30 Apr 2015 11:22:59: 3000000 INFO @ Thu, 30 Apr 2015 11:23:04: 4000000 INFO @ Thu, 30 Apr 2015 11:23:04: 4000000 INFO @ Thu, 30 Apr 2015 11:23:04: 4000000 INFO @ Thu, 30 Apr 2015 11:23:09: 5000000 INFO @ Thu, 30 Apr 2015 11:23:09: 5000000 INFO @ Thu, 30 Apr 2015 11:23:10: 5000000 INFO @ Thu, 30 Apr 2015 11:23:14: 6000000 INFO @ Thu, 30 Apr 2015 11:23:14: 6000000 INFO @ Thu, 30 Apr 2015 11:23:15: 6000000 INFO @ Thu, 30 Apr 2015 11:23:20: 7000000 INFO @ Thu, 30 Apr 2015 11:23:21: 7000000 INFO @ Thu, 30 Apr 2015 11:23:21: 7000000 INFO @ Thu, 30 Apr 2015 11:23:25: 8000000 INFO @ Thu, 30 Apr 2015 11:23:26: 8000000 INFO @ Thu, 30 Apr 2015 11:23:27: 8000000 INFO @ Thu, 30 Apr 2015 11:23:31: 9000000 INFO @ Thu, 30 Apr 2015 11:23:31: 9000000 INFO @ Thu, 30 Apr 2015 11:23:32: 9000000 INFO @ Thu, 30 Apr 2015 11:23:36: 10000000 INFO @ Thu, 30 Apr 2015 11:23:36: 10000000 INFO @ Thu, 30 Apr 2015 11:23:38: 10000000 INFO @ Thu, 30 Apr 2015 11:23:42: 11000000 INFO @ Thu, 30 Apr 2015 11:23:42: 11000000 INFO @ Thu, 30 Apr 2015 11:23:44: 11000000 INFO @ Thu, 30 Apr 2015 11:23:47: 12000000 INFO @ Thu, 30 Apr 2015 11:23:47: 12000000 INFO @ Thu, 30 Apr 2015 11:23:49: 12000000 INFO @ Thu, 30 Apr 2015 11:23:52: 13000000 INFO @ Thu, 30 Apr 2015 11:23:53: 13000000 INFO @ Thu, 30 Apr 2015 11:23:55: 13000000 INFO @ Thu, 30 Apr 2015 11:23:57: 14000000 INFO @ Thu, 30 Apr 2015 11:23:58: 14000000 INFO @ Thu, 30 Apr 2015 11:24:01: 14000000 INFO @ Thu, 30 Apr 2015 11:24:02: 15000000 INFO @ Thu, 30 Apr 2015 11:24:04: 15000000 INFO @ Thu, 30 Apr 2015 11:24:06: 15000000 INFO @ Thu, 30 Apr 2015 11:24:07: 16000000 INFO @ Thu, 30 Apr 2015 11:24:09: 16000000 INFO @ Thu, 30 Apr 2015 11:24:12: #1 tag size is determined as 42 bps INFO @ Thu, 30 Apr 2015 11:24:12: #1 tag size = 42 INFO @ Thu, 30 Apr 2015 11:24:12: #1 total tags in treatment: 16845003 INFO @ Thu, 30 Apr 2015 11:24:12: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:24:12: #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 11:24:12: 16000000 INFO @ Thu, 30 Apr 2015 11:24:15: #1 tag size is determined as 42 bps INFO @ Thu, 30 Apr 2015 11:24:15: #1 tag size = 42 INFO @ Thu, 30 Apr 2015 11:24:15: #1 total tags in treatment: 16845003 INFO @ Thu, 30 Apr 2015 11:24:15: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:24:15: #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 11:24:16: #1 tags after filtering in treatment: 16840293 INFO @ Thu, 30 Apr 2015 11:24:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:24:16: #1 finished! INFO @ Thu, 30 Apr 2015 11:24:16: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:24:17: #1 tag size is determined as 42 bps INFO @ Thu, 30 Apr 2015 11:24:17: #1 tag size = 42 INFO @ Thu, 30 Apr 2015 11:24:17: #1 total tags in treatment: 16845003 INFO @ Thu, 30 Apr 2015 11:24:17: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:24:17: #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 11:24:18: #1 tags after filtering in treatment: 16840293 INFO @ Thu, 30 Apr 2015 11:24:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:24:18: #1 finished! INFO @ Thu, 30 Apr 2015 11:24:18: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:24:19: #2 number of paired peaks: 189 WARNING @ Thu, 30 Apr 2015 11:24:19: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Thu, 30 Apr 2015 11:24:19: start model_add_line... INFO @ Thu, 30 Apr 2015 11:24:20: #1 tags after filtering in treatment: 16840293 INFO @ Thu, 30 Apr 2015 11:24:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:24:20: #1 finished! INFO @ Thu, 30 Apr 2015 11:24:20: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:24:21: #2 number of paired peaks: 189 WARNING @ Thu, 30 Apr 2015 11:24:21: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Thu, 30 Apr 2015 11:24:21: start model_add_line... INFO @ Thu, 30 Apr 2015 11:24:23: #2 number of paired peaks: 189 WARNING @ Thu, 30 Apr 2015 11:24:23: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Thu, 30 Apr 2015 11:24:23: start model_add_line... INFO @ Thu, 30 Apr 2015 11:24:24: start X-correlation... INFO @ Thu, 30 Apr 2015 11:24:24: end of X-cor INFO @ Thu, 30 Apr 2015 11:24:24: #2 finished! INFO @ Thu, 30 Apr 2015 11:24:24: #2 predicted fragment length is 38 bps INFO @ Thu, 30 Apr 2015 11:24:24: #2 alternative fragment length(s) may be 1,38,505,545,573 bps INFO @ Thu, 30 Apr 2015 11:24:24: #2.2 Generate R script for model : SRX063962.05_model.r WARNING @ Thu, 30 Apr 2015 11:24:24: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:24:24: #2 You may need to consider one of the other alternative d(s): 1,38,505,545,573 WARNING @ Thu, 30 Apr 2015 11:24:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:24:24: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:24:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:24:25: start X-correlation... INFO @ Thu, 30 Apr 2015 11:24:25: end of X-cor INFO @ Thu, 30 Apr 2015 11:24:25: #2 finished! INFO @ Thu, 30 Apr 2015 11:24:25: #2 predicted fragment length is 38 bps INFO @ Thu, 30 Apr 2015 11:24:25: #2 alternative fragment length(s) may be 1,38,505,545,573 bps INFO @ Thu, 30 Apr 2015 11:24:25: #2.2 Generate R script for model : SRX063962.10_model.r WARNING @ Thu, 30 Apr 2015 11:24:25: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:24:25: #2 You may need to consider one of the other alternative d(s): 1,38,505,545,573 WARNING @ Thu, 30 Apr 2015 11:24:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:24:25: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:24:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:24:27: start X-correlation... INFO @ Thu, 30 Apr 2015 11:24:27: end of X-cor INFO @ Thu, 30 Apr 2015 11:24:27: #2 finished! INFO @ Thu, 30 Apr 2015 11:24:27: #2 predicted fragment length is 38 bps INFO @ Thu, 30 Apr 2015 11:24:27: #2 alternative fragment length(s) may be 1,38,505,545,573 bps INFO @ Thu, 30 Apr 2015 11:24:27: #2.2 Generate R script for model : SRX063962.20_model.r WARNING @ Thu, 30 Apr 2015 11:24:27: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:24:27: #2 You may need to consider one of the other alternative d(s): 1,38,505,545,573 WARNING @ Thu, 30 Apr 2015 11:24:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:24:27: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:24:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:42: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:44: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:46: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:38: #4 Write output xls file... SRX063962.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:38: #4 Write peak in narrowPeak format file... SRX063962.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:38: #4 Write summits bed file... SRX063962.10_summits.bed INFO @ Thu, 30 Apr 2015 11:26:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (309 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:26:41: #4 Write output xls file... SRX063962.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:41: #4 Write peak in narrowPeak format file... SRX063962.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:41: #4 Write summits bed file... SRX063962.05_summits.bed INFO @ Thu, 30 Apr 2015 11:26:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (669 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:26:42: #4 Write output xls file... SRX063962.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:42: #4 Write peak in narrowPeak format file... SRX063962.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:42: #4 Write summits bed file... SRX063962.20_summits.bed INFO @ Thu, 30 Apr 2015 11:26:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (93 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。