Job ID = 2236847 sra ファイルのダウンロード中... Completed: 516406K bytes transferred in 11 seconds (359286K 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 34645 0 34645 0 0 45000 0 --:--:-- --:--:-- --:--:-- 59939 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 17396159 spots for /home/okishinya/chipatlas/results/ce10/SRX059223/SRR190663.sra Written 17396159 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: 00:03:42 17396159 reads; of these: 17396159 (100.00%) were unpaired; of these: 267896 (1.54%) aligned 0 times 13790583 (79.27%) aligned exactly 1 time 3337680 (19.19%) aligned >1 times 98.46% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 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] 2247608 / 17128263 = 0.1312 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 11:19:13: # Command line: callpeak -t SRX059223.bam -f BAM -g ce -n SRX059223.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059223.10 # format = BAM # ChIP-seq file = ['SRX059223.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 11:19:13: # Command line: callpeak -t SRX059223.bam -f BAM -g ce -n SRX059223.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059223.05 # format = BAM # ChIP-seq file = ['SRX059223.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 11:19:13: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:19:13: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:19:13: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:19:13: # Command line: callpeak -t SRX059223.bam -f BAM -g ce -n SRX059223.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059223.20 # format = BAM # ChIP-seq file = ['SRX059223.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 11:19:13: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:19:13: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:19:13: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:19:18: 1000000 INFO @ Thu, 30 Apr 2015 11:19:18: 1000000 INFO @ Thu, 30 Apr 2015 11:19:18: 1000000 INFO @ Thu, 30 Apr 2015 11:19:23: 2000000 INFO @ Thu, 30 Apr 2015 11:19:23: 2000000 INFO @ Thu, 30 Apr 2015 11:19:24: 2000000 INFO @ Thu, 30 Apr 2015 11:19:28: 3000000 INFO @ Thu, 30 Apr 2015 11:19:28: 3000000 INFO @ Thu, 30 Apr 2015 11:19:29: 3000000 INFO @ Thu, 30 Apr 2015 11:19:33: 4000000 INFO @ Thu, 30 Apr 2015 11:19:34: 4000000 INFO @ Thu, 30 Apr 2015 11:19:34: 4000000 INFO @ Thu, 30 Apr 2015 11:19:39: 5000000 INFO @ Thu, 30 Apr 2015 11:19:39: 5000000 INFO @ Thu, 30 Apr 2015 11:19:40: 5000000 INFO @ Thu, 30 Apr 2015 11:19:44: 6000000 INFO @ Thu, 30 Apr 2015 11:19:44: 6000000 INFO @ Thu, 30 Apr 2015 11:19:45: 6000000 INFO @ Thu, 30 Apr 2015 11:19:49: 7000000 INFO @ Thu, 30 Apr 2015 11:19:49: 7000000 INFO @ Thu, 30 Apr 2015 11:19:50: 7000000 INFO @ Thu, 30 Apr 2015 11:19:54: 8000000 INFO @ Thu, 30 Apr 2015 11:19:54: 8000000 INFO @ Thu, 30 Apr 2015 11:19:55: 8000000 INFO @ Thu, 30 Apr 2015 11:19:59: 9000000 INFO @ Thu, 30 Apr 2015 11:19:59: 9000000 INFO @ Thu, 30 Apr 2015 11:20:01: 9000000 INFO @ Thu, 30 Apr 2015 11:20:04: 10000000 INFO @ Thu, 30 Apr 2015 11:20:04: 10000000 INFO @ Thu, 30 Apr 2015 11:20:06: 10000000 INFO @ Thu, 30 Apr 2015 11:20:09: 11000000 INFO @ Thu, 30 Apr 2015 11:20:10: 11000000 INFO @ Thu, 30 Apr 2015 11:20:11: 11000000 INFO @ Thu, 30 Apr 2015 11:20:15: 12000000 INFO @ Thu, 30 Apr 2015 11:20:15: 12000000 INFO @ Thu, 30 Apr 2015 11:20:16: 12000000 INFO @ Thu, 30 Apr 2015 11:20:20: 13000000 INFO @ Thu, 30 Apr 2015 11:20:20: 13000000 INFO @ Thu, 30 Apr 2015 11:20:22: 13000000 INFO @ Thu, 30 Apr 2015 11:20:25: 14000000 INFO @ Thu, 30 Apr 2015 11:20:25: 14000000 INFO @ Thu, 30 Apr 2015 11:20:27: 14000000 INFO @ Thu, 30 Apr 2015 11:20:30: #1 tag size is determined as 42 bps INFO @ Thu, 30 Apr 2015 11:20:30: #1 tag size = 42 INFO @ Thu, 30 Apr 2015 11:20:30: #1 total tags in treatment: 14880655 INFO @ Thu, 30 Apr 2015 11:20:30: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:20:30: #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 11:20:30: #1 tag size is determined as 42 bps INFO @ Thu, 30 Apr 2015 11:20:30: #1 tag size = 42 INFO @ Thu, 30 Apr 2015 11:20:30: #1 total tags in treatment: 14880655 INFO @ Thu, 30 Apr 2015 11:20:30: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:20:30: #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 11:20:32: #1 tag size is determined as 42 bps INFO @ Thu, 30 Apr 2015 11:20:32: #1 tag size = 42 INFO @ Thu, 30 Apr 2015 11:20:32: #1 total tags in treatment: 14880655 INFO @ Thu, 30 Apr 2015 11:20:32: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:20:32: #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 11:20:32: #1 tags after filtering in treatment: 14875584 INFO @ Thu, 30 Apr 2015 11:20:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:20:32: #1 finished! INFO @ Thu, 30 Apr 2015 11:20:32: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:20:33: #1 tags after filtering in treatment: 14875584 INFO @ Thu, 30 Apr 2015 11:20:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:20:33: #1 finished! INFO @ Thu, 30 Apr 2015 11:20:33: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:20:35: #1 tags after filtering in treatment: 14875584 INFO @ Thu, 30 Apr 2015 11:20:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:20:35: #1 finished! INFO @ Thu, 30 Apr 2015 11:20:35: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:20:35: #2 number of paired peaks: 253 WARNING @ Thu, 30 Apr 2015 11:20:35: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Thu, 30 Apr 2015 11:20:35: start model_add_line... INFO @ Thu, 30 Apr 2015 11:20:35: #2 number of paired peaks: 253 WARNING @ Thu, 30 Apr 2015 11:20:35: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Thu, 30 Apr 2015 11:20:35: start model_add_line... INFO @ Thu, 30 Apr 2015 11:20:37: #2 number of paired peaks: 253 WARNING @ Thu, 30 Apr 2015 11:20:37: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Thu, 30 Apr 2015 11:20:37: start model_add_line... INFO @ Thu, 30 Apr 2015 11:20:40: start X-correlation... INFO @ Thu, 30 Apr 2015 11:20:40: end of X-cor INFO @ Thu, 30 Apr 2015 11:20:40: #2 finished! INFO @ Thu, 30 Apr 2015 11:20:40: #2 predicted fragment length is 40 bps INFO @ Thu, 30 Apr 2015 11:20:40: #2 alternative fragment length(s) may be 3,40,565,573 bps INFO @ Thu, 30 Apr 2015 11:20:40: #2.2 Generate R script for model : SRX059223.20_model.r WARNING @ Thu, 30 Apr 2015 11:20:40: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:20:40: #2 You may need to consider one of the other alternative d(s): 3,40,565,573 WARNING @ Thu, 30 Apr 2015 11:20:40: #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 11:20:40: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:20:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:20:40: start X-correlation... INFO @ Thu, 30 Apr 2015 11:20:40: end of X-cor INFO @ Thu, 30 Apr 2015 11:20:40: #2 finished! INFO @ Thu, 30 Apr 2015 11:20:40: #2 predicted fragment length is 40 bps INFO @ Thu, 30 Apr 2015 11:20:40: #2 alternative fragment length(s) may be 3,40,565,573 bps INFO @ Thu, 30 Apr 2015 11:20:40: #2.2 Generate R script for model : SRX059223.05_model.r WARNING @ Thu, 30 Apr 2015 11:20:40: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:20:40: #2 You may need to consider one of the other alternative d(s): 3,40,565,573 WARNING @ Thu, 30 Apr 2015 11:20:40: #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 11:20:40: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:20:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:20:41: start X-correlation... INFO @ Thu, 30 Apr 2015 11:20:41: end of X-cor INFO @ Thu, 30 Apr 2015 11:20:41: #2 finished! INFO @ Thu, 30 Apr 2015 11:20:41: #2 predicted fragment length is 40 bps INFO @ Thu, 30 Apr 2015 11:20:41: #2 alternative fragment length(s) may be 3,40,565,573 bps INFO @ Thu, 30 Apr 2015 11:20:41: #2.2 Generate R script for model : SRX059223.10_model.r WARNING @ Thu, 30 Apr 2015 11:20:41: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:20:41: #2 You may need to consider one of the other alternative d(s): 3,40,565,573 WARNING @ Thu, 30 Apr 2015 11:20:41: #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 11:20:41: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:20:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:21:48: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:21:49: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:21:50: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:22:38: #4 Write output xls file... SRX059223.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:22:38: #4 Write peak in narrowPeak format file... SRX059223.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:22:38: #4 Write summits bed file... SRX059223.20_summits.bed INFO @ Thu, 30 Apr 2015 11:22:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (161 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:22:41: #4 Write output xls file... SRX059223.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:22:41: #4 Write peak in narrowPeak format file... SRX059223.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:22:41: #4 Write summits bed file... SRX059223.10_summits.bed INFO @ Thu, 30 Apr 2015 11:22:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1608 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:22:44: #4 Write output xls file... SRX059223.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:22:45: #4 Write peak in narrowPeak format file... SRX059223.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:22:45: #4 Write summits bed file... SRX059223.05_summits.bed INFO @ Thu, 30 Apr 2015 11:22:45: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (10817 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。