Job ID = 2236881 sra ファイルのダウンロード中... Completed: 333548K bytes transferred in 23 seconds (117830K 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 16345 0 16345 0 0 20635 0 --:--:-- --:--:-- --:--:-- 27196 100 35233 0 35233 0 0 44427 0 --:--:-- --:--:-- --:--:-- 58526 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 14398666 spots for /home/okishinya/chipatlas/results/ce10/SRX059257/SRR190697.sra Written 14398666 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: 00:02:55 14398666 reads; of these: 14398666 (100.00%) were unpaired; of these: 497372 (3.45%) aligned 0 times 11326618 (78.66%) aligned exactly 1 time 2574676 (17.88%) aligned >1 times 96.55% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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_rmdupse_core] 1612478 / 13901294 = 0.1160 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 11:17:47: # Command line: callpeak -t SRX059257.bam -f BAM -g ce -n SRX059257.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059257.05 # format = BAM # ChIP-seq file = ['SRX059257.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 11:17:47: # Command line: callpeak -t SRX059257.bam -f BAM -g ce -n SRX059257.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059257.20 # format = BAM # ChIP-seq file = ['SRX059257.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 11:17:47: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:17:47: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:17:47: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:17:47: # Command line: callpeak -t SRX059257.bam -f BAM -g ce -n SRX059257.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059257.10 # format = BAM # ChIP-seq file = ['SRX059257.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 11:17:47: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:17:47: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:17:47: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:17:54: 1000000 INFO @ Thu, 30 Apr 2015 11:17:54: 1000000 INFO @ Thu, 30 Apr 2015 11:17:54: 1000000 INFO @ Thu, 30 Apr 2015 11:18:00: 2000000 INFO @ Thu, 30 Apr 2015 11:18:00: 2000000 INFO @ Thu, 30 Apr 2015 11:18:00: 2000000 INFO @ Thu, 30 Apr 2015 11:18:06: 3000000 INFO @ Thu, 30 Apr 2015 11:18:07: 3000000 INFO @ Thu, 30 Apr 2015 11:18:07: 3000000 INFO @ Thu, 30 Apr 2015 11:18:13: 4000000 INFO @ Thu, 30 Apr 2015 11:18:13: 4000000 INFO @ Thu, 30 Apr 2015 11:18:13: 4000000 INFO @ Thu, 30 Apr 2015 11:18:19: 5000000 INFO @ Thu, 30 Apr 2015 11:18:20: 5000000 INFO @ Thu, 30 Apr 2015 11:18:20: 5000000 INFO @ Thu, 30 Apr 2015 11:18:26: 6000000 INFO @ Thu, 30 Apr 2015 11:18:26: 6000000 INFO @ Thu, 30 Apr 2015 11:18:26: 6000000 INFO @ Thu, 30 Apr 2015 11:18:32: 7000000 INFO @ Thu, 30 Apr 2015 11:18:33: 7000000 INFO @ Thu, 30 Apr 2015 11:18:33: 7000000 INFO @ Thu, 30 Apr 2015 11:18:39: 8000000 INFO @ Thu, 30 Apr 2015 11:18:40: 8000000 INFO @ Thu, 30 Apr 2015 11:18:40: 8000000 INFO @ Thu, 30 Apr 2015 11:18:46: 9000000 INFO @ Thu, 30 Apr 2015 11:18:46: 9000000 INFO @ Thu, 30 Apr 2015 11:18:46: 9000000 INFO @ Thu, 30 Apr 2015 11:18:52: 10000000 INFO @ Thu, 30 Apr 2015 11:18:53: 10000000 INFO @ Thu, 30 Apr 2015 11:18:53: 10000000 INFO @ Thu, 30 Apr 2015 11:18:59: 11000000 INFO @ Thu, 30 Apr 2015 11:19:00: 11000000 INFO @ Thu, 30 Apr 2015 11:19:00: 11000000 INFO @ Thu, 30 Apr 2015 11:19:06: 12000000 INFO @ Thu, 30 Apr 2015 11:19:07: 12000000 INFO @ Thu, 30 Apr 2015 11:19:07: 12000000 INFO @ Thu, 30 Apr 2015 11:19:08: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:19:08: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:19:08: #1 total tags in treatment: 12288816 INFO @ Thu, 30 Apr 2015 11:19:08: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:19:08: #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 11:19:08: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:19:08: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:19:08: #1 total tags in treatment: 12288816 INFO @ Thu, 30 Apr 2015 11:19:08: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:19:08: #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 11:19:08: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:19:08: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:19:08: #1 total tags in treatment: 12288816 INFO @ Thu, 30 Apr 2015 11:19:08: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:19:08: #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 11:19:10: #1 tags after filtering in treatment: 12288056 INFO @ Thu, 30 Apr 2015 11:19:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:19:10: #1 finished! INFO @ Thu, 30 Apr 2015 11:19:10: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:19:11: #1 tags after filtering in treatment: 12288056 INFO @ Thu, 30 Apr 2015 11:19:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:19:11: #1 finished! INFO @ Thu, 30 Apr 2015 11:19:11: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:19:11: #1 tags after filtering in treatment: 12288056 INFO @ Thu, 30 Apr 2015 11:19:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:19:11: #1 finished! INFO @ Thu, 30 Apr 2015 11:19:11: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:19:12: #2 number of paired peaks: 332 WARNING @ Thu, 30 Apr 2015 11:19:12: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Thu, 30 Apr 2015 11:19:12: start model_add_line... INFO @ Thu, 30 Apr 2015 11:19:13: #2 number of paired peaks: 332 WARNING @ Thu, 30 Apr 2015 11:19:13: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Thu, 30 Apr 2015 11:19:13: start model_add_line... INFO @ Thu, 30 Apr 2015 11:19:13: #2 number of paired peaks: 332 WARNING @ Thu, 30 Apr 2015 11:19:13: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Thu, 30 Apr 2015 11:19:13: start model_add_line... INFO @ Thu, 30 Apr 2015 11:19:17: start X-correlation... INFO @ Thu, 30 Apr 2015 11:19:17: end of X-cor INFO @ Thu, 30 Apr 2015 11:19:17: #2 finished! INFO @ Thu, 30 Apr 2015 11:19:17: #2 predicted fragment length is 37 bps INFO @ Thu, 30 Apr 2015 11:19:17: #2 alternative fragment length(s) may be 2,37,573 bps INFO @ Thu, 30 Apr 2015 11:19:17: #2.2 Generate R script for model : SRX059257.20_model.r WARNING @ Thu, 30 Apr 2015 11:19:17: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:19:17: #2 You may need to consider one of the other alternative d(s): 2,37,573 WARNING @ Thu, 30 Apr 2015 11:19:17: #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 11:19:17: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:19:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:19:18: start X-correlation... INFO @ Thu, 30 Apr 2015 11:19:18: end of X-cor INFO @ Thu, 30 Apr 2015 11:19:18: #2 finished! INFO @ Thu, 30 Apr 2015 11:19:18: #2 predicted fragment length is 37 bps INFO @ Thu, 30 Apr 2015 11:19:18: #2 alternative fragment length(s) may be 2,37,573 bps INFO @ Thu, 30 Apr 2015 11:19:18: #2.2 Generate R script for model : SRX059257.05_model.r WARNING @ Thu, 30 Apr 2015 11:19:18: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:19:18: #2 You may need to consider one of the other alternative d(s): 2,37,573 WARNING @ Thu, 30 Apr 2015 11:19:18: #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 11:19:18: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:19:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:19:18: start X-correlation... INFO @ Thu, 30 Apr 2015 11:19:18: end of X-cor INFO @ Thu, 30 Apr 2015 11:19:18: #2 finished! INFO @ Thu, 30 Apr 2015 11:19:18: #2 predicted fragment length is 37 bps INFO @ Thu, 30 Apr 2015 11:19:18: #2 alternative fragment length(s) may be 2,37,573 bps INFO @ Thu, 30 Apr 2015 11:19:18: #2.2 Generate R script for model : SRX059257.10_model.r WARNING @ Thu, 30 Apr 2015 11:19:18: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:19:18: #2 You may need to consider one of the other alternative d(s): 2,37,573 WARNING @ Thu, 30 Apr 2015 11:19:18: #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 11:19:18: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:19:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:20:19: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:20:20: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:20:22: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:21:04: #4 Write output xls file... SRX059257.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:21:04: #4 Write peak in narrowPeak format file... SRX059257.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:21:04: #4 Write summits bed file... SRX059257.20_summits.bed INFO @ Thu, 30 Apr 2015 11:21:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (493 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:21:07: #4 Write output xls file... SRX059257.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:21:07: #4 Write peak in narrowPeak format file... SRX059257.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:21:07: #4 Write summits bed file... SRX059257.10_summits.bed INFO @ Thu, 30 Apr 2015 11:21:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1090 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:21:08: #4 Write output xls file... SRX059257.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:21:08: #4 Write peak in narrowPeak format file... SRX059257.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:21:08: #4 Write summits bed file... SRX059257.05_summits.bed INFO @ Thu, 30 Apr 2015 11:21:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1791 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。