Job ID = 2236873 sra ファイルのダウンロード中... Completed: 142584K bytes transferred in 13 seconds (85445K 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 5459 0 5459 0 0 9734 0 --:--:-- --:--:-- --:--:-- 14754 100 35096 0 35096 0 0 46764 0 --:--:-- --:--:-- --:--:-- 62671 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 9011548 spots for /home/okishinya/chipatlas/results/ce10/SRX059249/SRR190689.sra Written 9011548 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: 00:01:34 9011548 reads; of these: 9011548 (100.00%) were unpaired; of these: 25430 (0.28%) aligned 0 times 7439006 (82.55%) aligned exactly 1 time 1547112 (17.17%) aligned >1 times 99.72% overall alignment rate Time searching: 00:01:34 Overall time: 00:01:34 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] 570706 / 8986118 = 0.0635 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 11:14:29: # Command line: callpeak -t SRX059249.bam -f BAM -g ce -n SRX059249.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059249.05 # format = BAM # ChIP-seq file = ['SRX059249.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 11:14:29: # Command line: callpeak -t SRX059249.bam -f BAM -g ce -n SRX059249.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059249.20 # format = BAM # ChIP-seq file = ['SRX059249.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 11:14:29: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:14:29: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:14:29: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:14:29: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:14:29: # Command line: callpeak -t SRX059249.bam -f BAM -g ce -n SRX059249.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059249.10 # format = BAM # ChIP-seq file = ['SRX059249.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 11:14:29: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:14:29: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:14:34: 1000000 INFO @ Thu, 30 Apr 2015 11:14:34: 1000000 INFO @ Thu, 30 Apr 2015 11:14:34: 1000000 INFO @ Thu, 30 Apr 2015 11:14:39: 2000000 INFO @ Thu, 30 Apr 2015 11:14:39: 2000000 INFO @ Thu, 30 Apr 2015 11:14:39: 2000000 INFO @ Thu, 30 Apr 2015 11:14:43: 3000000 INFO @ Thu, 30 Apr 2015 11:14:44: 3000000 INFO @ Thu, 30 Apr 2015 11:14:44: 3000000 INFO @ Thu, 30 Apr 2015 11:14:48: 4000000 INFO @ Thu, 30 Apr 2015 11:14:49: 4000000 INFO @ Thu, 30 Apr 2015 11:14:49: 4000000 INFO @ Thu, 30 Apr 2015 11:14:53: 5000000 INFO @ Thu, 30 Apr 2015 11:14:54: 5000000 INFO @ Thu, 30 Apr 2015 11:14:54: 5000000 INFO @ Thu, 30 Apr 2015 11:14:58: 6000000 INFO @ Thu, 30 Apr 2015 11:14:59: 6000000 INFO @ Thu, 30 Apr 2015 11:14:59: 6000000 INFO @ Thu, 30 Apr 2015 11:15:02: 7000000 INFO @ Thu, 30 Apr 2015 11:15:03: 7000000 INFO @ Thu, 30 Apr 2015 11:15:04: 7000000 INFO @ Thu, 30 Apr 2015 11:15:07: 8000000 INFO @ Thu, 30 Apr 2015 11:15:08: 8000000 INFO @ Thu, 30 Apr 2015 11:15:09: 8000000 INFO @ Thu, 30 Apr 2015 11:15:09: #1 tag size is determined as 28 bps INFO @ Thu, 30 Apr 2015 11:15:09: #1 tag size = 28 INFO @ Thu, 30 Apr 2015 11:15:09: #1 total tags in treatment: 8415412 INFO @ Thu, 30 Apr 2015 11:15:09: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:15:09: #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 11:15:10: #1 tag size is determined as 28 bps INFO @ Thu, 30 Apr 2015 11:15:10: #1 tag size = 28 INFO @ Thu, 30 Apr 2015 11:15:10: #1 total tags in treatment: 8415412 INFO @ Thu, 30 Apr 2015 11:15:10: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:15:10: #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 11:15:11: #1 tags after filtering in treatment: 8415360 INFO @ Thu, 30 Apr 2015 11:15:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:15:11: #1 finished! INFO @ Thu, 30 Apr 2015 11:15:11: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:15:11: #1 tag size is determined as 28 bps INFO @ Thu, 30 Apr 2015 11:15:11: #1 tag size = 28 INFO @ Thu, 30 Apr 2015 11:15:11: #1 total tags in treatment: 8415412 INFO @ Thu, 30 Apr 2015 11:15:11: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:15:11: #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 11:15:12: #1 tags after filtering in treatment: 8415360 INFO @ Thu, 30 Apr 2015 11:15:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:15:12: #1 finished! INFO @ Thu, 30 Apr 2015 11:15:12: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:15:12: #2 number of paired peaks: 353 WARNING @ Thu, 30 Apr 2015 11:15:12: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Thu, 30 Apr 2015 11:15:12: start model_add_line... INFO @ Thu, 30 Apr 2015 11:15:12: #1 tags after filtering in treatment: 8415360 INFO @ Thu, 30 Apr 2015 11:15:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:15:12: #1 finished! INFO @ Thu, 30 Apr 2015 11:15:12: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:15:14: #2 number of paired peaks: 353 WARNING @ Thu, 30 Apr 2015 11:15:14: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Thu, 30 Apr 2015 11:15:14: start model_add_line... INFO @ Thu, 30 Apr 2015 11:15:14: #2 number of paired peaks: 353 WARNING @ Thu, 30 Apr 2015 11:15:14: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Thu, 30 Apr 2015 11:15:14: start model_add_line... INFO @ Thu, 30 Apr 2015 11:15:16: start X-correlation... INFO @ Thu, 30 Apr 2015 11:15:16: end of X-cor INFO @ Thu, 30 Apr 2015 11:15:16: #2 finished! INFO @ Thu, 30 Apr 2015 11:15:16: #2 predicted fragment length is 28 bps INFO @ Thu, 30 Apr 2015 11:15:16: #2 alternative fragment length(s) may be 2,28,536 bps INFO @ Thu, 30 Apr 2015 11:15:16: #2.2 Generate R script for model : SRX059249.10_model.r WARNING @ Thu, 30 Apr 2015 11:15:16: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:15:16: #2 You may need to consider one of the other alternative d(s): 2,28,536 WARNING @ Thu, 30 Apr 2015 11:15:16: #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 11:15:16: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:15:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:15:18: start X-correlation... INFO @ Thu, 30 Apr 2015 11:15:18: end of X-cor INFO @ Thu, 30 Apr 2015 11:15:18: #2 finished! INFO @ Thu, 30 Apr 2015 11:15:18: #2 predicted fragment length is 28 bps INFO @ Thu, 30 Apr 2015 11:15:18: #2 alternative fragment length(s) may be 2,28,536 bps INFO @ Thu, 30 Apr 2015 11:15:18: #2.2 Generate R script for model : SRX059249.05_model.r WARNING @ Thu, 30 Apr 2015 11:15:18: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:15:18: #2 You may need to consider one of the other alternative d(s): 2,28,536 WARNING @ Thu, 30 Apr 2015 11:15:18: #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 11:15:18: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:15:18: start X-correlation... INFO @ Thu, 30 Apr 2015 11:15:18: end of X-cor INFO @ Thu, 30 Apr 2015 11:15:18: #2 finished! INFO @ Thu, 30 Apr 2015 11:15:18: #2 predicted fragment length is 28 bps INFO @ Thu, 30 Apr 2015 11:15:18: #2 alternative fragment length(s) may be 2,28,536 bps INFO @ Thu, 30 Apr 2015 11:15:18: #2.2 Generate R script for model : SRX059249.20_model.r WARNING @ Thu, 30 Apr 2015 11:15:18: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:15:18: #2 You may need to consider one of the other alternative d(s): 2,28,536 WARNING @ Thu, 30 Apr 2015 11:15:18: #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 11:15:18: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:16:00: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:16:02: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:16:05: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:16:33: #4 Write output xls file... SRX059249.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:16:33: #4 Write peak in narrowPeak format file... SRX059249.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:16:33: #4 Write summits bed file... SRX059249.05_summits.bed INFO @ Thu, 30 Apr 2015 11:16:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (535 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:16:34: #4 Write output xls file... SRX059249.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:16:34: #4 Write peak in narrowPeak format file... SRX059249.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:16:34: #4 Write summits bed file... SRX059249.10_summits.bed INFO @ Thu, 30 Apr 2015 11:16:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:16:39: #4 Write output xls file... SRX059249.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:16:39: #4 Write peak in narrowPeak format file... SRX059249.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:16:39: #4 Write summits bed file... SRX059249.20_summits.bed INFO @ Thu, 30 Apr 2015 11:16:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (65 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。