Job ID = 2237071 sra ファイルのダウンロード中... Completed: 323816K bytes transferred in 7 seconds (352855K 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 36890 0 36890 0 0 50558 0 --:--:-- --:--:-- --:--:-- 68568 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 14958099 spots for /home/okishinya/chipatlas/results/ce10/SRX113609/SRR393709.sra Written 14958099 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: 00:03:52 14958099 reads; of these: 14958099 (100.00%) were unpaired; of these: 1038771 (6.94%) aligned 0 times 10640523 (71.14%) aligned exactly 1 time 3278805 (21.92%) aligned >1 times 93.06% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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] 5090651 / 13919328 = 0.3657 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 11:33:48: # Command line: callpeak -t SRX113609.bam -f BAM -g ce -n SRX113609.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX113609.20 # format = BAM # ChIP-seq file = ['SRX113609.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 11:33:48: # Command line: callpeak -t SRX113609.bam -f BAM -g ce -n SRX113609.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX113609.10 # format = BAM # ChIP-seq file = ['SRX113609.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 11:33:48: # Command line: callpeak -t SRX113609.bam -f BAM -g ce -n SRX113609.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX113609.05 # format = BAM # ChIP-seq file = ['SRX113609.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 11:33:48: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:33:48: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:33:48: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:33:48: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:33:48: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:33:48: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:33:54: 1000000 INFO @ Thu, 30 Apr 2015 11:33:54: 1000000 INFO @ Thu, 30 Apr 2015 11:33:54: 1000000 INFO @ Thu, 30 Apr 2015 11:34:01: 2000000 INFO @ Thu, 30 Apr 2015 11:34:01: 2000000 INFO @ Thu, 30 Apr 2015 11:34:01: 2000000 INFO @ Thu, 30 Apr 2015 11:34:07: 3000000 INFO @ Thu, 30 Apr 2015 11:34:07: 3000000 INFO @ Thu, 30 Apr 2015 11:34:07: 3000000 INFO @ Thu, 30 Apr 2015 11:34:13: 4000000 INFO @ Thu, 30 Apr 2015 11:34:13: 4000000 INFO @ Thu, 30 Apr 2015 11:34:13: 4000000 INFO @ Thu, 30 Apr 2015 11:34:19: 5000000 INFO @ Thu, 30 Apr 2015 11:34:19: 5000000 INFO @ Thu, 30 Apr 2015 11:34:20: 5000000 INFO @ Thu, 30 Apr 2015 11:34:25: 6000000 INFO @ Thu, 30 Apr 2015 11:34:25: 6000000 INFO @ Thu, 30 Apr 2015 11:34:26: 6000000 INFO @ Thu, 30 Apr 2015 11:34:31: 7000000 INFO @ Thu, 30 Apr 2015 11:34:32: 7000000 INFO @ Thu, 30 Apr 2015 11:34:32: 7000000 INFO @ Thu, 30 Apr 2015 11:34:37: 8000000 INFO @ Thu, 30 Apr 2015 11:34:38: 8000000 INFO @ Thu, 30 Apr 2015 11:34:39: 8000000 INFO @ Thu, 30 Apr 2015 11:34:43: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:34:43: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:34:43: #1 total tags in treatment: 8828677 INFO @ Thu, 30 Apr 2015 11:34:43: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:34:43: #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 11:34:44: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:34:44: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:34:44: #1 total tags in treatment: 8828677 INFO @ Thu, 30 Apr 2015 11:34:44: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:34:44: #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 11:34:44: #1 tags after filtering in treatment: 8803012 INFO @ Thu, 30 Apr 2015 11:34:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:34:44: #1 finished! INFO @ Thu, 30 Apr 2015 11:34:44: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:34:44: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:34:44: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:34:44: #1 total tags in treatment: 8828677 INFO @ Thu, 30 Apr 2015 11:34:44: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:34:44: #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 11:34:46: #2 number of paired peaks: 221 WARNING @ Thu, 30 Apr 2015 11:34:46: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Thu, 30 Apr 2015 11:34:46: start model_add_line... INFO @ Thu, 30 Apr 2015 11:34:46: #1 tags after filtering in treatment: 8803012 INFO @ Thu, 30 Apr 2015 11:34:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:34:46: #1 finished! INFO @ Thu, 30 Apr 2015 11:34:46: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:34:46: #1 tags after filtering in treatment: 8803012 INFO @ Thu, 30 Apr 2015 11:34:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:34:46: #1 finished! INFO @ Thu, 30 Apr 2015 11:34:46: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:34:47: #2 number of paired peaks: 221 WARNING @ Thu, 30 Apr 2015 11:34:47: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Thu, 30 Apr 2015 11:34:47: start model_add_line... INFO @ Thu, 30 Apr 2015 11:34:47: #2 number of paired peaks: 221 WARNING @ Thu, 30 Apr 2015 11:34:47: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Thu, 30 Apr 2015 11:34:47: start model_add_line... INFO @ Thu, 30 Apr 2015 11:34:48: start X-correlation... INFO @ Thu, 30 Apr 2015 11:34:48: end of X-cor INFO @ Thu, 30 Apr 2015 11:34:48: #2 finished! INFO @ Thu, 30 Apr 2015 11:34:48: #2 predicted fragment length is 28 bps INFO @ Thu, 30 Apr 2015 11:34:48: #2 alternative fragment length(s) may be 1,28,102,134,456,474,536,556,585,587 bps INFO @ Thu, 30 Apr 2015 11:34:48: #2.2 Generate R script for model : SRX113609.20_model.r WARNING @ Thu, 30 Apr 2015 11:34:48: #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 11:34:48: #2 You may need to consider one of the other alternative d(s): 1,28,102,134,456,474,536,556,585,587 WARNING @ Thu, 30 Apr 2015 11:34:48: #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 11:34:48: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:34:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:34:50: start X-correlation... INFO @ Thu, 30 Apr 2015 11:34:50: end of X-cor INFO @ Thu, 30 Apr 2015 11:34:50: #2 finished! INFO @ Thu, 30 Apr 2015 11:34:50: #2 predicted fragment length is 28 bps INFO @ Thu, 30 Apr 2015 11:34:50: #2 alternative fragment length(s) may be 1,28,102,134,456,474,536,556,585,587 bps INFO @ Thu, 30 Apr 2015 11:34:50: #2.2 Generate R script for model : SRX113609.10_model.r WARNING @ Thu, 30 Apr 2015 11:34:50: #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 11:34:50: #2 You may need to consider one of the other alternative d(s): 1,28,102,134,456,474,536,556,585,587 WARNING @ Thu, 30 Apr 2015 11:34:50: #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 11:34:50: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:34:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:34:50: start X-correlation... INFO @ Thu, 30 Apr 2015 11:34:50: end of X-cor INFO @ Thu, 30 Apr 2015 11:34:50: #2 finished! INFO @ Thu, 30 Apr 2015 11:34:50: #2 predicted fragment length is 28 bps INFO @ Thu, 30 Apr 2015 11:34:50: #2 alternative fragment length(s) may be 1,28,102,134,456,474,536,556,585,587 bps INFO @ Thu, 30 Apr 2015 11:34:50: #2.2 Generate R script for model : SRX113609.05_model.r WARNING @ Thu, 30 Apr 2015 11:34:50: #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 11:34:50: #2 You may need to consider one of the other alternative d(s): 1,28,102,134,456,474,536,556,585,587 WARNING @ Thu, 30 Apr 2015 11:34:50: #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 11:34:50: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:34:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:35:35: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:35:36: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:35:37: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:36:06: #4 Write output xls file... SRX113609.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:36:06: #4 Write peak in narrowPeak format file... SRX113609.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:36:06: #4 Write summits bed file... SRX113609.10_summits.bed INFO @ Thu, 30 Apr 2015 11:36:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (49 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:36:08: #4 Write output xls file... SRX113609.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:36:08: #4 Write peak in narrowPeak format file... SRX113609.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:36:08: #4 Write summits bed file... SRX113609.20_summits.bed INFO @ Thu, 30 Apr 2015 11:36:08: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:36:12: #4 Write output xls file... SRX113609.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:36:12: #4 Write peak in narrowPeak format file... SRX113609.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:36:12: #4 Write summits bed file... SRX113609.05_summits.bed INFO @ Thu, 30 Apr 2015 11:36:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (251 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。