Job ID = 9370024 sra ファイルのダウンロード中... Completed: 937742K bytes transferred in 68 seconds (111983K bits/sec), in 1 file, 2 directories. 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 27553640 spots for /home/okishinya/chipatlas/results/ce10/SRX2710285/SRR5418739.sra Written 27553640 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: 00:17:12 27553640 reads; of these: 27553640 (100.00%) were unpaired; of these: 5963377 (21.64%) aligned 0 times 12665071 (45.97%) aligned exactly 1 time 8925192 (32.39%) aligned >1 times 78.36% overall alignment rate Time searching: 00:17:12 Overall time: 00:17:12 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 12 files... [bam_rmdupse_core] 8926842 / 21590263 = 0.4135 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 @ Fri, 04 Aug 2017 12:21:07: # Command line: callpeak -t SRX2710285.bam -f BAM -g ce -n SRX2710285.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2710285.20 # format = BAM # ChIP-seq file = ['SRX2710285.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 # Paired-End mode is off INFO @ Fri, 04 Aug 2017 12:21:07: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:21:07: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:21:07: # Command line: callpeak -t SRX2710285.bam -f BAM -g ce -n SRX2710285.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2710285.05 # format = BAM # ChIP-seq file = ['SRX2710285.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 # Paired-End mode is off INFO @ Fri, 04 Aug 2017 12:21:07: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:21:07: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:21:07: # Command line: callpeak -t SRX2710285.bam -f BAM -g ce -n SRX2710285.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2710285.10 # format = BAM # ChIP-seq file = ['SRX2710285.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 # Paired-End mode is off INFO @ Fri, 04 Aug 2017 12:21:07: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:21:07: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:21:21: 1000000 INFO @ Fri, 04 Aug 2017 12:21:21: 1000000 INFO @ Fri, 04 Aug 2017 12:21:22: 1000000 INFO @ Fri, 04 Aug 2017 12:21:36: 2000000 INFO @ Fri, 04 Aug 2017 12:21:36: 2000000 INFO @ Fri, 04 Aug 2017 12:21:36: 2000000 INFO @ Fri, 04 Aug 2017 12:21:46: 3000000 INFO @ Fri, 04 Aug 2017 12:21:49: 3000000 INFO @ Fri, 04 Aug 2017 12:21:50: 3000000 INFO @ Fri, 04 Aug 2017 12:21:58: 4000000 INFO @ Fri, 04 Aug 2017 12:22:02: 4000000 INFO @ Fri, 04 Aug 2017 12:22:04: 4000000 INFO @ Fri, 04 Aug 2017 12:22:09: 5000000 INFO @ Fri, 04 Aug 2017 12:22:13: 5000000 INFO @ Fri, 04 Aug 2017 12:22:17: 5000000 INFO @ Fri, 04 Aug 2017 12:22:20: 6000000 INFO @ Fri, 04 Aug 2017 12:22:23: 6000000 INFO @ Fri, 04 Aug 2017 12:22:31: 7000000 INFO @ Fri, 04 Aug 2017 12:22:32: 6000000 INFO @ Fri, 04 Aug 2017 12:22:36: 7000000 INFO @ Fri, 04 Aug 2017 12:22:42: 8000000 INFO @ Fri, 04 Aug 2017 12:22:49: 7000000 INFO @ Fri, 04 Aug 2017 12:22:52: 9000000 INFO @ Fri, 04 Aug 2017 12:22:52: 8000000 INFO @ Fri, 04 Aug 2017 12:23:04: 10000000 INFO @ Fri, 04 Aug 2017 12:23:05: 8000000 INFO @ Fri, 04 Aug 2017 12:23:09: 9000000 INFO @ Fri, 04 Aug 2017 12:23:20: 11000000 INFO @ Fri, 04 Aug 2017 12:23:20: 9000000 INFO @ Fri, 04 Aug 2017 12:23:25: 10000000 INFO @ Fri, 04 Aug 2017 12:23:36: 12000000 INFO @ Fri, 04 Aug 2017 12:23:39: 10000000 INFO @ Fri, 04 Aug 2017 12:23:43: 11000000 INFO @ Fri, 04 Aug 2017 12:23:46: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 12:23:46: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 12:23:46: #1 total tags in treatment: 12663421 INFO @ Fri, 04 Aug 2017 12:23:46: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:23:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:23:46: #1 tags after filtering in treatment: 12663421 INFO @ Fri, 04 Aug 2017 12:23:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 12:23:46: #1 finished! INFO @ Fri, 04 Aug 2017 12:23:46: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:23:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:23:48: #2 number of paired peaks: 868 WARNING @ Fri, 04 Aug 2017 12:23:48: Fewer paired peaks (868) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 868 pairs to build model! INFO @ Fri, 04 Aug 2017 12:23:48: start model_add_line... INFO @ Fri, 04 Aug 2017 12:23:48: start X-correlation... INFO @ Fri, 04 Aug 2017 12:23:48: end of X-cor INFO @ Fri, 04 Aug 2017 12:23:48: #2 finished! INFO @ Fri, 04 Aug 2017 12:23:48: #2 predicted fragment length is 62 bps INFO @ Fri, 04 Aug 2017 12:23:48: #2 alternative fragment length(s) may be 2,62 bps INFO @ Fri, 04 Aug 2017 12:23:48: #2.2 Generate R script for model : SRX2710285.10_model.r WARNING @ Fri, 04 Aug 2017 12:23:48: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 12:23:48: #2 You may need to consider one of the other alternative d(s): 2,62 WARNING @ Fri, 04 Aug 2017 12:23:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 12:23:48: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:23:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:24:00: 11000000 INFO @ Fri, 04 Aug 2017 12:24:00: 12000000 INFO @ Fri, 04 Aug 2017 12:24:11: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 12:24:11: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 12:24:11: #1 total tags in treatment: 12663421 INFO @ Fri, 04 Aug 2017 12:24:11: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:24:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:24:11: #1 tags after filtering in treatment: 12663421 INFO @ Fri, 04 Aug 2017 12:24:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 12:24:11: #1 finished! INFO @ Fri, 04 Aug 2017 12:24:11: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:24:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:24:13: #2 number of paired peaks: 868 WARNING @ Fri, 04 Aug 2017 12:24:13: Fewer paired peaks (868) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 868 pairs to build model! INFO @ Fri, 04 Aug 2017 12:24:13: start model_add_line... INFO @ Fri, 04 Aug 2017 12:24:13: start X-correlation... INFO @ Fri, 04 Aug 2017 12:24:13: end of X-cor INFO @ Fri, 04 Aug 2017 12:24:13: #2 finished! INFO @ Fri, 04 Aug 2017 12:24:13: #2 predicted fragment length is 62 bps INFO @ Fri, 04 Aug 2017 12:24:13: #2 alternative fragment length(s) may be 2,62 bps INFO @ Fri, 04 Aug 2017 12:24:13: #2.2 Generate R script for model : SRX2710285.05_model.r WARNING @ Fri, 04 Aug 2017 12:24:13: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 12:24:13: #2 You may need to consider one of the other alternative d(s): 2,62 WARNING @ Fri, 04 Aug 2017 12:24:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 12:24:13: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:24:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:24:16: 12000000 INFO @ Fri, 04 Aug 2017 12:24:25: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 12:24:25: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 12:24:25: #1 total tags in treatment: 12663421 INFO @ Fri, 04 Aug 2017 12:24:25: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:24:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:24:26: #1 tags after filtering in treatment: 12663421 INFO @ Fri, 04 Aug 2017 12:24:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 12:24:26: #1 finished! INFO @ Fri, 04 Aug 2017 12:24:26: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:24:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:24:27: #2 number of paired peaks: 868 WARNING @ Fri, 04 Aug 2017 12:24:27: Fewer paired peaks (868) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 868 pairs to build model! INFO @ Fri, 04 Aug 2017 12:24:27: start model_add_line... INFO @ Fri, 04 Aug 2017 12:24:27: start X-correlation... INFO @ Fri, 04 Aug 2017 12:24:27: end of X-cor INFO @ Fri, 04 Aug 2017 12:24:27: #2 finished! INFO @ Fri, 04 Aug 2017 12:24:27: #2 predicted fragment length is 62 bps INFO @ Fri, 04 Aug 2017 12:24:27: #2 alternative fragment length(s) may be 2,62 bps INFO @ Fri, 04 Aug 2017 12:24:27: #2.2 Generate R script for model : SRX2710285.20_model.r WARNING @ Fri, 04 Aug 2017 12:24:28: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 12:24:28: #2 You may need to consider one of the other alternative d(s): 2,62 WARNING @ Fri, 04 Aug 2017 12:24:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 12:24:28: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:24:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:24:29: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:24:53: #4 Write output xls file... SRX2710285.10_peaks.xls INFO @ Fri, 04 Aug 2017 12:24:53: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:24:53: #4 Write peak in narrowPeak format file... SRX2710285.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:24:53: #4 Write summits bed file... SRX2710285.10_summits.bed INFO @ Fri, 04 Aug 2017 12:24:53: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3150 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:25:11: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:25:15: #4 Write output xls file... SRX2710285.05_peaks.xls INFO @ Fri, 04 Aug 2017 12:25:15: #4 Write peak in narrowPeak format file... SRX2710285.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:25:16: #4 Write summits bed file... SRX2710285.05_summits.bed INFO @ Fri, 04 Aug 2017 12:25:16: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (7711 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:25:43: #4 Write output xls file... SRX2710285.20_peaks.xls INFO @ Fri, 04 Aug 2017 12:25:43: #4 Write peak in narrowPeak format file... SRX2710285.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:25:43: #4 Write summits bed file... SRX2710285.20_summits.bed INFO @ Fri, 04 Aug 2017 12:25:43: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (820 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。