Job ID = 9157355 sra ファイルのダウンロード中... Completed: 567922K bytes transferred in 8 seconds (526798K 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 19263987 spots for /home/okishinya/chipatlas/results/ce10/SRX060165/SRR192330.sra Written 19263987 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: 00:04:22 19263987 reads; of these: 19263987 (100.00%) were unpaired; of these: 287138 (1.49%) aligned 0 times 15656738 (81.27%) aligned exactly 1 time 3320111 (17.23%) aligned >1 times 98.51% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 1890199 / 18976849 = 0.0996 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 @ Tue, 27 Jun 2017 11:36:14: # Command line: callpeak -t SRX060165.bam -f BAM -g ce -n SRX060165.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX060165.10 # format = BAM # ChIP-seq file = ['SRX060165.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 @ Tue, 27 Jun 2017 11:36:14: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:36:14: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:36:14: # Command line: callpeak -t SRX060165.bam -f BAM -g ce -n SRX060165.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX060165.05 # format = BAM # ChIP-seq file = ['SRX060165.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 @ Tue, 27 Jun 2017 11:36:14: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:36:14: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:36:14: # Command line: callpeak -t SRX060165.bam -f BAM -g ce -n SRX060165.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX060165.20 # format = BAM # ChIP-seq file = ['SRX060165.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 @ Tue, 27 Jun 2017 11:36:14: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:36:14: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:36:20: 1000000 INFO @ Tue, 27 Jun 2017 11:36:21: 1000000 INFO @ Tue, 27 Jun 2017 11:36:21: 1000000 INFO @ Tue, 27 Jun 2017 11:36:27: 2000000 INFO @ Tue, 27 Jun 2017 11:36:28: 2000000 INFO @ Tue, 27 Jun 2017 11:36:29: 2000000 INFO @ Tue, 27 Jun 2017 11:36:34: 3000000 INFO @ Tue, 27 Jun 2017 11:36:36: 3000000 INFO @ Tue, 27 Jun 2017 11:36:36: 3000000 INFO @ Tue, 27 Jun 2017 11:36:40: 4000000 INFO @ Tue, 27 Jun 2017 11:36:43: 4000000 INFO @ Tue, 27 Jun 2017 11:36:44: 4000000 INFO @ Tue, 27 Jun 2017 11:36:47: 5000000 INFO @ Tue, 27 Jun 2017 11:36:51: 5000000 INFO @ Tue, 27 Jun 2017 11:36:51: 5000000 INFO @ Tue, 27 Jun 2017 11:36:53: 6000000 INFO @ Tue, 27 Jun 2017 11:36:59: 6000000 INFO @ Tue, 27 Jun 2017 11:37:00: 6000000 INFO @ Tue, 27 Jun 2017 11:37:00: 7000000 INFO @ Tue, 27 Jun 2017 11:37:06: 8000000 INFO @ Tue, 27 Jun 2017 11:37:07: 7000000 INFO @ Tue, 27 Jun 2017 11:37:08: 7000000 INFO @ Tue, 27 Jun 2017 11:37:13: 9000000 INFO @ Tue, 27 Jun 2017 11:37:14: 8000000 INFO @ Tue, 27 Jun 2017 11:37:16: 8000000 INFO @ Tue, 27 Jun 2017 11:37:20: 10000000 INFO @ Tue, 27 Jun 2017 11:37:22: 9000000 INFO @ Tue, 27 Jun 2017 11:37:23: 9000000 INFO @ Tue, 27 Jun 2017 11:37:26: 11000000 INFO @ Tue, 27 Jun 2017 11:37:29: 10000000 INFO @ Tue, 27 Jun 2017 11:37:31: 10000000 INFO @ Tue, 27 Jun 2017 11:37:32: 12000000 INFO @ Tue, 27 Jun 2017 11:37:37: 11000000 INFO @ Tue, 27 Jun 2017 11:37:38: 13000000 INFO @ Tue, 27 Jun 2017 11:37:39: 11000000 INFO @ Tue, 27 Jun 2017 11:37:44: 12000000 INFO @ Tue, 27 Jun 2017 11:37:45: 14000000 INFO @ Tue, 27 Jun 2017 11:37:46: 12000000 INFO @ Tue, 27 Jun 2017 11:37:51: 15000000 INFO @ Tue, 27 Jun 2017 11:37:51: 13000000 INFO @ Tue, 27 Jun 2017 11:37:54: 13000000 INFO @ Tue, 27 Jun 2017 11:37:58: 16000000 INFO @ Tue, 27 Jun 2017 11:37:58: 14000000 INFO @ Tue, 27 Jun 2017 11:38:01: 14000000 INFO @ Tue, 27 Jun 2017 11:38:04: 17000000 INFO @ Tue, 27 Jun 2017 11:38:05: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 11:38:05: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 11:38:05: #1 total tags in treatment: 17086650 INFO @ Tue, 27 Jun 2017 11:38:05: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:38:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:38:05: #1 tags after filtering in treatment: 17086650 INFO @ Tue, 27 Jun 2017 11:38:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:38:05: #1 finished! INFO @ Tue, 27 Jun 2017 11:38:05: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:38:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:38:06: 15000000 INFO @ Tue, 27 Jun 2017 11:38:06: #2 number of paired peaks: 194 WARNING @ Tue, 27 Jun 2017 11:38:06: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Tue, 27 Jun 2017 11:38:06: start model_add_line... INFO @ Tue, 27 Jun 2017 11:38:07: start X-correlation... INFO @ Tue, 27 Jun 2017 11:38:07: end of X-cor INFO @ Tue, 27 Jun 2017 11:38:07: #2 finished! INFO @ Tue, 27 Jun 2017 11:38:07: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:38:07: #2 alternative fragment length(s) may be 1,22,518,522,531,561 bps INFO @ Tue, 27 Jun 2017 11:38:07: #2.2 Generate R script for model : SRX060165.20_model.r WARNING @ Tue, 27 Jun 2017 11:38:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:38:07: #2 You may need to consider one of the other alternative d(s): 1,22,518,522,531,561 WARNING @ Tue, 27 Jun 2017 11:38:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:38:07: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:38:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:38:08: 15000000 INFO @ Tue, 27 Jun 2017 11:38:13: 16000000 INFO @ Tue, 27 Jun 2017 11:38:16: 16000000 INFO @ Tue, 27 Jun 2017 11:38:20: 17000000 INFO @ Tue, 27 Jun 2017 11:38:21: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 11:38:21: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 11:38:21: #1 total tags in treatment: 17086650 INFO @ Tue, 27 Jun 2017 11:38:21: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:38:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:38:21: #1 tags after filtering in treatment: 17086650 INFO @ Tue, 27 Jun 2017 11:38:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:38:21: #1 finished! INFO @ Tue, 27 Jun 2017 11:38:21: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:38:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:38:22: #2 number of paired peaks: 194 WARNING @ Tue, 27 Jun 2017 11:38:22: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Tue, 27 Jun 2017 11:38:22: start model_add_line... INFO @ Tue, 27 Jun 2017 11:38:22: start X-correlation... INFO @ Tue, 27 Jun 2017 11:38:22: end of X-cor INFO @ Tue, 27 Jun 2017 11:38:22: #2 finished! INFO @ Tue, 27 Jun 2017 11:38:22: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:38:22: #2 alternative fragment length(s) may be 1,22,518,522,531,561 bps INFO @ Tue, 27 Jun 2017 11:38:22: #2.2 Generate R script for model : SRX060165.05_model.r WARNING @ Tue, 27 Jun 2017 11:38:22: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:38:22: #2 You may need to consider one of the other alternative d(s): 1,22,518,522,531,561 WARNING @ Tue, 27 Jun 2017 11:38:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:38:22: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:38:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:38:23: 17000000 INFO @ Tue, 27 Jun 2017 11:38:23: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 11:38:23: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 11:38:23: #1 total tags in treatment: 17086650 INFO @ Tue, 27 Jun 2017 11:38:23: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:38:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:38:24: #1 tags after filtering in treatment: 17086650 INFO @ Tue, 27 Jun 2017 11:38:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:38:24: #1 finished! INFO @ Tue, 27 Jun 2017 11:38:24: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:38:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:38:25: #2 number of paired peaks: 194 WARNING @ Tue, 27 Jun 2017 11:38:25: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Tue, 27 Jun 2017 11:38:25: start model_add_line... INFO @ Tue, 27 Jun 2017 11:38:25: start X-correlation... INFO @ Tue, 27 Jun 2017 11:38:25: end of X-cor INFO @ Tue, 27 Jun 2017 11:38:25: #2 finished! INFO @ Tue, 27 Jun 2017 11:38:25: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:38:25: #2 alternative fragment length(s) may be 1,22,518,522,531,561 bps INFO @ Tue, 27 Jun 2017 11:38:25: #2.2 Generate R script for model : SRX060165.10_model.r WARNING @ Tue, 27 Jun 2017 11:38:25: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:38:25: #2 You may need to consider one of the other alternative d(s): 1,22,518,522,531,561 WARNING @ Tue, 27 Jun 2017 11:38:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:38:25: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:38:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:38:35: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:38:50: #4 Write output xls file... SRX060165.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:38:50: #4 Write peak in narrowPeak format file... SRX060165.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:38:50: #4 Write summits bed file... SRX060165.20_summits.bed INFO @ Tue, 27 Jun 2017 11:38:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:38:53: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:38:53: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:39:08: #4 Write output xls file... SRX060165.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:39:08: #4 Write peak in narrowPeak format file... SRX060165.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:39:08: #4 Write summits bed file... SRX060165.10_summits.bed INFO @ Tue, 27 Jun 2017 11:39:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:39:10: #4 Write output xls file... SRX060165.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:39:10: #4 Write peak in narrowPeak format file... SRX060165.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:39:10: #4 Write summits bed file... SRX060165.05_summits.bed INFO @ Tue, 27 Jun 2017 11:39:10: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。