Job ID = 9157301 sra ファイルのダウンロード中... Completed: 917287K bytes transferred in 29 seconds (256177K 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 19070323 spots for /home/okishinya/chipatlas/results/ce10/SRX2761388/SRR5476962.sra Written 19070323 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:52 19070323 reads; of these: 19070323 (100.00%) were unpaired; of these: 2373504 (12.45%) aligned 0 times 13620839 (71.42%) aligned exactly 1 time 3075980 (16.13%) aligned >1 times 87.55% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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] 1460641 / 16696819 = 0.0875 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 11:31:44: # Command line: callpeak -t SRX2761388.bam -f BAM -g ce -n SRX2761388.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2761388.10 # format = BAM # ChIP-seq file = ['SRX2761388.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 11:31:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:31:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:31:44: # Command line: callpeak -t SRX2761388.bam -f BAM -g ce -n SRX2761388.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2761388.20 # format = BAM # ChIP-seq file = ['SRX2761388.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 11:31:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:31:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:31:44: # Command line: callpeak -t SRX2761388.bam -f BAM -g ce -n SRX2761388.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2761388.05 # format = BAM # ChIP-seq file = ['SRX2761388.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 11:31:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:31:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:31:50: 1000000 INFO @ Tue, 27 Jun 2017 11:31:50: 1000000 INFO @ Tue, 27 Jun 2017 11:31:50: 1000000 INFO @ Tue, 27 Jun 2017 11:31:57: 2000000 INFO @ Tue, 27 Jun 2017 11:31:57: 2000000 INFO @ Tue, 27 Jun 2017 11:31:57: 2000000 INFO @ Tue, 27 Jun 2017 11:32:03: 3000000 INFO @ Tue, 27 Jun 2017 11:32:04: 3000000 INFO @ Tue, 27 Jun 2017 11:32:04: 3000000 INFO @ Tue, 27 Jun 2017 11:32:10: 4000000 INFO @ Tue, 27 Jun 2017 11:32:11: 4000000 INFO @ Tue, 27 Jun 2017 11:32:11: 4000000 INFO @ Tue, 27 Jun 2017 11:32:16: 5000000 INFO @ Tue, 27 Jun 2017 11:32:17: 5000000 INFO @ Tue, 27 Jun 2017 11:32:18: 5000000 INFO @ Tue, 27 Jun 2017 11:32:23: 6000000 INFO @ Tue, 27 Jun 2017 11:32:24: 6000000 INFO @ Tue, 27 Jun 2017 11:32:25: 6000000 INFO @ Tue, 27 Jun 2017 11:32:30: 7000000 INFO @ Tue, 27 Jun 2017 11:32:31: 7000000 INFO @ Tue, 27 Jun 2017 11:32:32: 7000000 INFO @ Tue, 27 Jun 2017 11:32:36: 8000000 INFO @ Tue, 27 Jun 2017 11:32:38: 8000000 INFO @ Tue, 27 Jun 2017 11:32:38: 8000000 INFO @ Tue, 27 Jun 2017 11:32:43: 9000000 INFO @ Tue, 27 Jun 2017 11:32:45: 9000000 INFO @ Tue, 27 Jun 2017 11:32:45: 9000000 INFO @ Tue, 27 Jun 2017 11:32:49: 10000000 INFO @ Tue, 27 Jun 2017 11:32:52: 10000000 INFO @ Tue, 27 Jun 2017 11:32:53: 10000000 INFO @ Tue, 27 Jun 2017 11:32:55: 11000000 INFO @ Tue, 27 Jun 2017 11:32:59: 11000000 INFO @ Tue, 27 Jun 2017 11:33:00: 11000000 INFO @ Tue, 27 Jun 2017 11:33:02: 12000000 INFO @ Tue, 27 Jun 2017 11:33:07: 12000000 INFO @ Tue, 27 Jun 2017 11:33:07: 12000000 INFO @ Tue, 27 Jun 2017 11:33:08: 13000000 INFO @ Tue, 27 Jun 2017 11:33:14: 13000000 INFO @ Tue, 27 Jun 2017 11:33:15: 13000000 INFO @ Tue, 27 Jun 2017 11:33:15: 14000000 INFO @ Tue, 27 Jun 2017 11:33:21: 14000000 INFO @ Tue, 27 Jun 2017 11:33:21: 15000000 INFO @ Tue, 27 Jun 2017 11:33:22: 14000000 INFO @ Tue, 27 Jun 2017 11:33:23: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:33:23: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:33:23: #1 total tags in treatment: 15236178 INFO @ Tue, 27 Jun 2017 11:33:23: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:33:23: #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 11:33:23: #1 tags after filtering in treatment: 15236178 INFO @ Tue, 27 Jun 2017 11:33:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:33:23: #1 finished! INFO @ Tue, 27 Jun 2017 11:33:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:33:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:33:24: #2 number of paired peaks: 342 WARNING @ Tue, 27 Jun 2017 11:33:24: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Tue, 27 Jun 2017 11:33:24: start model_add_line... INFO @ Tue, 27 Jun 2017 11:33:24: start X-correlation... INFO @ Tue, 27 Jun 2017 11:33:24: end of X-cor INFO @ Tue, 27 Jun 2017 11:33:24: #2 finished! INFO @ Tue, 27 Jun 2017 11:33:24: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:33:24: #2 alternative fragment length(s) may be 1,28,33,42,553,596 bps INFO @ Tue, 27 Jun 2017 11:33:24: #2.2 Generate R script for model : SRX2761388.10_model.r WARNING @ Tue, 27 Jun 2017 11:33:24: #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 11:33:24: #2 You may need to consider one of the other alternative d(s): 1,28,33,42,553,596 WARNING @ Tue, 27 Jun 2017 11:33:24: #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 11:33:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:33:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:33:28: 15000000 INFO @ Tue, 27 Jun 2017 11:33:29: 15000000 INFO @ Tue, 27 Jun 2017 11:33:30: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:33:30: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:33:30: #1 total tags in treatment: 15236178 INFO @ Tue, 27 Jun 2017 11:33:30: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:33:30: #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 11:33:30: #1 tags after filtering in treatment: 15236178 INFO @ Tue, 27 Jun 2017 11:33:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:33:30: #1 finished! INFO @ Tue, 27 Jun 2017 11:33:30: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:33:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:33:31: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:33:31: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:33:31: #1 total tags in treatment: 15236178 INFO @ Tue, 27 Jun 2017 11:33:31: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:33:31: #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 11:33:31: #2 number of paired peaks: 342 WARNING @ Tue, 27 Jun 2017 11:33:31: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Tue, 27 Jun 2017 11:33:31: start model_add_line... INFO @ Tue, 27 Jun 2017 11:33:31: #1 tags after filtering in treatment: 15236178 INFO @ Tue, 27 Jun 2017 11:33:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:33:31: #1 finished! INFO @ Tue, 27 Jun 2017 11:33:31: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:33:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:33:32: start X-correlation... INFO @ Tue, 27 Jun 2017 11:33:32: end of X-cor INFO @ Tue, 27 Jun 2017 11:33:32: #2 finished! INFO @ Tue, 27 Jun 2017 11:33:32: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:33:32: #2 alternative fragment length(s) may be 1,28,33,42,553,596 bps INFO @ Tue, 27 Jun 2017 11:33:32: #2.2 Generate R script for model : SRX2761388.20_model.r WARNING @ Tue, 27 Jun 2017 11:33:32: #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 11:33:32: #2 You may need to consider one of the other alternative d(s): 1,28,33,42,553,596 WARNING @ Tue, 27 Jun 2017 11:33:32: #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 11:33:32: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:33:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:33:33: #2 number of paired peaks: 342 WARNING @ Tue, 27 Jun 2017 11:33:33: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Tue, 27 Jun 2017 11:33:33: start model_add_line... INFO @ Tue, 27 Jun 2017 11:33:33: start X-correlation... INFO @ Tue, 27 Jun 2017 11:33:33: end of X-cor INFO @ Tue, 27 Jun 2017 11:33:33: #2 finished! INFO @ Tue, 27 Jun 2017 11:33:33: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:33:33: #2 alternative fragment length(s) may be 1,28,33,42,553,596 bps INFO @ Tue, 27 Jun 2017 11:33:33: #2.2 Generate R script for model : SRX2761388.05_model.r WARNING @ Tue, 27 Jun 2017 11:33:33: #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 11:33:33: #2 You may need to consider one of the other alternative d(s): 1,28,33,42,553,596 WARNING @ Tue, 27 Jun 2017 11:33:33: #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 11:33:33: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:33:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:33:51: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:33:58: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:33:59: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:34:06: #4 Write output xls file... SRX2761388.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:34:06: #4 Write peak in narrowPeak format file... SRX2761388.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:34:06: #4 Write summits bed file... SRX2761388.10_summits.bed INFO @ Tue, 27 Jun 2017 11:34:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:34:12: #4 Write output xls file... SRX2761388.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:34:12: #4 Write peak in narrowPeak format file... SRX2761388.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:34:12: #4 Write summits bed file... SRX2761388.05_summits.bed INFO @ Tue, 27 Jun 2017 11:34:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:34:13: #4 Write output xls file... SRX2761388.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:34:13: #4 Write peak in narrowPeak format file... SRX2761388.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:34:13: #4 Write summits bed file... SRX2761388.20_summits.bed INFO @ Tue, 27 Jun 2017 11:34:13: 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。