Job ID = 9157389 sra ファイルのダウンロード中... Completed: 1320195K bytes transferred in 16 seconds (665142K bits/sec), in 2 files, 3 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 21894547 spots for /home/okishinya/chipatlas/results/ce10/SRX1844113/SRR3665606.sra Written 21894547 spots total Written 22258098 spots for /home/okishinya/chipatlas/results/ce10/SRX1844113/SRR3665605.sra Written 22258098 spots total 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: 00:12:15 44152645 reads; of these: 44152645 (100.00%) were unpaired; of these: 11259438 (25.50%) aligned 0 times 28557763 (64.68%) aligned exactly 1 time 4335444 (9.82%) aligned >1 times 74.50% overall alignment rate Time searching: 00:12:15 Overall time: 00:12:15 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 16 files... [bam_rmdupse_core] 18959300 / 32893207 = 0.5764 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 11:59:14: # Command line: callpeak -t SRX1844113.bam -f BAM -g ce -n SRX1844113.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1844113.05 # format = BAM # ChIP-seq file = ['SRX1844113.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 11:59:14: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:59:14: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:59:14: # Command line: callpeak -t SRX1844113.bam -f BAM -g ce -n SRX1844113.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1844113.20 # format = BAM # ChIP-seq file = ['SRX1844113.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 11:59:14: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:59:14: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:59:14: # Command line: callpeak -t SRX1844113.bam -f BAM -g ce -n SRX1844113.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1844113.10 # format = BAM # ChIP-seq file = ['SRX1844113.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 11:59:14: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:59:14: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:59:21: 1000000 INFO @ Tue, 27 Jun 2017 11:59:21: 1000000 INFO @ Tue, 27 Jun 2017 11:59:21: 1000000 INFO @ Tue, 27 Jun 2017 11:59:28: 2000000 INFO @ Tue, 27 Jun 2017 11:59:29: 2000000 INFO @ Tue, 27 Jun 2017 11:59:29: 2000000 INFO @ Tue, 27 Jun 2017 11:59:35: 3000000 INFO @ Tue, 27 Jun 2017 11:59:36: 3000000 INFO @ Tue, 27 Jun 2017 11:59:36: 3000000 INFO @ Tue, 27 Jun 2017 11:59:41: 4000000 INFO @ Tue, 27 Jun 2017 11:59:43: 4000000 INFO @ Tue, 27 Jun 2017 11:59:44: 4000000 INFO @ Tue, 27 Jun 2017 11:59:48: 5000000 INFO @ Tue, 27 Jun 2017 11:59:51: 5000000 INFO @ Tue, 27 Jun 2017 11:59:52: 5000000 INFO @ Tue, 27 Jun 2017 11:59:55: 6000000 INFO @ Tue, 27 Jun 2017 11:59:59: 6000000 INFO @ Tue, 27 Jun 2017 12:00:00: 6000000 INFO @ Tue, 27 Jun 2017 12:00:01: 7000000 INFO @ Tue, 27 Jun 2017 12:00:07: 7000000 INFO @ Tue, 27 Jun 2017 12:00:08: 8000000 INFO @ Tue, 27 Jun 2017 12:00:09: 7000000 INFO @ Tue, 27 Jun 2017 12:00:14: 9000000 INFO @ Tue, 27 Jun 2017 12:00:14: 8000000 INFO @ Tue, 27 Jun 2017 12:00:17: 8000000 INFO @ Tue, 27 Jun 2017 12:00:21: 10000000 INFO @ Tue, 27 Jun 2017 12:00:22: 9000000 INFO @ Tue, 27 Jun 2017 12:00:25: 9000000 INFO @ Tue, 27 Jun 2017 12:00:28: 11000000 INFO @ Tue, 27 Jun 2017 12:00:30: 10000000 INFO @ Tue, 27 Jun 2017 12:00:33: 10000000 INFO @ Tue, 27 Jun 2017 12:00:36: 12000000 INFO @ Tue, 27 Jun 2017 12:00:38: 11000000 INFO @ Tue, 27 Jun 2017 12:00:41: 11000000 INFO @ Tue, 27 Jun 2017 12:00:42: 13000000 INFO @ Tue, 27 Jun 2017 12:00:45: 12000000 INFO @ Tue, 27 Jun 2017 12:00:48: #1 tag size is determined as 45 bps INFO @ Tue, 27 Jun 2017 12:00:48: #1 tag size = 45 INFO @ Tue, 27 Jun 2017 12:00:48: #1 total tags in treatment: 13933907 INFO @ Tue, 27 Jun 2017 12:00:48: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:00:48: #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 12:00:49: #1 tags after filtering in treatment: 13933907 INFO @ Tue, 27 Jun 2017 12:00:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:00:49: #1 finished! INFO @ Tue, 27 Jun 2017 12:00:49: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:00:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:00:50: 12000000 INFO @ Tue, 27 Jun 2017 12:00:50: #2 number of paired peaks: 127 WARNING @ Tue, 27 Jun 2017 12:00:50: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Tue, 27 Jun 2017 12:00:50: start model_add_line... INFO @ Tue, 27 Jun 2017 12:00:50: start X-correlation... INFO @ Tue, 27 Jun 2017 12:00:50: end of X-cor INFO @ Tue, 27 Jun 2017 12:00:50: #2 finished! INFO @ Tue, 27 Jun 2017 12:00:50: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 12:00:50: #2 alternative fragment length(s) may be 2,33,63,86,578 bps INFO @ Tue, 27 Jun 2017 12:00:50: #2.2 Generate R script for model : SRX1844113.10_model.r WARNING @ Tue, 27 Jun 2017 12:00:50: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 12:00:50: #2 You may need to consider one of the other alternative d(s): 2,33,63,86,578 WARNING @ Tue, 27 Jun 2017 12:00:50: #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 12:00:50: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:00:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:00:53: 13000000 INFO @ Tue, 27 Jun 2017 12:00:58: 13000000 INFO @ Tue, 27 Jun 2017 12:01:00: #1 tag size is determined as 45 bps INFO @ Tue, 27 Jun 2017 12:01:00: #1 tag size = 45 INFO @ Tue, 27 Jun 2017 12:01:00: #1 total tags in treatment: 13933907 INFO @ Tue, 27 Jun 2017 12:01:00: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:01:00: #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 12:01:01: #1 tags after filtering in treatment: 13933907 INFO @ Tue, 27 Jun 2017 12:01:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:01:01: #1 finished! INFO @ Tue, 27 Jun 2017 12:01:01: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:01:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:01:01: #2 number of paired peaks: 127 WARNING @ Tue, 27 Jun 2017 12:01:01: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Tue, 27 Jun 2017 12:01:01: start model_add_line... INFO @ Tue, 27 Jun 2017 12:01:02: start X-correlation... INFO @ Tue, 27 Jun 2017 12:01:02: end of X-cor INFO @ Tue, 27 Jun 2017 12:01:02: #2 finished! INFO @ Tue, 27 Jun 2017 12:01:02: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 12:01:02: #2 alternative fragment length(s) may be 2,33,63,86,578 bps INFO @ Tue, 27 Jun 2017 12:01:02: #2.2 Generate R script for model : SRX1844113.20_model.r WARNING @ Tue, 27 Jun 2017 12:01:02: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 12:01:02: #2 You may need to consider one of the other alternative d(s): 2,33,63,86,578 WARNING @ Tue, 27 Jun 2017 12:01:02: #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 12:01:02: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:01:05: #1 tag size is determined as 45 bps INFO @ Tue, 27 Jun 2017 12:01:05: #1 tag size = 45 INFO @ Tue, 27 Jun 2017 12:01:05: #1 total tags in treatment: 13933907 INFO @ Tue, 27 Jun 2017 12:01:05: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:01:05: #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 12:01:05: #1 tags after filtering in treatment: 13933907 INFO @ Tue, 27 Jun 2017 12:01:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:01:05: #1 finished! INFO @ Tue, 27 Jun 2017 12:01:05: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:01:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:01:06: #2 number of paired peaks: 127 WARNING @ Tue, 27 Jun 2017 12:01:06: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Tue, 27 Jun 2017 12:01:06: start model_add_line... INFO @ Tue, 27 Jun 2017 12:01:06: start X-correlation... INFO @ Tue, 27 Jun 2017 12:01:06: end of X-cor INFO @ Tue, 27 Jun 2017 12:01:06: #2 finished! INFO @ Tue, 27 Jun 2017 12:01:06: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 12:01:06: #2 alternative fragment length(s) may be 2,33,63,86,578 bps INFO @ Tue, 27 Jun 2017 12:01:06: #2.2 Generate R script for model : SRX1844113.05_model.r WARNING @ Tue, 27 Jun 2017 12:01:06: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 12:01:06: #2 You may need to consider one of the other alternative d(s): 2,33,63,86,578 WARNING @ Tue, 27 Jun 2017 12:01:06: #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 12:01:06: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:01:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:01:14: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:01:26: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:01:29: #4 Write output xls file... SRX1844113.10_peaks.xls INFO @ Tue, 27 Jun 2017 12:01:29: #4 Write peak in narrowPeak format file... SRX1844113.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:01:29: #4 Write summits bed file... SRX1844113.10_summits.bed INFO @ Tue, 27 Jun 2017 12:01:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:01:31: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:01:41: #4 Write output xls file... SRX1844113.20_peaks.xls INFO @ Tue, 27 Jun 2017 12:01:41: #4 Write peak in narrowPeak format file... SRX1844113.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:01:41: #4 Write summits bed file... SRX1844113.20_summits.bed INFO @ Tue, 27 Jun 2017 12:01:41: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:01:44: #4 Write output xls file... SRX1844113.05_peaks.xls INFO @ Tue, 27 Jun 2017 12:01:44: #4 Write peak in narrowPeak format file... SRX1844113.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:01:44: #4 Write summits bed file... SRX1844113.05_summits.bed INFO @ Tue, 27 Jun 2017 12:01:44: 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。