Job ID = 9158490 sra ファイルのダウンロード中... Completed: 1526939K bytes transferred in 15 seconds (811982K 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 49142444 spots for /home/okishinya/chipatlas/results/dm3/SRX1361351/SRR2749789.sra Written 49142444 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: 00:00:01 Multiseed full-index search: 00:25:23 49142444 reads; of these: 49142444 (100.00%) were unpaired; of these: 3194508 (6.50%) aligned 0 times 22390085 (45.56%) aligned exactly 1 time 23557851 (47.94%) aligned >1 times 93.50% overall alignment rate Time searching: 00:25:24 Overall time: 00:25:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 14897556 / 45947936 = 0.3242 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 17:44:50: # Command line: callpeak -t SRX1361351.bam -f BAM -g dm -n SRX1361351.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1361351.10 # format = BAM # ChIP-seq file = ['SRX1361351.bam'] # control file = None # effective genome size = 1.20e+08 # 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 17:44:50: # Command line: callpeak -t SRX1361351.bam -f BAM -g dm -n SRX1361351.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1361351.20 # format = BAM # ChIP-seq file = ['SRX1361351.bam'] # control file = None # effective genome size = 1.20e+08 # 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 17:44:50: # Command line: callpeak -t SRX1361351.bam -f BAM -g dm -n SRX1361351.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1361351.05 # format = BAM # ChIP-seq file = ['SRX1361351.bam'] # control file = None # effective genome size = 1.20e+08 # 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 17:44:50: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:44:50: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:44:50: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:44:50: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:44:50: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:44:50: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:44:58: 1000000 INFO @ Tue, 27 Jun 2017 17:44:58: 1000000 INFO @ Tue, 27 Jun 2017 17:44:58: 1000000 INFO @ Tue, 27 Jun 2017 17:45:06: 2000000 INFO @ Tue, 27 Jun 2017 17:45:07: 2000000 INFO @ Tue, 27 Jun 2017 17:45:07: 2000000 INFO @ Tue, 27 Jun 2017 17:45:14: 3000000 INFO @ Tue, 27 Jun 2017 17:45:16: 3000000 INFO @ Tue, 27 Jun 2017 17:45:16: 3000000 INFO @ Tue, 27 Jun 2017 17:45:21: 4000000 INFO @ Tue, 27 Jun 2017 17:45:24: 4000000 INFO @ Tue, 27 Jun 2017 17:45:24: 4000000 INFO @ Tue, 27 Jun 2017 17:45:29: 5000000 INFO @ Tue, 27 Jun 2017 17:45:33: 5000000 INFO @ Tue, 27 Jun 2017 17:45:33: 5000000 INFO @ Tue, 27 Jun 2017 17:45:37: 6000000 INFO @ Tue, 27 Jun 2017 17:45:42: 6000000 INFO @ Tue, 27 Jun 2017 17:45:42: 6000000 INFO @ Tue, 27 Jun 2017 17:45:45: 7000000 INFO @ Tue, 27 Jun 2017 17:45:51: 7000000 INFO @ Tue, 27 Jun 2017 17:45:51: 7000000 INFO @ Tue, 27 Jun 2017 17:45:52: 8000000 INFO @ Tue, 27 Jun 2017 17:46:00: 8000000 INFO @ Tue, 27 Jun 2017 17:46:00: 8000000 INFO @ Tue, 27 Jun 2017 17:46:00: 9000000 INFO @ Tue, 27 Jun 2017 17:46:08: 10000000 INFO @ Tue, 27 Jun 2017 17:46:09: 9000000 INFO @ Tue, 27 Jun 2017 17:46:09: 9000000 INFO @ Tue, 27 Jun 2017 17:46:15: 11000000 INFO @ Tue, 27 Jun 2017 17:46:17: 10000000 INFO @ Tue, 27 Jun 2017 17:46:17: 10000000 INFO @ Tue, 27 Jun 2017 17:46:23: 12000000 INFO @ Tue, 27 Jun 2017 17:46:26: 11000000 INFO @ Tue, 27 Jun 2017 17:46:26: 11000000 INFO @ Tue, 27 Jun 2017 17:46:31: 13000000 INFO @ Tue, 27 Jun 2017 17:46:35: 12000000 INFO @ Tue, 27 Jun 2017 17:46:35: 12000000 INFO @ Tue, 27 Jun 2017 17:46:38: 14000000 INFO @ Tue, 27 Jun 2017 17:46:44: 13000000 INFO @ Tue, 27 Jun 2017 17:46:44: 13000000 INFO @ Tue, 27 Jun 2017 17:46:46: 15000000 INFO @ Tue, 27 Jun 2017 17:46:53: 14000000 INFO @ Tue, 27 Jun 2017 17:46:53: 14000000 INFO @ Tue, 27 Jun 2017 17:46:54: 16000000 INFO @ Tue, 27 Jun 2017 17:47:01: 17000000 INFO @ Tue, 27 Jun 2017 17:47:01: 15000000 INFO @ Tue, 27 Jun 2017 17:47:01: 15000000 INFO @ Tue, 27 Jun 2017 17:47:09: 18000000 INFO @ Tue, 27 Jun 2017 17:47:11: 16000000 INFO @ Tue, 27 Jun 2017 17:47:11: 16000000 INFO @ Tue, 27 Jun 2017 17:47:16: 19000000 INFO @ Tue, 27 Jun 2017 17:47:20: 17000000 INFO @ Tue, 27 Jun 2017 17:47:20: 17000000 INFO @ Tue, 27 Jun 2017 17:47:24: 20000000 INFO @ Tue, 27 Jun 2017 17:47:29: 18000000 INFO @ Tue, 27 Jun 2017 17:47:29: 18000000 INFO @ Tue, 27 Jun 2017 17:47:31: 21000000 INFO @ Tue, 27 Jun 2017 17:47:38: 19000000 INFO @ Tue, 27 Jun 2017 17:47:38: 19000000 INFO @ Tue, 27 Jun 2017 17:47:38: 22000000 INFO @ Tue, 27 Jun 2017 17:47:46: 23000000 INFO @ Tue, 27 Jun 2017 17:47:47: 20000000 INFO @ Tue, 27 Jun 2017 17:47:47: 20000000 INFO @ Tue, 27 Jun 2017 17:47:53: 24000000 INFO @ Tue, 27 Jun 2017 17:47:56: 21000000 INFO @ Tue, 27 Jun 2017 17:47:56: 21000000 INFO @ Tue, 27 Jun 2017 17:48:00: 25000000 INFO @ Tue, 27 Jun 2017 17:48:06: 22000000 INFO @ Tue, 27 Jun 2017 17:48:06: 22000000 INFO @ Tue, 27 Jun 2017 17:48:08: 26000000 INFO @ Tue, 27 Jun 2017 17:48:15: 23000000 INFO @ Tue, 27 Jun 2017 17:48:15: 23000000 INFO @ Tue, 27 Jun 2017 17:48:15: 27000000 INFO @ Tue, 27 Jun 2017 17:48:22: 28000000 INFO @ Tue, 27 Jun 2017 17:48:24: 24000000 INFO @ Tue, 27 Jun 2017 17:48:24: 24000000 INFO @ Tue, 27 Jun 2017 17:48:30: 29000000 INFO @ Tue, 27 Jun 2017 17:48:33: 25000000 INFO @ Tue, 27 Jun 2017 17:48:33: 25000000 INFO @ Tue, 27 Jun 2017 17:48:37: 30000000 INFO @ Tue, 27 Jun 2017 17:48:42: 26000000 INFO @ Tue, 27 Jun 2017 17:48:42: 26000000 INFO @ Tue, 27 Jun 2017 17:48:44: 31000000 INFO @ Tue, 27 Jun 2017 17:48:45: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 17:48:45: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 17:48:45: #1 total tags in treatment: 31050380 INFO @ Tue, 27 Jun 2017 17:48:45: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 17:48:45: #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 17:48:46: #1 tags after filtering in treatment: 31050380 INFO @ Tue, 27 Jun 2017 17:48:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 17:48:46: #1 finished! INFO @ Tue, 27 Jun 2017 17:48:46: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 17:48:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 17:48:48: #2 number of paired peaks: 253 WARNING @ Tue, 27 Jun 2017 17:48:48: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 27 Jun 2017 17:48:48: start model_add_line... INFO @ Tue, 27 Jun 2017 17:48:48: start X-correlation... INFO @ Tue, 27 Jun 2017 17:48:48: end of X-cor INFO @ Tue, 27 Jun 2017 17:48:48: #2 finished! INFO @ Tue, 27 Jun 2017 17:48:48: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 17:48:48: #2 alternative fragment length(s) may be 1,31 bps INFO @ Tue, 27 Jun 2017 17:48:48: #2.2 Generate R script for model : SRX1361351.05_model.r WARNING @ Tue, 27 Jun 2017 17:48:48: #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 17:48:48: #2 You may need to consider one of the other alternative d(s): 1,31 WARNING @ Tue, 27 Jun 2017 17:48:48: #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 17:48:48: #3 Call peaks... INFO @ Tue, 27 Jun 2017 17:48:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 17:48:50: 27000000 INFO @ Tue, 27 Jun 2017 17:48:51: 27000000 INFO @ Tue, 27 Jun 2017 17:48:58: 28000000 INFO @ Tue, 27 Jun 2017 17:49:00: 28000000 INFO @ Tue, 27 Jun 2017 17:49:06: 29000000 INFO @ Tue, 27 Jun 2017 17:49:09: 29000000 INFO @ Tue, 27 Jun 2017 17:49:14: 30000000 INFO @ Tue, 27 Jun 2017 17:49:17: 30000000 INFO @ Tue, 27 Jun 2017 17:49:22: 31000000 INFO @ Tue, 27 Jun 2017 17:49:23: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 17:49:23: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 17:49:23: #1 total tags in treatment: 31050380 INFO @ Tue, 27 Jun 2017 17:49:23: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 17:49:23: #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 17:49:24: #1 tags after filtering in treatment: 31050380 INFO @ Tue, 27 Jun 2017 17:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 17:49:24: #1 finished! INFO @ Tue, 27 Jun 2017 17:49:24: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 17:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 17:49:26: #2 number of paired peaks: 253 WARNING @ Tue, 27 Jun 2017 17:49:26: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 27 Jun 2017 17:49:26: start model_add_line... INFO @ Tue, 27 Jun 2017 17:49:26: start X-correlation... INFO @ Tue, 27 Jun 2017 17:49:26: end of X-cor INFO @ Tue, 27 Jun 2017 17:49:26: #2 finished! INFO @ Tue, 27 Jun 2017 17:49:26: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 17:49:26: #2 alternative fragment length(s) may be 1,31 bps INFO @ Tue, 27 Jun 2017 17:49:26: #2.2 Generate R script for model : SRX1361351.20_model.r WARNING @ Tue, 27 Jun 2017 17:49:26: #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 17:49:26: #2 You may need to consider one of the other alternative d(s): 1,31 WARNING @ Tue, 27 Jun 2017 17:49:26: #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 17:49:26: #3 Call peaks... INFO @ Tue, 27 Jun 2017 17:49:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 17:49:26: 31000000 INFO @ Tue, 27 Jun 2017 17:49:27: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 17:49:27: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 17:49:27: #1 total tags in treatment: 31050380 INFO @ Tue, 27 Jun 2017 17:49:27: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 17:49:27: #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 17:49:27: #1 tags after filtering in treatment: 31050380 INFO @ Tue, 27 Jun 2017 17:49:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 17:49:27: #1 finished! INFO @ Tue, 27 Jun 2017 17:49:27: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 17:49:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 17:49:29: #2 number of paired peaks: 253 WARNING @ Tue, 27 Jun 2017 17:49:29: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 27 Jun 2017 17:49:29: start model_add_line... INFO @ Tue, 27 Jun 2017 17:49:29: start X-correlation... INFO @ Tue, 27 Jun 2017 17:49:29: end of X-cor INFO @ Tue, 27 Jun 2017 17:49:29: #2 finished! INFO @ Tue, 27 Jun 2017 17:49:29: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 17:49:29: #2 alternative fragment length(s) may be 1,31 bps INFO @ Tue, 27 Jun 2017 17:49:29: #2.2 Generate R script for model : SRX1361351.10_model.r WARNING @ Tue, 27 Jun 2017 17:49:29: #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 17:49:29: #2 You may need to consider one of the other alternative d(s): 1,31 WARNING @ Tue, 27 Jun 2017 17:49:29: #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 17:49:29: #3 Call peaks... INFO @ Tue, 27 Jun 2017 17:49:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 17:49:40: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 17:50:05: #4 Write output xls file... SRX1361351.05_peaks.xls INFO @ Tue, 27 Jun 2017 17:50:05: #4 Write peak in narrowPeak format file... SRX1361351.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 17:50:05: #4 Write summits bed file... SRX1361351.05_summits.bed INFO @ Tue, 27 Jun 2017 17:50:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 17:50:14: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 17:50:21: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 17:50:41: #4 Write output xls file... SRX1361351.20_peaks.xls INFO @ Tue, 27 Jun 2017 17:50:41: #4 Write peak in narrowPeak format file... SRX1361351.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 17:50:41: #4 Write summits bed file... SRX1361351.20_summits.bed INFO @ Tue, 27 Jun 2017 17:50:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 17:50:47: #4 Write output xls file... SRX1361351.10_peaks.xls INFO @ Tue, 27 Jun 2017 17:50:47: #4 Write peak in narrowPeak format file... SRX1361351.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 17:50:47: #4 Write summits bed file... SRX1361351.10_summits.bed INFO @ Tue, 27 Jun 2017 17:50:47: Done! pass1 - making usageList (0 chroms): 1 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。