Job ID = 10714369 sra ファイルのダウンロード中... Completed: 697301K bytes transferred in 71 seconds (80213K bits/sec), in 1 file. 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... Read 42454831 spots for /home/okishinya/chipatlas/results/ce10/SRX2985928/SRR5807078.sra Written 42454831 spots for /home/okishinya/chipatlas/results/ce10/SRX2985928/SRR5807078.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:12:01 42454831 reads; of these: 42454831 (100.00%) were unpaired; of these: 1022627 (2.41%) aligned 0 times 32364497 (76.23%) aligned exactly 1 time 9067707 (21.36%) aligned >1 times 97.59% overall alignment rate Time searching: 00:12:01 Overall time: 00:12:01 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 20 files... [bam_rmdupse_core] 11946684 / 41432204 = 0.2883 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 @ Sun, 03 Jun 2018 12:52:09: # Command line: callpeak -t SRX2985928.bam -f BAM -g ce -n SRX2985928.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2985928.20 # format = BAM # ChIP-seq file = ['SRX2985928.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 @ Sun, 03 Jun 2018 12:52:09: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:52:09: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:52:09: # Command line: callpeak -t SRX2985928.bam -f BAM -g ce -n SRX2985928.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2985928.10 # format = BAM # ChIP-seq file = ['SRX2985928.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 @ Sun, 03 Jun 2018 12:52:09: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:52:09: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:52:09: # Command line: callpeak -t SRX2985928.bam -f BAM -g ce -n SRX2985928.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2985928.05 # format = BAM # ChIP-seq file = ['SRX2985928.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 @ Sun, 03 Jun 2018 12:52:09: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:52:09: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:52:17: 1000000 INFO @ Sun, 03 Jun 2018 12:52:18: 1000000 INFO @ Sun, 03 Jun 2018 12:52:18: 1000000 INFO @ Sun, 03 Jun 2018 12:52:25: 2000000 INFO @ Sun, 03 Jun 2018 12:52:26: 2000000 INFO @ Sun, 03 Jun 2018 12:52:26: 2000000 INFO @ Sun, 03 Jun 2018 12:52:33: 3000000 INFO @ Sun, 03 Jun 2018 12:52:34: 3000000 INFO @ Sun, 03 Jun 2018 12:52:34: 3000000 INFO @ Sun, 03 Jun 2018 12:52:40: 4000000 INFO @ Sun, 03 Jun 2018 12:52:42: 4000000 INFO @ Sun, 03 Jun 2018 12:52:42: 4000000 INFO @ Sun, 03 Jun 2018 12:52:48: 5000000 INFO @ Sun, 03 Jun 2018 12:52:50: 5000000 INFO @ Sun, 03 Jun 2018 12:52:50: 5000000 INFO @ Sun, 03 Jun 2018 12:52:56: 6000000 INFO @ Sun, 03 Jun 2018 12:52:58: 6000000 INFO @ Sun, 03 Jun 2018 12:52:58: 6000000 INFO @ Sun, 03 Jun 2018 12:53:03: 7000000 INFO @ Sun, 03 Jun 2018 12:53:06: 7000000 INFO @ Sun, 03 Jun 2018 12:53:06: 7000000 INFO @ Sun, 03 Jun 2018 12:53:11: 8000000 INFO @ Sun, 03 Jun 2018 12:53:15: 8000000 INFO @ Sun, 03 Jun 2018 12:53:15: 8000000 INFO @ Sun, 03 Jun 2018 12:53:19: 9000000 INFO @ Sun, 03 Jun 2018 12:53:23: 9000000 INFO @ Sun, 03 Jun 2018 12:53:23: 9000000 INFO @ Sun, 03 Jun 2018 12:53:27: 10000000 INFO @ Sun, 03 Jun 2018 12:53:31: 10000000 INFO @ Sun, 03 Jun 2018 12:53:31: 10000000 INFO @ Sun, 03 Jun 2018 12:53:34: 11000000 INFO @ Sun, 03 Jun 2018 12:53:39: 11000000 INFO @ Sun, 03 Jun 2018 12:53:39: 11000000 INFO @ Sun, 03 Jun 2018 12:53:42: 12000000 INFO @ Sun, 03 Jun 2018 12:53:47: 12000000 INFO @ Sun, 03 Jun 2018 12:53:47: 12000000 INFO @ Sun, 03 Jun 2018 12:53:48: 13000000 INFO @ Sun, 03 Jun 2018 12:53:55: 14000000 INFO @ Sun, 03 Jun 2018 12:53:56: 13000000 INFO @ Sun, 03 Jun 2018 12:53:56: 13000000 INFO @ Sun, 03 Jun 2018 12:54:01: 15000000 INFO @ Sun, 03 Jun 2018 12:54:03: 14000000 INFO @ Sun, 03 Jun 2018 12:54:03: 14000000 INFO @ Sun, 03 Jun 2018 12:54:08: 16000000 INFO @ Sun, 03 Jun 2018 12:54:10: 15000000 INFO @ Sun, 03 Jun 2018 12:54:10: 15000000 INFO @ Sun, 03 Jun 2018 12:54:14: 17000000 INFO @ Sun, 03 Jun 2018 12:54:18: 16000000 INFO @ Sun, 03 Jun 2018 12:54:18: 16000000 INFO @ Sun, 03 Jun 2018 12:54:21: 18000000 INFO @ Sun, 03 Jun 2018 12:54:25: 17000000 INFO @ Sun, 03 Jun 2018 12:54:25: 17000000 INFO @ Sun, 03 Jun 2018 12:54:27: 19000000 INFO @ Sun, 03 Jun 2018 12:54:32: 18000000 INFO @ Sun, 03 Jun 2018 12:54:32: 18000000 INFO @ Sun, 03 Jun 2018 12:54:33: 20000000 INFO @ Sun, 03 Jun 2018 12:54:39: 19000000 INFO @ Sun, 03 Jun 2018 12:54:39: 19000000 INFO @ Sun, 03 Jun 2018 12:54:40: 21000000 INFO @ Sun, 03 Jun 2018 12:54:46: 22000000 INFO @ Sun, 03 Jun 2018 12:54:46: 20000000 INFO @ Sun, 03 Jun 2018 12:54:46: 20000000 INFO @ Sun, 03 Jun 2018 12:54:53: 23000000 INFO @ Sun, 03 Jun 2018 12:54:54: 21000000 INFO @ Sun, 03 Jun 2018 12:54:54: 21000000 INFO @ Sun, 03 Jun 2018 12:54:59: 24000000 INFO @ Sun, 03 Jun 2018 12:55:01: 22000000 INFO @ Sun, 03 Jun 2018 12:55:01: 22000000 INFO @ Sun, 03 Jun 2018 12:55:05: 25000000 INFO @ Sun, 03 Jun 2018 12:55:08: 23000000 INFO @ Sun, 03 Jun 2018 12:55:08: 23000000 INFO @ Sun, 03 Jun 2018 12:55:12: 26000000 INFO @ Sun, 03 Jun 2018 12:55:15: 24000000 INFO @ Sun, 03 Jun 2018 12:55:15: 24000000 INFO @ Sun, 03 Jun 2018 12:55:18: 27000000 INFO @ Sun, 03 Jun 2018 12:55:22: 25000000 INFO @ Sun, 03 Jun 2018 12:55:22: 25000000 INFO @ Sun, 03 Jun 2018 12:55:24: 28000000 INFO @ Sun, 03 Jun 2018 12:55:29: 26000000 INFO @ Sun, 03 Jun 2018 12:55:29: 26000000 INFO @ Sun, 03 Jun 2018 12:55:31: 29000000 INFO @ Sun, 03 Jun 2018 12:55:34: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:55:34: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:55:34: #1 total tags in treatment: 29485520 INFO @ Sun, 03 Jun 2018 12:55:34: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:55:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:55:35: #1 tags after filtering in treatment: 29485520 INFO @ Sun, 03 Jun 2018 12:55:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:55:35: #1 finished! INFO @ Sun, 03 Jun 2018 12:55:35: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:55:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:55:36: 27000000 INFO @ Sun, 03 Jun 2018 12:55:36: 27000000 INFO @ Sun, 03 Jun 2018 12:55:37: #2 number of paired peaks: 160 WARNING @ Sun, 03 Jun 2018 12:55:37: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sun, 03 Jun 2018 12:55:37: start model_add_line... INFO @ Sun, 03 Jun 2018 12:55:37: start X-correlation... INFO @ Sun, 03 Jun 2018 12:55:37: end of X-cor INFO @ Sun, 03 Jun 2018 12:55:37: #2 finished! INFO @ Sun, 03 Jun 2018 12:55:37: #2 predicted fragment length is 1 bps INFO @ Sun, 03 Jun 2018 12:55:37: #2 alternative fragment length(s) may be 1,15,42,510 bps INFO @ Sun, 03 Jun 2018 12:55:37: #2.2 Generate R script for model : SRX2985928.05_model.r WARNING @ Sun, 03 Jun 2018 12:55:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:55:37: #2 You may need to consider one of the other alternative d(s): 1,15,42,510 WARNING @ Sun, 03 Jun 2018 12:55:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:55:37: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:55:43: 28000000 INFO @ Sun, 03 Jun 2018 12:55:43: 28000000 INFO @ Sun, 03 Jun 2018 12:55:49: 29000000 INFO @ Sun, 03 Jun 2018 12:55:49: 29000000 INFO @ Sun, 03 Jun 2018 12:55:53: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:55:53: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:55:53: #1 total tags in treatment: 29485520 INFO @ Sun, 03 Jun 2018 12:55:53: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:55:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:55:53: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:55:53: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:55:53: #1 total tags in treatment: 29485520 INFO @ Sun, 03 Jun 2018 12:55:53: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:55:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:55:53: #1 tags after filtering in treatment: 29485520 INFO @ Sun, 03 Jun 2018 12:55:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:55:53: #1 finished! INFO @ Sun, 03 Jun 2018 12:55:53: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:55:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:55:54: #1 tags after filtering in treatment: 29485520 INFO @ Sun, 03 Jun 2018 12:55:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:55:54: #1 finished! INFO @ Sun, 03 Jun 2018 12:55:54: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:55:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:55:55: #2 number of paired peaks: 160 WARNING @ Sun, 03 Jun 2018 12:55:55: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sun, 03 Jun 2018 12:55:55: start model_add_line... INFO @ Sun, 03 Jun 2018 12:55:55: #2 number of paired peaks: 160 WARNING @ Sun, 03 Jun 2018 12:55:55: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sun, 03 Jun 2018 12:55:55: start model_add_line... INFO @ Sun, 03 Jun 2018 12:55:56: start X-correlation... INFO @ Sun, 03 Jun 2018 12:55:56: end of X-cor INFO @ Sun, 03 Jun 2018 12:55:56: #2 finished! INFO @ Sun, 03 Jun 2018 12:55:56: #2 predicted fragment length is 1 bps INFO @ Sun, 03 Jun 2018 12:55:56: #2 alternative fragment length(s) may be 1,15,42,510 bps INFO @ Sun, 03 Jun 2018 12:55:56: #2.2 Generate R script for model : SRX2985928.10_model.r WARNING @ Sun, 03 Jun 2018 12:55:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:55:56: #2 You may need to consider one of the other alternative d(s): 1,15,42,510 WARNING @ Sun, 03 Jun 2018 12:55:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:55:56: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:55:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:55:56: start X-correlation... INFO @ Sun, 03 Jun 2018 12:55:56: end of X-cor INFO @ Sun, 03 Jun 2018 12:55:56: #2 finished! INFO @ Sun, 03 Jun 2018 12:55:56: #2 predicted fragment length is 1 bps INFO @ Sun, 03 Jun 2018 12:55:56: #2 alternative fragment length(s) may be 1,15,42,510 bps INFO @ Sun, 03 Jun 2018 12:55:56: #2.2 Generate R script for model : SRX2985928.20_model.r WARNING @ Sun, 03 Jun 2018 12:55:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:55:56: #2 You may need to consider one of the other alternative d(s): 1,15,42,510 WARNING @ Sun, 03 Jun 2018 12:55:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:55:56: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:55:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:56:22: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:56:37: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:56:38: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:56:44: #4 Write output xls file... SRX2985928.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:56:44: #4 Write peak in narrowPeak format file... SRX2985928.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:56:44: #4 Write summits bed file... SRX2985928.05_summits.bed INFO @ Sun, 03 Jun 2018 12:56:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:56:59: #4 Write output xls file... SRX2985928.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:56:59: #4 Write peak in narrowPeak format file... SRX2985928.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:56:59: #4 Write summits bed file... SRX2985928.10_summits.bed INFO @ Sun, 03 Jun 2018 12:56:59: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:57:00: #4 Write output xls file... SRX2985928.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:57:00: #4 Write peak in narrowPeak format file... SRX2985928.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:57:00: #4 Write summits bed file... SRX2985928.20_summits.bed INFO @ Sun, 03 Jun 2018 12:57:00: 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。