Job ID = 9157384 sra ファイルのダウンロード中... Completed: 1345944K bytes transferred in 15 seconds (696448K 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 58288493 spots for /home/okishinya/chipatlas/results/ce10/SRX1674101/SRR3320147.sra Written 58288493 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: 00:16:31 58288493 reads; of these: 58288493 (100.00%) were unpaired; of these: 1869972 (3.21%) aligned 0 times 50298498 (86.29%) aligned exactly 1 time 6120023 (10.50%) aligned >1 times 96.79% overall alignment rate Time searching: 00:16:31 Overall time: 00:16:31 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 24 files... [bam_rmdupse_core] 23734910 / 56418521 = 0.4207 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 12:06:55: # Command line: callpeak -t SRX1674101.bam -f BAM -g ce -n SRX1674101.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1674101.05 # format = BAM # ChIP-seq file = ['SRX1674101.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 12:06:55: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:06:55: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:06:55: # Command line: callpeak -t SRX1674101.bam -f BAM -g ce -n SRX1674101.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1674101.20 # format = BAM # ChIP-seq file = ['SRX1674101.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 12:06:55: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:06:55: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:06:55: # Command line: callpeak -t SRX1674101.bam -f BAM -g ce -n SRX1674101.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1674101.10 # format = BAM # ChIP-seq file = ['SRX1674101.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 12:06:55: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:06:55: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:07:03: 1000000 INFO @ Tue, 27 Jun 2017 12:07:03: 1000000 INFO @ Tue, 27 Jun 2017 12:07:03: 1000000 INFO @ Tue, 27 Jun 2017 12:07:10: 2000000 INFO @ Tue, 27 Jun 2017 12:07:11: 2000000 INFO @ Tue, 27 Jun 2017 12:07:12: 2000000 INFO @ Tue, 27 Jun 2017 12:07:19: 3000000 INFO @ Tue, 27 Jun 2017 12:07:19: 3000000 INFO @ Tue, 27 Jun 2017 12:07:20: 3000000 INFO @ Tue, 27 Jun 2017 12:07:27: 4000000 INFO @ Tue, 27 Jun 2017 12:07:27: 4000000 INFO @ Tue, 27 Jun 2017 12:07:29: 4000000 INFO @ Tue, 27 Jun 2017 12:07:34: 5000000 INFO @ Tue, 27 Jun 2017 12:07:35: 5000000 INFO @ Tue, 27 Jun 2017 12:07:38: 5000000 INFO @ Tue, 27 Jun 2017 12:07:42: 6000000 INFO @ Tue, 27 Jun 2017 12:07:43: 6000000 INFO @ Tue, 27 Jun 2017 12:07:47: 6000000 INFO @ Tue, 27 Jun 2017 12:07:50: 7000000 INFO @ Tue, 27 Jun 2017 12:07:52: 7000000 INFO @ Tue, 27 Jun 2017 12:07:56: 7000000 INFO @ Tue, 27 Jun 2017 12:07:57: 8000000 INFO @ Tue, 27 Jun 2017 12:08:00: 8000000 INFO @ Tue, 27 Jun 2017 12:08:05: 8000000 INFO @ Tue, 27 Jun 2017 12:08:05: 9000000 INFO @ Tue, 27 Jun 2017 12:08:08: 9000000 INFO @ Tue, 27 Jun 2017 12:08:12: 10000000 INFO @ Tue, 27 Jun 2017 12:08:13: 9000000 INFO @ Tue, 27 Jun 2017 12:08:17: 10000000 INFO @ Tue, 27 Jun 2017 12:08:20: 11000000 INFO @ Tue, 27 Jun 2017 12:08:22: 10000000 INFO @ Tue, 27 Jun 2017 12:08:25: 11000000 INFO @ Tue, 27 Jun 2017 12:08:27: 12000000 INFO @ Tue, 27 Jun 2017 12:08:31: 11000000 INFO @ Tue, 27 Jun 2017 12:08:33: 12000000 INFO @ Tue, 27 Jun 2017 12:08:34: 13000000 INFO @ Tue, 27 Jun 2017 12:08:40: 12000000 INFO @ Tue, 27 Jun 2017 12:08:41: 14000000 INFO @ Tue, 27 Jun 2017 12:08:41: 13000000 INFO @ Tue, 27 Jun 2017 12:08:48: 15000000 INFO @ Tue, 27 Jun 2017 12:08:49: 13000000 INFO @ Tue, 27 Jun 2017 12:08:50: 14000000 INFO @ Tue, 27 Jun 2017 12:08:55: 16000000 INFO @ Tue, 27 Jun 2017 12:08:57: 14000000 INFO @ Tue, 27 Jun 2017 12:08:58: 15000000 INFO @ Tue, 27 Jun 2017 12:09:02: 17000000 INFO @ Tue, 27 Jun 2017 12:09:06: 16000000 INFO @ Tue, 27 Jun 2017 12:09:06: 15000000 INFO @ Tue, 27 Jun 2017 12:09:10: 18000000 INFO @ Tue, 27 Jun 2017 12:09:14: 17000000 INFO @ Tue, 27 Jun 2017 12:09:15: 16000000 INFO @ Tue, 27 Jun 2017 12:09:17: 19000000 INFO @ Tue, 27 Jun 2017 12:09:23: 18000000 INFO @ Tue, 27 Jun 2017 12:09:24: 17000000 INFO @ Tue, 27 Jun 2017 12:09:24: 20000000 INFO @ Tue, 27 Jun 2017 12:09:31: 19000000 INFO @ Tue, 27 Jun 2017 12:09:31: 21000000 INFO @ Tue, 27 Jun 2017 12:09:33: 18000000 INFO @ Tue, 27 Jun 2017 12:09:38: 22000000 INFO @ Tue, 27 Jun 2017 12:09:39: 20000000 INFO @ Tue, 27 Jun 2017 12:09:42: 19000000 INFO @ Tue, 27 Jun 2017 12:09:45: 23000000 INFO @ Tue, 27 Jun 2017 12:09:47: 21000000 INFO @ Tue, 27 Jun 2017 12:09:50: 20000000 INFO @ Tue, 27 Jun 2017 12:09:52: 24000000 INFO @ Tue, 27 Jun 2017 12:09:55: 22000000 INFO @ Tue, 27 Jun 2017 12:09:59: 21000000 INFO @ Tue, 27 Jun 2017 12:09:59: 25000000 INFO @ Tue, 27 Jun 2017 12:10:04: 23000000 INFO @ Tue, 27 Jun 2017 12:10:07: 26000000 INFO @ Tue, 27 Jun 2017 12:10:08: 22000000 INFO @ Tue, 27 Jun 2017 12:10:12: 24000000 INFO @ Tue, 27 Jun 2017 12:10:14: 27000000 INFO @ Tue, 27 Jun 2017 12:10:17: 23000000 INFO @ Tue, 27 Jun 2017 12:10:20: 25000000 INFO @ Tue, 27 Jun 2017 12:10:21: 28000000 INFO @ Tue, 27 Jun 2017 12:10:26: 24000000 INFO @ Tue, 27 Jun 2017 12:10:28: 29000000 INFO @ Tue, 27 Jun 2017 12:10:29: 26000000 INFO @ Tue, 27 Jun 2017 12:10:35: 25000000 INFO @ Tue, 27 Jun 2017 12:10:35: 30000000 INFO @ Tue, 27 Jun 2017 12:10:37: 27000000 INFO @ Tue, 27 Jun 2017 12:10:42: 31000000 INFO @ Tue, 27 Jun 2017 12:10:44: 26000000 INFO @ Tue, 27 Jun 2017 12:10:45: 28000000 INFO @ Tue, 27 Jun 2017 12:10:49: 32000000 INFO @ Tue, 27 Jun 2017 12:10:53: 27000000 INFO @ Tue, 27 Jun 2017 12:10:54: 29000000 INFO @ Tue, 27 Jun 2017 12:10:54: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 12:10:54: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 12:10:54: #1 total tags in treatment: 32683611 INFO @ Tue, 27 Jun 2017 12:10:54: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:10:54: #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 12:10:55: #1 tags after filtering in treatment: 32683611 INFO @ Tue, 27 Jun 2017 12:10:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:10:55: #1 finished! INFO @ Tue, 27 Jun 2017 12:10:55: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:10:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:10:57: #2 number of paired peaks: 428 WARNING @ Tue, 27 Jun 2017 12:10:57: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 27 Jun 2017 12:10:57: start model_add_line... INFO @ Tue, 27 Jun 2017 12:10:57: start X-correlation... INFO @ Tue, 27 Jun 2017 12:10:57: end of X-cor INFO @ Tue, 27 Jun 2017 12:10:57: #2 finished! INFO @ Tue, 27 Jun 2017 12:10:57: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 12:10:57: #2 alternative fragment length(s) may be 1,39,78,97,123,154,178,205,236 bps INFO @ Tue, 27 Jun 2017 12:10:57: #2.2 Generate R script for model : SRX1674101.05_model.r WARNING @ Tue, 27 Jun 2017 12:10:57: #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 12:10:57: #2 You may need to consider one of the other alternative d(s): 1,39,78,97,123,154,178,205,236 WARNING @ Tue, 27 Jun 2017 12:10:57: #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 12:10:57: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:10:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:11:02: 28000000 INFO @ Tue, 27 Jun 2017 12:11:02: 30000000 INFO @ Tue, 27 Jun 2017 12:11:11: 29000000 INFO @ Tue, 27 Jun 2017 12:11:11: 31000000 INFO @ Tue, 27 Jun 2017 12:11:20: 32000000 INFO @ Tue, 27 Jun 2017 12:11:20: 30000000 INFO @ Tue, 27 Jun 2017 12:11:26: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 12:11:26: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 12:11:26: #1 total tags in treatment: 32683611 INFO @ Tue, 27 Jun 2017 12:11:26: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:11:26: #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 12:11:26: #1 tags after filtering in treatment: 32683611 INFO @ Tue, 27 Jun 2017 12:11:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:11:26: #1 finished! INFO @ Tue, 27 Jun 2017 12:11:26: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:11:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:11:28: 31000000 INFO @ Tue, 27 Jun 2017 12:11:29: #2 number of paired peaks: 428 WARNING @ Tue, 27 Jun 2017 12:11:29: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 27 Jun 2017 12:11:29: start model_add_line... INFO @ Tue, 27 Jun 2017 12:11:29: start X-correlation... INFO @ Tue, 27 Jun 2017 12:11:29: end of X-cor INFO @ Tue, 27 Jun 2017 12:11:29: #2 finished! INFO @ Tue, 27 Jun 2017 12:11:29: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 12:11:29: #2 alternative fragment length(s) may be 1,39,78,97,123,154,178,205,236 bps INFO @ Tue, 27 Jun 2017 12:11:29: #2.2 Generate R script for model : SRX1674101.10_model.r WARNING @ Tue, 27 Jun 2017 12:11:29: #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 12:11:29: #2 You may need to consider one of the other alternative d(s): 1,39,78,97,123,154,178,205,236 WARNING @ Tue, 27 Jun 2017 12:11:29: #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 12:11:29: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:11:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:11:36: 32000000 INFO @ Tue, 27 Jun 2017 12:11:39: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:11:42: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 12:11:42: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 12:11:42: #1 total tags in treatment: 32683611 INFO @ Tue, 27 Jun 2017 12:11:42: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:11:42: #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 12:11:42: #1 tags after filtering in treatment: 32683611 INFO @ Tue, 27 Jun 2017 12:11:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:11:42: #1 finished! INFO @ Tue, 27 Jun 2017 12:11:42: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:11:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:11:44: #2 number of paired peaks: 428 WARNING @ Tue, 27 Jun 2017 12:11:44: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 27 Jun 2017 12:11:44: start model_add_line... INFO @ Tue, 27 Jun 2017 12:11:45: start X-correlation... INFO @ Tue, 27 Jun 2017 12:11:45: end of X-cor INFO @ Tue, 27 Jun 2017 12:11:45: #2 finished! INFO @ Tue, 27 Jun 2017 12:11:45: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 12:11:45: #2 alternative fragment length(s) may be 1,39,78,97,123,154,178,205,236 bps INFO @ Tue, 27 Jun 2017 12:11:45: #2.2 Generate R script for model : SRX1674101.20_model.r WARNING @ Tue, 27 Jun 2017 12:11:45: #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 12:11:45: #2 You may need to consider one of the other alternative d(s): 1,39,78,97,123,154,178,205,236 WARNING @ Tue, 27 Jun 2017 12:11:45: #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 12:11:45: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:11:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:11:59: #4 Write output xls file... SRX1674101.05_peaks.xls INFO @ Tue, 27 Jun 2017 12:11:59: #4 Write peak in narrowPeak format file... SRX1674101.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:11:59: #4 Write summits bed file... SRX1674101.05_summits.bed INFO @ Tue, 27 Jun 2017 12:11:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:12:12: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:12:26: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:12:31: #4 Write output xls file... SRX1674101.10_peaks.xls INFO @ Tue, 27 Jun 2017 12:12:31: #4 Write peak in narrowPeak format file... SRX1674101.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:12:31: #4 Write summits bed file... SRX1674101.10_summits.bed INFO @ Tue, 27 Jun 2017 12:12:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:12:45: #4 Write output xls file... SRX1674101.20_peaks.xls INFO @ Tue, 27 Jun 2017 12:12:45: #4 Write peak in narrowPeak format file... SRX1674101.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:12:45: #4 Write summits bed file... SRX1674101.20_summits.bed INFO @ Tue, 27 Jun 2017 12:12:45: 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。