Job ID = 9157351 sra ファイルのダウンロード中... Completed: 569305K bytes transferred in 9 seconds (501868K 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 37296098 spots for /home/okishinya/chipatlas/results/ce10/SRX059266/SRR190706.sra Written 37296098 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:42 37296098 reads; of these: 37296098 (100.00%) were unpaired; of these: 5740923 (15.39%) aligned 0 times 25916534 (69.49%) aligned exactly 1 time 5638641 (15.12%) aligned >1 times 84.61% overall alignment rate Time searching: 00:06:43 Overall time: 00:06:43 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] 4251317 / 31555175 = 0.1347 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 11:39:53: # Command line: callpeak -t SRX059266.bam -f BAM -g ce -n SRX059266.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059266.05 # format = BAM # ChIP-seq file = ['SRX059266.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 11:39:53: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:39:53: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:39:53: # Command line: callpeak -t SRX059266.bam -f BAM -g ce -n SRX059266.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059266.20 # format = BAM # ChIP-seq file = ['SRX059266.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 11:39:53: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:39:53: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:39:53: # Command line: callpeak -t SRX059266.bam -f BAM -g ce -n SRX059266.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059266.10 # format = BAM # ChIP-seq file = ['SRX059266.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 11:39:53: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:39:53: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:39:59: 1000000 INFO @ Tue, 27 Jun 2017 11:39:59: 1000000 INFO @ Tue, 27 Jun 2017 11:39:59: 1000000 INFO @ Tue, 27 Jun 2017 11:40:06: 2000000 INFO @ Tue, 27 Jun 2017 11:40:06: 2000000 INFO @ Tue, 27 Jun 2017 11:40:06: 2000000 INFO @ Tue, 27 Jun 2017 11:40:12: 3000000 INFO @ Tue, 27 Jun 2017 11:40:12: 3000000 INFO @ Tue, 27 Jun 2017 11:40:12: 3000000 INFO @ Tue, 27 Jun 2017 11:40:19: 4000000 INFO @ Tue, 27 Jun 2017 11:40:19: 4000000 INFO @ Tue, 27 Jun 2017 11:40:19: 4000000 INFO @ Tue, 27 Jun 2017 11:40:25: 5000000 INFO @ Tue, 27 Jun 2017 11:40:25: 5000000 INFO @ Tue, 27 Jun 2017 11:40:25: 5000000 INFO @ Tue, 27 Jun 2017 11:40:31: 6000000 INFO @ Tue, 27 Jun 2017 11:40:31: 6000000 INFO @ Tue, 27 Jun 2017 11:40:31: 6000000 INFO @ Tue, 27 Jun 2017 11:40:37: 7000000 INFO @ Tue, 27 Jun 2017 11:40:38: 7000000 INFO @ Tue, 27 Jun 2017 11:40:38: 7000000 INFO @ Tue, 27 Jun 2017 11:40:44: 8000000 INFO @ Tue, 27 Jun 2017 11:40:44: 8000000 INFO @ Tue, 27 Jun 2017 11:40:44: 8000000 INFO @ Tue, 27 Jun 2017 11:40:50: 9000000 INFO @ Tue, 27 Jun 2017 11:40:50: 9000000 INFO @ Tue, 27 Jun 2017 11:40:51: 9000000 INFO @ Tue, 27 Jun 2017 11:40:56: 10000000 INFO @ Tue, 27 Jun 2017 11:40:57: 10000000 INFO @ Tue, 27 Jun 2017 11:40:57: 10000000 INFO @ Tue, 27 Jun 2017 11:41:02: 11000000 INFO @ Tue, 27 Jun 2017 11:41:03: 11000000 INFO @ Tue, 27 Jun 2017 11:41:04: 11000000 INFO @ Tue, 27 Jun 2017 11:41:09: 12000000 INFO @ Tue, 27 Jun 2017 11:41:10: 12000000 INFO @ Tue, 27 Jun 2017 11:41:10: 12000000 INFO @ Tue, 27 Jun 2017 11:41:15: 13000000 INFO @ Tue, 27 Jun 2017 11:41:16: 13000000 INFO @ Tue, 27 Jun 2017 11:41:16: 13000000 INFO @ Tue, 27 Jun 2017 11:41:21: 14000000 INFO @ Tue, 27 Jun 2017 11:41:23: 14000000 INFO @ Tue, 27 Jun 2017 11:41:23: 14000000 INFO @ Tue, 27 Jun 2017 11:41:28: 15000000 INFO @ Tue, 27 Jun 2017 11:41:29: 15000000 INFO @ Tue, 27 Jun 2017 11:41:29: 15000000 INFO @ Tue, 27 Jun 2017 11:41:34: 16000000 INFO @ Tue, 27 Jun 2017 11:41:35: 16000000 INFO @ Tue, 27 Jun 2017 11:41:36: 16000000 INFO @ Tue, 27 Jun 2017 11:41:40: 17000000 INFO @ Tue, 27 Jun 2017 11:41:42: 17000000 INFO @ Tue, 27 Jun 2017 11:41:42: 17000000 INFO @ Tue, 27 Jun 2017 11:41:46: 18000000 INFO @ Tue, 27 Jun 2017 11:41:48: 18000000 INFO @ Tue, 27 Jun 2017 11:41:49: 18000000 INFO @ Tue, 27 Jun 2017 11:41:53: 19000000 INFO @ Tue, 27 Jun 2017 11:41:55: 19000000 INFO @ Tue, 27 Jun 2017 11:41:55: 19000000 INFO @ Tue, 27 Jun 2017 11:41:59: 20000000 INFO @ Tue, 27 Jun 2017 11:42:01: 20000000 INFO @ Tue, 27 Jun 2017 11:42:01: 20000000 INFO @ Tue, 27 Jun 2017 11:42:05: 21000000 INFO @ Tue, 27 Jun 2017 11:42:07: 21000000 INFO @ Tue, 27 Jun 2017 11:42:08: 21000000 INFO @ Tue, 27 Jun 2017 11:42:11: 22000000 INFO @ Tue, 27 Jun 2017 11:42:14: 22000000 INFO @ Tue, 27 Jun 2017 11:42:14: 22000000 INFO @ Tue, 27 Jun 2017 11:42:18: 23000000 INFO @ Tue, 27 Jun 2017 11:42:20: 23000000 INFO @ Tue, 27 Jun 2017 11:42:20: 23000000 INFO @ Tue, 27 Jun 2017 11:42:24: 24000000 INFO @ Tue, 27 Jun 2017 11:42:26: 24000000 INFO @ Tue, 27 Jun 2017 11:42:27: 24000000 INFO @ Tue, 27 Jun 2017 11:42:30: 25000000 INFO @ Tue, 27 Jun 2017 11:42:33: 25000000 INFO @ Tue, 27 Jun 2017 11:42:33: 25000000 INFO @ Tue, 27 Jun 2017 11:42:37: 26000000 INFO @ Tue, 27 Jun 2017 11:42:39: 26000000 INFO @ Tue, 27 Jun 2017 11:42:40: 26000000 INFO @ Tue, 27 Jun 2017 11:42:43: 27000000 INFO @ Tue, 27 Jun 2017 11:42:45: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 11:42:45: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 11:42:45: #1 total tags in treatment: 27303858 INFO @ Tue, 27 Jun 2017 11:42:45: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:42:45: #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 11:42:46: #1 tags after filtering in treatment: 27303858 INFO @ Tue, 27 Jun 2017 11:42:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:42:46: #1 finished! INFO @ Tue, 27 Jun 2017 11:42:46: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:42:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:42:46: 27000000 INFO @ Tue, 27 Jun 2017 11:42:46: 27000000 INFO @ Tue, 27 Jun 2017 11:42:48: #2 number of paired peaks: 110 WARNING @ Tue, 27 Jun 2017 11:42:48: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 27 Jun 2017 11:42:48: start model_add_line... INFO @ Tue, 27 Jun 2017 11:42:48: start X-correlation... INFO @ Tue, 27 Jun 2017 11:42:48: end of X-cor INFO @ Tue, 27 Jun 2017 11:42:48: #2 finished! INFO @ Tue, 27 Jun 2017 11:42:48: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:42:48: #2 alternative fragment length(s) may be 1,32,527 bps INFO @ Tue, 27 Jun 2017 11:42:48: #2.2 Generate R script for model : SRX059266.10_model.r WARNING @ Tue, 27 Jun 2017 11:42:48: #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 11:42:48: #2 You may need to consider one of the other alternative d(s): 1,32,527 WARNING @ Tue, 27 Jun 2017 11:42:48: #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 11:42:48: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:42:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:42:48: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 11:42:48: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 11:42:48: #1 total tags in treatment: 27303858 INFO @ Tue, 27 Jun 2017 11:42:48: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:42:48: #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 11:42:48: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 11:42:48: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 11:42:48: #1 total tags in treatment: 27303858 INFO @ Tue, 27 Jun 2017 11:42:48: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:42:48: #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 11:42:48: #1 tags after filtering in treatment: 27303858 INFO @ Tue, 27 Jun 2017 11:42:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:42:48: #1 finished! INFO @ Tue, 27 Jun 2017 11:42:48: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:42:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:42:49: #1 tags after filtering in treatment: 27303858 INFO @ Tue, 27 Jun 2017 11:42:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:42:49: #1 finished! INFO @ Tue, 27 Jun 2017 11:42:49: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:42:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:42:50: #2 number of paired peaks: 110 WARNING @ Tue, 27 Jun 2017 11:42:50: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 27 Jun 2017 11:42:50: start model_add_line... INFO @ Tue, 27 Jun 2017 11:42:50: start X-correlation... INFO @ Tue, 27 Jun 2017 11:42:50: end of X-cor INFO @ Tue, 27 Jun 2017 11:42:50: #2 finished! INFO @ Tue, 27 Jun 2017 11:42:50: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:42:50: #2 alternative fragment length(s) may be 1,32,527 bps INFO @ Tue, 27 Jun 2017 11:42:50: #2.2 Generate R script for model : SRX059266.20_model.r WARNING @ Tue, 27 Jun 2017 11:42:50: #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 11:42:50: #2 You may need to consider one of the other alternative d(s): 1,32,527 WARNING @ Tue, 27 Jun 2017 11:42:50: #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 11:42:50: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:42:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:42:51: #2 number of paired peaks: 110 WARNING @ Tue, 27 Jun 2017 11:42:51: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 27 Jun 2017 11:42:51: start model_add_line... INFO @ Tue, 27 Jun 2017 11:42:51: start X-correlation... INFO @ Tue, 27 Jun 2017 11:42:51: end of X-cor INFO @ Tue, 27 Jun 2017 11:42:51: #2 finished! INFO @ Tue, 27 Jun 2017 11:42:51: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:42:51: #2 alternative fragment length(s) may be 1,32,527 bps INFO @ Tue, 27 Jun 2017 11:42:51: #2.2 Generate R script for model : SRX059266.05_model.r WARNING @ Tue, 27 Jun 2017 11:42:51: #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 11:42:51: #2 You may need to consider one of the other alternative d(s): 1,32,527 WARNING @ Tue, 27 Jun 2017 11:42:51: #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 11:42:51: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:42:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:43:29: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:43:30: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:43:32: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:43:48: #4 Write output xls file... SRX059266.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:43:48: #4 Write peak in narrowPeak format file... SRX059266.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:43:48: #4 Write summits bed file... SRX059266.10_summits.bed INFO @ Tue, 27 Jun 2017 11:43:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:43:49: #4 Write output xls file... SRX059266.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:43:49: #4 Write peak in narrowPeak format file... SRX059266.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:43:49: #4 Write summits bed file... SRX059266.05_summits.bed INFO @ Tue, 27 Jun 2017 11:43:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:43:52: #4 Write output xls file... SRX059266.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:43:52: #4 Write peak in narrowPeak format file... SRX059266.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:43:52: #4 Write summits bed file... SRX059266.20_summits.bed INFO @ Tue, 27 Jun 2017 11:43:52: 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。