Job ID = 9157347 sra ファイルのダウンロード中... Completed: 598816K bytes transferred in 10 seconds (461407K 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 20333805 spots for /home/okishinya/chipatlas/results/ce10/SRX059229/SRR190669.sra Written 20333805 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: 00:05:27 20333805 reads; of these: 20333805 (100.00%) were unpaired; of these: 243213 (1.20%) aligned 0 times 16211122 (79.72%) aligned exactly 1 time 3879470 (19.08%) aligned >1 times 98.80% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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] 2866983 / 20090592 = 0.1427 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 11:37:19: # Command line: callpeak -t SRX059229.bam -f BAM -g ce -n SRX059229.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059229.05 # format = BAM # ChIP-seq file = ['SRX059229.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 11:37:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:37:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:37:19: # Command line: callpeak -t SRX059229.bam -f BAM -g ce -n SRX059229.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059229.20 # format = BAM # ChIP-seq file = ['SRX059229.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 11:37:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:37:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:37:19: # Command line: callpeak -t SRX059229.bam -f BAM -g ce -n SRX059229.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059229.10 # format = BAM # ChIP-seq file = ['SRX059229.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 11:37:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:37:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:37:26: 1000000 INFO @ Tue, 27 Jun 2017 11:37:26: 1000000 INFO @ Tue, 27 Jun 2017 11:37:26: 1000000 INFO @ Tue, 27 Jun 2017 11:37:33: 2000000 INFO @ Tue, 27 Jun 2017 11:37:33: 2000000 INFO @ Tue, 27 Jun 2017 11:37:33: 2000000 INFO @ Tue, 27 Jun 2017 11:37:40: 3000000 INFO @ Tue, 27 Jun 2017 11:37:40: 3000000 INFO @ Tue, 27 Jun 2017 11:37:41: 3000000 INFO @ Tue, 27 Jun 2017 11:37:48: 4000000 INFO @ Tue, 27 Jun 2017 11:37:48: 4000000 INFO @ Tue, 27 Jun 2017 11:37:49: 4000000 INFO @ Tue, 27 Jun 2017 11:37:56: 5000000 INFO @ Tue, 27 Jun 2017 11:37:56: 5000000 INFO @ Tue, 27 Jun 2017 11:37:57: 5000000 INFO @ Tue, 27 Jun 2017 11:38:03: 6000000 INFO @ Tue, 27 Jun 2017 11:38:03: 6000000 INFO @ Tue, 27 Jun 2017 11:38:05: 6000000 INFO @ Tue, 27 Jun 2017 11:38:11: 7000000 INFO @ Tue, 27 Jun 2017 11:38:11: 7000000 INFO @ Tue, 27 Jun 2017 11:38:13: 7000000 INFO @ Tue, 27 Jun 2017 11:38:19: 8000000 INFO @ Tue, 27 Jun 2017 11:38:19: 8000000 INFO @ Tue, 27 Jun 2017 11:38:22: 8000000 INFO @ Tue, 27 Jun 2017 11:38:26: 9000000 INFO @ Tue, 27 Jun 2017 11:38:26: 9000000 INFO @ Tue, 27 Jun 2017 11:38:30: 9000000 INFO @ Tue, 27 Jun 2017 11:38:34: 10000000 INFO @ Tue, 27 Jun 2017 11:38:34: 10000000 INFO @ Tue, 27 Jun 2017 11:38:38: 10000000 INFO @ Tue, 27 Jun 2017 11:38:42: 11000000 INFO @ Tue, 27 Jun 2017 11:38:42: 11000000 INFO @ Tue, 27 Jun 2017 11:38:46: 11000000 INFO @ Tue, 27 Jun 2017 11:38:49: 12000000 INFO @ Tue, 27 Jun 2017 11:38:49: 12000000 INFO @ Tue, 27 Jun 2017 11:38:53: 12000000 INFO @ Tue, 27 Jun 2017 11:38:55: 13000000 INFO @ Tue, 27 Jun 2017 11:38:56: 13000000 INFO @ Tue, 27 Jun 2017 11:39:00: 13000000 INFO @ Tue, 27 Jun 2017 11:39:01: 14000000 INFO @ Tue, 27 Jun 2017 11:39:03: 14000000 INFO @ Tue, 27 Jun 2017 11:39:07: 14000000 INFO @ Tue, 27 Jun 2017 11:39:08: 15000000 INFO @ Tue, 27 Jun 2017 11:39:10: 15000000 INFO @ Tue, 27 Jun 2017 11:39:14: 16000000 INFO @ Tue, 27 Jun 2017 11:39:15: 15000000 INFO @ Tue, 27 Jun 2017 11:39:17: 16000000 INFO @ Tue, 27 Jun 2017 11:39:20: 17000000 INFO @ Tue, 27 Jun 2017 11:39:22: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 11:39:22: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 11:39:22: #1 total tags in treatment: 17223609 INFO @ Tue, 27 Jun 2017 11:39:22: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:39:22: #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 11:39:22: 16000000 INFO @ Tue, 27 Jun 2017 11:39:22: #1 tags after filtering in treatment: 17223609 INFO @ Tue, 27 Jun 2017 11:39:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:39:22: #1 finished! INFO @ Tue, 27 Jun 2017 11:39:22: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:39:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:39:23: #2 number of paired peaks: 211 WARNING @ Tue, 27 Jun 2017 11:39:23: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 27 Jun 2017 11:39:23: start model_add_line... INFO @ Tue, 27 Jun 2017 11:39:23: 17000000 INFO @ Tue, 27 Jun 2017 11:39:23: start X-correlation... INFO @ Tue, 27 Jun 2017 11:39:23: end of X-cor INFO @ Tue, 27 Jun 2017 11:39:23: #2 finished! INFO @ Tue, 27 Jun 2017 11:39:23: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:39:23: #2 alternative fragment length(s) may be 1,19,39,522,542,576 bps INFO @ Tue, 27 Jun 2017 11:39:23: #2.2 Generate R script for model : SRX059229.20_model.r WARNING @ Tue, 27 Jun 2017 11:39:23: #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 11:39:23: #2 You may need to consider one of the other alternative d(s): 1,19,39,522,542,576 WARNING @ Tue, 27 Jun 2017 11:39:23: #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 11:39:23: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:39:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:39:25: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 11:39:25: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 11:39:25: #1 total tags in treatment: 17223609 INFO @ Tue, 27 Jun 2017 11:39:25: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:39:25: #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 11:39:25: #1 tags after filtering in treatment: 17223609 INFO @ Tue, 27 Jun 2017 11:39:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:39:25: #1 finished! INFO @ Tue, 27 Jun 2017 11:39:25: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:39:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:39:26: #2 number of paired peaks: 211 WARNING @ Tue, 27 Jun 2017 11:39:26: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 27 Jun 2017 11:39:26: start model_add_line... INFO @ Tue, 27 Jun 2017 11:39:27: start X-correlation... INFO @ Tue, 27 Jun 2017 11:39:27: end of X-cor INFO @ Tue, 27 Jun 2017 11:39:27: #2 finished! INFO @ Tue, 27 Jun 2017 11:39:27: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:39:27: #2 alternative fragment length(s) may be 1,19,39,522,542,576 bps INFO @ Tue, 27 Jun 2017 11:39:27: #2.2 Generate R script for model : SRX059229.05_model.r WARNING @ Tue, 27 Jun 2017 11:39:27: #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 11:39:27: #2 You may need to consider one of the other alternative d(s): 1,19,39,522,542,576 WARNING @ Tue, 27 Jun 2017 11:39:27: #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 11:39:27: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:39:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:39:29: 17000000 INFO @ Tue, 27 Jun 2017 11:39:31: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 11:39:31: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 11:39:31: #1 total tags in treatment: 17223609 INFO @ Tue, 27 Jun 2017 11:39:31: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:39:31: #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 11:39:31: #1 tags after filtering in treatment: 17223609 INFO @ Tue, 27 Jun 2017 11:39:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:39:31: #1 finished! INFO @ Tue, 27 Jun 2017 11:39:31: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:39:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:39:32: #2 number of paired peaks: 211 WARNING @ Tue, 27 Jun 2017 11:39:32: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 27 Jun 2017 11:39:32: start model_add_line... INFO @ Tue, 27 Jun 2017 11:39:33: start X-correlation... INFO @ Tue, 27 Jun 2017 11:39:33: end of X-cor INFO @ Tue, 27 Jun 2017 11:39:33: #2 finished! INFO @ Tue, 27 Jun 2017 11:39:33: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:39:33: #2 alternative fragment length(s) may be 1,19,39,522,542,576 bps INFO @ Tue, 27 Jun 2017 11:39:33: #2.2 Generate R script for model : SRX059229.10_model.r WARNING @ Tue, 27 Jun 2017 11:39:33: #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 11:39:33: #2 You may need to consider one of the other alternative d(s): 1,19,39,522,542,576 WARNING @ Tue, 27 Jun 2017 11:39:33: #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 11:39:33: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:39:55: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:39:57: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:40:01: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:40:09: #4 Write output xls file... SRX059229.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:40:09: #4 Write peak in narrowPeak format file... SRX059229.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:40:09: #4 Write summits bed file... SRX059229.20_summits.bed INFO @ Tue, 27 Jun 2017 11:40:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:40:11: #4 Write output xls file... SRX059229.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:40:11: #4 Write peak in narrowPeak format file... SRX059229.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:40:11: #4 Write summits bed file... SRX059229.05_summits.bed INFO @ Tue, 27 Jun 2017 11:40:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:40:17: #4 Write output xls file... SRX059229.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:40:17: #4 Write peak in narrowPeak format file... SRX059229.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:40:17: #4 Write summits bed file... SRX059229.10_summits.bed INFO @ Tue, 27 Jun 2017 11:40:17: 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。