Job ID = 9371436 sra ファイルのダウンロード中... Completed: 498287K bytes transferred in 9 seconds (428542K 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 20754335 spots for /home/okishinya/chipatlas/results/dm3/SRX2520636/SRR5206755.sra Written 20754335 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: 00:16:53 20754335 reads; of these: 20754335 (100.00%) were unpaired; of these: 538814 (2.60%) aligned 0 times 15078477 (72.65%) aligned exactly 1 time 5137044 (24.75%) aligned >1 times 97.40% overall alignment rate Time searching: 00:16:54 Overall time: 00:16:54 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 12 files... [bam_rmdupse_core] 2873075 / 20215521 = 0.1421 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 @ Fri, 04 Aug 2017 15:15:13: # Command line: callpeak -t SRX2520636.bam -f BAM -g dm -n SRX2520636.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2520636.10 # format = BAM # ChIP-seq file = ['SRX2520636.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 @ Fri, 04 Aug 2017 15:15:13: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:15:13: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:15:13: # Command line: callpeak -t SRX2520636.bam -f BAM -g dm -n SRX2520636.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2520636.05 # format = BAM # ChIP-seq file = ['SRX2520636.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 @ Fri, 04 Aug 2017 15:15:13: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:15:13: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:15:13: # Command line: callpeak -t SRX2520636.bam -f BAM -g dm -n SRX2520636.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2520636.20 # format = BAM # ChIP-seq file = ['SRX2520636.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 @ Fri, 04 Aug 2017 15:15:13: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:15:13: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:15:26: 1000000 INFO @ Fri, 04 Aug 2017 15:15:26: 1000000 INFO @ Fri, 04 Aug 2017 15:15:27: 1000000 INFO @ Fri, 04 Aug 2017 15:15:38: 2000000 INFO @ Fri, 04 Aug 2017 15:15:38: 2000000 INFO @ Fri, 04 Aug 2017 15:15:40: 2000000 INFO @ Fri, 04 Aug 2017 15:15:51: 3000000 INFO @ Fri, 04 Aug 2017 15:15:51: 3000000 INFO @ Fri, 04 Aug 2017 15:15:53: 3000000 INFO @ Fri, 04 Aug 2017 15:16:05: 4000000 INFO @ Fri, 04 Aug 2017 15:16:05: 4000000 INFO @ Fri, 04 Aug 2017 15:16:06: 4000000 INFO @ Fri, 04 Aug 2017 15:16:21: 5000000 INFO @ Fri, 04 Aug 2017 15:16:22: 5000000 INFO @ Fri, 04 Aug 2017 15:16:24: 5000000 INFO @ Fri, 04 Aug 2017 15:16:33: 6000000 INFO @ Fri, 04 Aug 2017 15:16:37: 6000000 INFO @ Fri, 04 Aug 2017 15:16:39: 6000000 INFO @ Fri, 04 Aug 2017 15:16:46: 7000000 INFO @ Fri, 04 Aug 2017 15:16:53: 7000000 INFO @ Fri, 04 Aug 2017 15:16:54: 7000000 INFO @ Fri, 04 Aug 2017 15:16:58: 8000000 INFO @ Fri, 04 Aug 2017 15:17:11: 8000000 INFO @ Fri, 04 Aug 2017 15:17:11: 8000000 INFO @ Fri, 04 Aug 2017 15:17:11: 9000000 INFO @ Fri, 04 Aug 2017 15:17:26: 10000000 INFO @ Fri, 04 Aug 2017 15:17:27: 9000000 INFO @ Fri, 04 Aug 2017 15:17:28: 9000000 INFO @ Fri, 04 Aug 2017 15:17:41: 10000000 INFO @ Fri, 04 Aug 2017 15:17:41: 10000000 INFO @ Fri, 04 Aug 2017 15:17:42: 11000000 INFO @ Fri, 04 Aug 2017 15:17:56: 11000000 INFO @ Fri, 04 Aug 2017 15:17:58: 11000000 INFO @ Fri, 04 Aug 2017 15:18:01: 12000000 INFO @ Fri, 04 Aug 2017 15:18:11: 12000000 INFO @ Fri, 04 Aug 2017 15:18:16: 12000000 INFO @ Fri, 04 Aug 2017 15:18:18: 13000000 INFO @ Fri, 04 Aug 2017 15:18:26: 13000000 INFO @ Fri, 04 Aug 2017 15:18:31: 13000000 INFO @ Fri, 04 Aug 2017 15:18:34: 14000000 INFO @ Fri, 04 Aug 2017 15:18:42: 14000000 INFO @ Fri, 04 Aug 2017 15:18:48: 14000000 INFO @ Fri, 04 Aug 2017 15:18:52: 15000000 INFO @ Fri, 04 Aug 2017 15:18:57: 15000000 INFO @ Fri, 04 Aug 2017 15:19:04: 15000000 INFO @ Fri, 04 Aug 2017 15:19:10: 16000000 INFO @ Fri, 04 Aug 2017 15:19:12: 16000000 INFO @ Fri, 04 Aug 2017 15:19:21: 17000000 INFO @ Fri, 04 Aug 2017 15:19:22: 16000000 INFO @ Fri, 04 Aug 2017 15:19:27: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:19:27: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:19:27: #1 total tags in treatment: 17342446 INFO @ Fri, 04 Aug 2017 15:19:27: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:19:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:19:28: #1 tags after filtering in treatment: 17342446 INFO @ Fri, 04 Aug 2017 15:19:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:19:28: #1 finished! INFO @ Fri, 04 Aug 2017 15:19:28: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:19:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:19:28: 17000000 INFO @ Fri, 04 Aug 2017 15:19:29: #2 number of paired peaks: 374 WARNING @ Fri, 04 Aug 2017 15:19:29: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Fri, 04 Aug 2017 15:19:29: start model_add_line... INFO @ Fri, 04 Aug 2017 15:19:30: start X-correlation... INFO @ Fri, 04 Aug 2017 15:19:30: end of X-cor INFO @ Fri, 04 Aug 2017 15:19:30: #2 finished! INFO @ Fri, 04 Aug 2017 15:19:30: #2 predicted fragment length is 45 bps INFO @ Fri, 04 Aug 2017 15:19:30: #2 alternative fragment length(s) may be 4,45 bps INFO @ Fri, 04 Aug 2017 15:19:30: #2.2 Generate R script for model : SRX2520636.20_model.r WARNING @ Fri, 04 Aug 2017 15:19:30: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:19:30: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Fri, 04 Aug 2017 15:19:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 15:19:30: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:19:34: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:19:34: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:19:34: #1 total tags in treatment: 17342446 INFO @ Fri, 04 Aug 2017 15:19:34: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:19:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:19:34: #1 tags after filtering in treatment: 17342446 INFO @ Fri, 04 Aug 2017 15:19:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:19:34: #1 finished! INFO @ Fri, 04 Aug 2017 15:19:34: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:19:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:19:36: #2 number of paired peaks: 374 WARNING @ Fri, 04 Aug 2017 15:19:36: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Fri, 04 Aug 2017 15:19:36: start model_add_line... INFO @ Fri, 04 Aug 2017 15:19:36: start X-correlation... INFO @ Fri, 04 Aug 2017 15:19:36: end of X-cor INFO @ Fri, 04 Aug 2017 15:19:36: #2 finished! INFO @ Fri, 04 Aug 2017 15:19:36: #2 predicted fragment length is 45 bps INFO @ Fri, 04 Aug 2017 15:19:36: #2 alternative fragment length(s) may be 4,45 bps INFO @ Fri, 04 Aug 2017 15:19:36: #2.2 Generate R script for model : SRX2520636.10_model.r WARNING @ Fri, 04 Aug 2017 15:19:36: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:19:36: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Fri, 04 Aug 2017 15:19:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 15:19:36: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:19:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:19:37: 17000000 INFO @ Fri, 04 Aug 2017 15:19:42: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:19:42: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:19:42: #1 total tags in treatment: 17342446 INFO @ Fri, 04 Aug 2017 15:19:42: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:19:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:19:43: #1 tags after filtering in treatment: 17342446 INFO @ Fri, 04 Aug 2017 15:19:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:19:43: #1 finished! INFO @ Fri, 04 Aug 2017 15:19:43: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:19:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:19:45: #2 number of paired peaks: 374 WARNING @ Fri, 04 Aug 2017 15:19:45: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Fri, 04 Aug 2017 15:19:45: start model_add_line... INFO @ Fri, 04 Aug 2017 15:19:45: start X-correlation... INFO @ Fri, 04 Aug 2017 15:19:45: end of X-cor INFO @ Fri, 04 Aug 2017 15:19:45: #2 finished! INFO @ Fri, 04 Aug 2017 15:19:45: #2 predicted fragment length is 45 bps INFO @ Fri, 04 Aug 2017 15:19:45: #2 alternative fragment length(s) may be 4,45 bps INFO @ Fri, 04 Aug 2017 15:19:45: #2.2 Generate R script for model : SRX2520636.05_model.r WARNING @ Fri, 04 Aug 2017 15:19:45: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:19:45: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Fri, 04 Aug 2017 15:19:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 15:19:45: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:19:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:20:22: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:20:29: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:20:36: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:20:51: #4 Write output xls file... SRX2520636.20_peaks.xls INFO @ Fri, 04 Aug 2017 15:20:51: #4 Write peak in narrowPeak format file... SRX2520636.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:20:51: #4 Write summits bed file... SRX2520636.20_summits.bed INFO @ Fri, 04 Aug 2017 15:20:51: Done! pass1 - making usageList (11 chroms): 6 millis pass2 - checking and writing primary data (948 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:20:59: #4 Write output xls file... SRX2520636.10_peaks.xls INFO @ Fri, 04 Aug 2017 15:20:59: #4 Write peak in narrowPeak format file... SRX2520636.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:20:59: #4 Write summits bed file... SRX2520636.10_summits.bed INFO @ Fri, 04 Aug 2017 15:20:59: Done! pass1 - making usageList (14 chroms): 9 millis pass2 - checking and writing primary data (2178 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:21:05: #4 Write output xls file... SRX2520636.05_peaks.xls INFO @ Fri, 04 Aug 2017 15:21:05: #4 Write peak in narrowPeak format file... SRX2520636.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:21:05: #4 Write summits bed file... SRX2520636.05_summits.bed INFO @ Fri, 04 Aug 2017 15:21:05: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (3450 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。