Job ID = 10609121 sra ファイルのダウンロード中... Completed: 734089K bytes transferred in 53 seconds (112258K 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 50285491 spots for /home/okishinya/chipatlas/results/dm3/SRX3011266/SRR5834742.sra Written 50285491 spots for /home/okishinya/chipatlas/results/dm3/SRX3011266/SRR5834742.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: 00:11:29 50285491 reads; of these: 50285491 (100.00%) were unpaired; of these: 5731863 (11.40%) aligned 0 times 35235969 (70.07%) aligned exactly 1 time 9317659 (18.53%) aligned >1 times 88.60% overall alignment rate Time searching: 00:11:29 Overall time: 00:11:29 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] 15428559 / 44553628 = 0.3463 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 May 2018 07:24:20: # Command line: callpeak -t SRX3011266.bam -f BAM -g dm -n SRX3011266.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011266.10 # format = BAM # ChIP-seq file = ['SRX3011266.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 May 2018 07:24:20: # Command line: callpeak -t SRX3011266.bam -f BAM -g dm -n SRX3011266.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011266.05 # format = BAM # ChIP-seq file = ['SRX3011266.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 May 2018 07:24:20: # Command line: callpeak -t SRX3011266.bam -f BAM -g dm -n SRX3011266.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011266.20 # format = BAM # ChIP-seq file = ['SRX3011266.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 May 2018 07:24:20: #1 read tag files... INFO @ Fri, 04 May 2018 07:24:20: #1 read tag files... INFO @ Fri, 04 May 2018 07:24:20: #1 read tag files... INFO @ Fri, 04 May 2018 07:24:20: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:24:20: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:24:20: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:24:26: 1000000 INFO @ Fri, 04 May 2018 07:24:26: 1000000 INFO @ Fri, 04 May 2018 07:24:26: 1000000 INFO @ Fri, 04 May 2018 07:24:32: 2000000 INFO @ Fri, 04 May 2018 07:24:32: 2000000 INFO @ Fri, 04 May 2018 07:24:32: 2000000 INFO @ Fri, 04 May 2018 07:24:37: 3000000 INFO @ Fri, 04 May 2018 07:24:38: 3000000 INFO @ Fri, 04 May 2018 07:24:38: 3000000 INFO @ Fri, 04 May 2018 07:24:43: 4000000 INFO @ Fri, 04 May 2018 07:24:43: 4000000 INFO @ Fri, 04 May 2018 07:24:44: 4000000 INFO @ Fri, 04 May 2018 07:24:49: 5000000 INFO @ Fri, 04 May 2018 07:24:49: 5000000 INFO @ Fri, 04 May 2018 07:24:50: 5000000 INFO @ Fri, 04 May 2018 07:24:55: 6000000 INFO @ Fri, 04 May 2018 07:24:55: 6000000 INFO @ Fri, 04 May 2018 07:24:56: 6000000 INFO @ Fri, 04 May 2018 07:25:00: 7000000 INFO @ Fri, 04 May 2018 07:25:02: 7000000 INFO @ Fri, 04 May 2018 07:25:03: 7000000 INFO @ Fri, 04 May 2018 07:25:06: 8000000 INFO @ Fri, 04 May 2018 07:25:08: 8000000 INFO @ Fri, 04 May 2018 07:25:09: 8000000 INFO @ Fri, 04 May 2018 07:25:12: 9000000 INFO @ Fri, 04 May 2018 07:25:14: 9000000 INFO @ Fri, 04 May 2018 07:25:15: 9000000 INFO @ Fri, 04 May 2018 07:25:17: 10000000 INFO @ Fri, 04 May 2018 07:25:20: 10000000 INFO @ Fri, 04 May 2018 07:25:22: 10000000 INFO @ Fri, 04 May 2018 07:25:23: 11000000 INFO @ Fri, 04 May 2018 07:25:26: 11000000 INFO @ Fri, 04 May 2018 07:25:28: 11000000 INFO @ Fri, 04 May 2018 07:25:29: 12000000 INFO @ Fri, 04 May 2018 07:25:32: 12000000 INFO @ Fri, 04 May 2018 07:25:34: 12000000 INFO @ Fri, 04 May 2018 07:25:35: 13000000 INFO @ Fri, 04 May 2018 07:25:38: 13000000 INFO @ Fri, 04 May 2018 07:25:39: 13000000 INFO @ Fri, 04 May 2018 07:25:41: 14000000 INFO @ Fri, 04 May 2018 07:25:44: 14000000 INFO @ Fri, 04 May 2018 07:25:45: 14000000 INFO @ Fri, 04 May 2018 07:25:46: 15000000 INFO @ Fri, 04 May 2018 07:25:50: 15000000 INFO @ Fri, 04 May 2018 07:25:51: 15000000 INFO @ Fri, 04 May 2018 07:25:53: 16000000 INFO @ Fri, 04 May 2018 07:25:56: 16000000 INFO @ Fri, 04 May 2018 07:25:57: 16000000 INFO @ Fri, 04 May 2018 07:25:59: 17000000 INFO @ Fri, 04 May 2018 07:26:02: 17000000 INFO @ Fri, 04 May 2018 07:26:03: 17000000 INFO @ Fri, 04 May 2018 07:26:04: 18000000 INFO @ Fri, 04 May 2018 07:26:08: 18000000 INFO @ Fri, 04 May 2018 07:26:09: 18000000 INFO @ Fri, 04 May 2018 07:26:10: 19000000 INFO @ Fri, 04 May 2018 07:26:14: 19000000 INFO @ Fri, 04 May 2018 07:26:15: 19000000 INFO @ Fri, 04 May 2018 07:26:16: 20000000 INFO @ Fri, 04 May 2018 07:26:20: 20000000 INFO @ Fri, 04 May 2018 07:26:21: 20000000 INFO @ Fri, 04 May 2018 07:26:22: 21000000 INFO @ Fri, 04 May 2018 07:26:26: 21000000 INFO @ Fri, 04 May 2018 07:26:27: 21000000 INFO @ Fri, 04 May 2018 07:26:28: 22000000 INFO @ Fri, 04 May 2018 07:26:32: 22000000 INFO @ Fri, 04 May 2018 07:26:33: 22000000 INFO @ Fri, 04 May 2018 07:26:34: 23000000 INFO @ Fri, 04 May 2018 07:26:38: 23000000 INFO @ Fri, 04 May 2018 07:26:38: 23000000 INFO @ Fri, 04 May 2018 07:26:40: 24000000 INFO @ Fri, 04 May 2018 07:26:44: 24000000 INFO @ Fri, 04 May 2018 07:26:44: 24000000 INFO @ Fri, 04 May 2018 07:26:46: 25000000 INFO @ Fri, 04 May 2018 07:26:50: 25000000 INFO @ Fri, 04 May 2018 07:26:50: 25000000 INFO @ Fri, 04 May 2018 07:26:52: 26000000 INFO @ Fri, 04 May 2018 07:26:56: 26000000 INFO @ Fri, 04 May 2018 07:26:56: 26000000 INFO @ Fri, 04 May 2018 07:26:58: 27000000 INFO @ Fri, 04 May 2018 07:27:02: 27000000 INFO @ Fri, 04 May 2018 07:27:02: 27000000 INFO @ Fri, 04 May 2018 07:27:04: 28000000 INFO @ Fri, 04 May 2018 07:27:08: 28000000 INFO @ Fri, 04 May 2018 07:27:08: 28000000 INFO @ Fri, 04 May 2018 07:27:10: 29000000 INFO @ Fri, 04 May 2018 07:27:11: #1 tag size is determined as 40 bps INFO @ Fri, 04 May 2018 07:27:11: #1 tag size = 40 INFO @ Fri, 04 May 2018 07:27:11: #1 total tags in treatment: 29125069 INFO @ Fri, 04 May 2018 07:27:11: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:27:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:27:11: #1 tags after filtering in treatment: 29125069 INFO @ Fri, 04 May 2018 07:27:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:27:11: #1 finished! INFO @ Fri, 04 May 2018 07:27:11: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:27:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:27:13: #2 number of paired peaks: 819 WARNING @ Fri, 04 May 2018 07:27:13: Fewer paired peaks (819) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 819 pairs to build model! INFO @ Fri, 04 May 2018 07:27:13: start model_add_line... INFO @ Fri, 04 May 2018 07:27:14: start X-correlation... INFO @ Fri, 04 May 2018 07:27:14: end of X-cor INFO @ Fri, 04 May 2018 07:27:14: #2 finished! INFO @ Fri, 04 May 2018 07:27:14: #2 predicted fragment length is 142 bps INFO @ Fri, 04 May 2018 07:27:14: #2 alternative fragment length(s) may be 142 bps INFO @ Fri, 04 May 2018 07:27:14: #2.2 Generate R script for model : SRX3011266.10_model.r INFO @ Fri, 04 May 2018 07:27:14: #3 Call peaks... INFO @ Fri, 04 May 2018 07:27:14: 29000000 INFO @ Fri, 04 May 2018 07:27:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:27:14: 29000000 INFO @ Fri, 04 May 2018 07:27:15: #1 tag size is determined as 40 bps INFO @ Fri, 04 May 2018 07:27:15: #1 tag size = 40 INFO @ Fri, 04 May 2018 07:27:15: #1 total tags in treatment: 29125069 INFO @ Fri, 04 May 2018 07:27:15: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:27:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:27:15: #1 tag size is determined as 40 bps INFO @ Fri, 04 May 2018 07:27:15: #1 tag size = 40 INFO @ Fri, 04 May 2018 07:27:15: #1 total tags in treatment: 29125069 INFO @ Fri, 04 May 2018 07:27:15: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:27:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:27:16: #1 tags after filtering in treatment: 29125069 INFO @ Fri, 04 May 2018 07:27:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:27:16: #1 finished! INFO @ Fri, 04 May 2018 07:27:16: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:27:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:27:16: #1 tags after filtering in treatment: 29125069 INFO @ Fri, 04 May 2018 07:27:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:27:16: #1 finished! INFO @ Fri, 04 May 2018 07:27:16: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:27:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:27:18: #2 number of paired peaks: 819 WARNING @ Fri, 04 May 2018 07:27:18: Fewer paired peaks (819) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 819 pairs to build model! INFO @ Fri, 04 May 2018 07:27:18: start model_add_line... INFO @ Fri, 04 May 2018 07:27:18: #2 number of paired peaks: 819 WARNING @ Fri, 04 May 2018 07:27:18: Fewer paired peaks (819) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 819 pairs to build model! INFO @ Fri, 04 May 2018 07:27:18: start model_add_line... INFO @ Fri, 04 May 2018 07:27:18: start X-correlation... INFO @ Fri, 04 May 2018 07:27:18: end of X-cor INFO @ Fri, 04 May 2018 07:27:18: #2 finished! INFO @ Fri, 04 May 2018 07:27:18: #2 predicted fragment length is 142 bps INFO @ Fri, 04 May 2018 07:27:18: #2 alternative fragment length(s) may be 142 bps INFO @ Fri, 04 May 2018 07:27:18: #2.2 Generate R script for model : SRX3011266.05_model.r INFO @ Fri, 04 May 2018 07:27:18: #3 Call peaks... INFO @ Fri, 04 May 2018 07:27:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:27:18: start X-correlation... INFO @ Fri, 04 May 2018 07:27:18: end of X-cor INFO @ Fri, 04 May 2018 07:27:18: #2 finished! INFO @ Fri, 04 May 2018 07:27:18: #2 predicted fragment length is 142 bps INFO @ Fri, 04 May 2018 07:27:18: #2 alternative fragment length(s) may be 142 bps INFO @ Fri, 04 May 2018 07:27:18: #2.2 Generate R script for model : SRX3011266.20_model.r INFO @ Fri, 04 May 2018 07:27:18: #3 Call peaks... INFO @ Fri, 04 May 2018 07:27:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:28:21: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:28:22: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:28:24: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:28:55: #4 Write output xls file... SRX3011266.05_peaks.xls INFO @ Fri, 04 May 2018 07:28:55: #4 Write peak in narrowPeak format file... SRX3011266.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:28:55: #4 Write summits bed file... SRX3011266.05_summits.bed INFO @ Fri, 04 May 2018 07:28:55: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (16786 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:28:58: #4 Write output xls file... SRX3011266.10_peaks.xls INFO @ Fri, 04 May 2018 07:28:58: #4 Write peak in narrowPeak format file... SRX3011266.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:28:58: #4 Write summits bed file... SRX3011266.10_summits.bed INFO @ Fri, 04 May 2018 07:28:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12051 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:29:00: #4 Write output xls file... SRX3011266.20_peaks.xls INFO @ Fri, 04 May 2018 07:29:00: #4 Write peak in narrowPeak format file... SRX3011266.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:29:00: #4 Write summits bed file... SRX3011266.20_summits.bed INFO @ Fri, 04 May 2018 07:29:00: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6655 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。