Job ID = 10609111 sra ファイルのダウンロード中... Completed: 464542K bytes transferred in 59 seconds (64345K 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 16318116 spots for /home/okishinya/chipatlas/results/dm3/SRX3011249/SRR5834726.sra Written 16318116 spots for /home/okishinya/chipatlas/results/dm3/SRX3011249/SRR5834726.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: 00:07:18 16318116 reads; of these: 16318116 (100.00%) were unpaired; of these: 230266 (1.41%) aligned 0 times 12195868 (74.74%) aligned exactly 1 time 3891982 (23.85%) aligned >1 times 98.59% overall alignment rate Time searching: 00:07:18 Overall time: 00:07:19 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 8 files... [bam_rmdupse_core] 6223296 / 16087850 = 0.3868 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 07:15:29: # Command line: callpeak -t SRX3011249.bam -f BAM -g dm -n SRX3011249.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011249.10 # format = BAM # ChIP-seq file = ['SRX3011249.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 07:15:29: # Command line: callpeak -t SRX3011249.bam -f BAM -g dm -n SRX3011249.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011249.05 # format = BAM # ChIP-seq file = ['SRX3011249.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 07:15:29: # Command line: callpeak -t SRX3011249.bam -f BAM -g dm -n SRX3011249.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011249.20 # format = BAM # ChIP-seq file = ['SRX3011249.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 07:15:29: #1 read tag files... INFO @ Fri, 04 May 2018 07:15:29: #1 read tag files... INFO @ Fri, 04 May 2018 07:15:29: #1 read tag files... INFO @ Fri, 04 May 2018 07:15:29: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:15:29: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:15:29: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:15:37: 1000000 INFO @ Fri, 04 May 2018 07:15:37: 1000000 INFO @ Fri, 04 May 2018 07:15:37: 1000000 INFO @ Fri, 04 May 2018 07:15:44: 2000000 INFO @ Fri, 04 May 2018 07:15:44: 2000000 INFO @ Fri, 04 May 2018 07:15:45: 2000000 INFO @ Fri, 04 May 2018 07:15:51: 3000000 INFO @ Fri, 04 May 2018 07:15:52: 3000000 INFO @ Fri, 04 May 2018 07:15:53: 3000000 INFO @ Fri, 04 May 2018 07:15:58: 4000000 INFO @ Fri, 04 May 2018 07:16:00: 4000000 INFO @ Fri, 04 May 2018 07:16:01: 4000000 INFO @ Fri, 04 May 2018 07:16:05: 5000000 INFO @ Fri, 04 May 2018 07:16:07: 5000000 INFO @ Fri, 04 May 2018 07:16:10: 5000000 INFO @ Fri, 04 May 2018 07:16:12: 6000000 INFO @ Fri, 04 May 2018 07:16:15: 6000000 INFO @ Fri, 04 May 2018 07:16:18: 6000000 INFO @ Fri, 04 May 2018 07:16:19: 7000000 INFO @ Fri, 04 May 2018 07:16:23: 7000000 INFO @ Fri, 04 May 2018 07:16:26: 7000000 INFO @ Fri, 04 May 2018 07:16:26: 8000000 INFO @ Fri, 04 May 2018 07:16:31: 8000000 INFO @ Fri, 04 May 2018 07:16:34: 9000000 INFO @ Fri, 04 May 2018 07:16:34: 8000000 INFO @ Fri, 04 May 2018 07:16:38: 9000000 INFO @ Fri, 04 May 2018 07:16:40: #1 tag size is determined as 80 bps INFO @ Fri, 04 May 2018 07:16:40: #1 tag size = 80 INFO @ Fri, 04 May 2018 07:16:40: #1 total tags in treatment: 9864554 INFO @ Fri, 04 May 2018 07:16:40: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:16:40: #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 07:16:40: #1 tags after filtering in treatment: 9864554 INFO @ Fri, 04 May 2018 07:16:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:16:40: #1 finished! INFO @ Fri, 04 May 2018 07:16:40: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:16:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:16:41: #2 number of paired peaks: 1725 INFO @ Fri, 04 May 2018 07:16:41: start model_add_line... INFO @ Fri, 04 May 2018 07:16:41: start X-correlation... INFO @ Fri, 04 May 2018 07:16:42: end of X-cor INFO @ Fri, 04 May 2018 07:16:42: #2 finished! INFO @ Fri, 04 May 2018 07:16:42: #2 predicted fragment length is 143 bps INFO @ Fri, 04 May 2018 07:16:42: #2 alternative fragment length(s) may be 143 bps INFO @ Fri, 04 May 2018 07:16:42: #2.2 Generate R script for model : SRX3011249.20_model.r WARNING @ Fri, 04 May 2018 07:16:42: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:16:42: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Fri, 04 May 2018 07:16:42: #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 May 2018 07:16:42: #3 Call peaks... INFO @ Fri, 04 May 2018 07:16:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:16:42: 9000000 INFO @ Fri, 04 May 2018 07:16:44: #1 tag size is determined as 80 bps INFO @ Fri, 04 May 2018 07:16:44: #1 tag size = 80 INFO @ Fri, 04 May 2018 07:16:44: #1 total tags in treatment: 9864554 INFO @ Fri, 04 May 2018 07:16:44: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:16:44: #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 07:16:44: #1 tags after filtering in treatment: 9864554 INFO @ Fri, 04 May 2018 07:16:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:16:44: #1 finished! INFO @ Fri, 04 May 2018 07:16:44: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:16:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:16:45: #2 number of paired peaks: 1725 INFO @ Fri, 04 May 2018 07:16:45: start model_add_line... INFO @ Fri, 04 May 2018 07:16:45: start X-correlation... INFO @ Fri, 04 May 2018 07:16:45: end of X-cor INFO @ Fri, 04 May 2018 07:16:45: #2 finished! INFO @ Fri, 04 May 2018 07:16:45: #2 predicted fragment length is 143 bps INFO @ Fri, 04 May 2018 07:16:45: #2 alternative fragment length(s) may be 143 bps INFO @ Fri, 04 May 2018 07:16:45: #2.2 Generate R script for model : SRX3011249.10_model.r WARNING @ Fri, 04 May 2018 07:16:45: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:16:45: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Fri, 04 May 2018 07:16:45: #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 May 2018 07:16:45: #3 Call peaks... INFO @ Fri, 04 May 2018 07:16:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:16:48: #1 tag size is determined as 80 bps INFO @ Fri, 04 May 2018 07:16:48: #1 tag size = 80 INFO @ Fri, 04 May 2018 07:16:48: #1 total tags in treatment: 9864554 INFO @ Fri, 04 May 2018 07:16:48: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:16:48: #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 07:16:49: #1 tags after filtering in treatment: 9864554 INFO @ Fri, 04 May 2018 07:16:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:16:49: #1 finished! INFO @ Fri, 04 May 2018 07:16:49: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:16:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:16:50: #2 number of paired peaks: 1725 INFO @ Fri, 04 May 2018 07:16:50: start model_add_line... INFO @ Fri, 04 May 2018 07:16:50: start X-correlation... INFO @ Fri, 04 May 2018 07:16:50: end of X-cor INFO @ Fri, 04 May 2018 07:16:50: #2 finished! INFO @ Fri, 04 May 2018 07:16:50: #2 predicted fragment length is 143 bps INFO @ Fri, 04 May 2018 07:16:50: #2 alternative fragment length(s) may be 143 bps INFO @ Fri, 04 May 2018 07:16:50: #2.2 Generate R script for model : SRX3011249.05_model.r WARNING @ Fri, 04 May 2018 07:16:50: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:16:50: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Fri, 04 May 2018 07:16:50: #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 May 2018 07:16:50: #3 Call peaks... INFO @ Fri, 04 May 2018 07:16:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:17:07: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:17:10: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:17:15: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:17:21: #4 Write output xls file... SRX3011249.20_peaks.xls INFO @ Fri, 04 May 2018 07:17:21: #4 Write peak in narrowPeak format file... SRX3011249.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:17:21: #4 Write summits bed file... SRX3011249.20_summits.bed INFO @ Fri, 04 May 2018 07:17:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2443 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:17:25: #4 Write output xls file... SRX3011249.10_peaks.xls INFO @ Fri, 04 May 2018 07:17:25: #4 Write peak in narrowPeak format file... SRX3011249.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:17:25: #4 Write summits bed file... SRX3011249.10_summits.bed INFO @ Fri, 04 May 2018 07:17:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5111 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:17:29: #4 Write output xls file... SRX3011249.05_peaks.xls INFO @ Fri, 04 May 2018 07:17:29: #4 Write peak in narrowPeak format file... SRX3011249.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:17:29: #4 Write summits bed file... SRX3011249.05_summits.bed INFO @ Fri, 04 May 2018 07:17:29: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8584 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。