Job ID = 10194987 sra ファイルのダウンロード中... Completed: 54146K bytes transferred in 3 seconds (126345K bits/sec), in 1 file. Completed: 35268K bytes transferred in 3 seconds (89542K 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... Written 1731853 spots for /home/okishinya/chipatlas/results/rn6/SRX695945/SRR1569508.sra Written 1731853 spots total Written 2637016 spots for /home/okishinya/chipatlas/results/rn6/SRX695945/SRR1569507.sra Written 2637016 spots total 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 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:27 4368869 reads; of these: 4368869 (100.00%) were unpaired; of these: 115812 (2.65%) aligned 0 times 3805557 (87.11%) aligned exactly 1 time 447500 (10.24%) aligned >1 times 97.35% overall alignment rate Time searching: 00:01:29 Overall time: 00:01:29 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 2402162 / 4253057 = 0.5648 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, 10 Nov 2017 18:39:34: # Command line: callpeak -t SRX695945.bam -f BAM -g 2.15e9 -n SRX695945.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX695945.10 # format = BAM # ChIP-seq file = ['SRX695945.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Nov 2017 18:39:34: # Command line: callpeak -t SRX695945.bam -f BAM -g 2.15e9 -n SRX695945.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX695945.20 # format = BAM # ChIP-seq file = ['SRX695945.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Nov 2017 18:39:34: # Command line: callpeak -t SRX695945.bam -f BAM -g 2.15e9 -n SRX695945.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX695945.05 # format = BAM # ChIP-seq file = ['SRX695945.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Nov 2017 18:39:34: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:39:34: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:39:34: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:39:34: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:39:34: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:39:34: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:39:41: 1000000 INFO @ Fri, 10 Nov 2017 18:39:41: 1000000 INFO @ Fri, 10 Nov 2017 18:39:41: 1000000 INFO @ Fri, 10 Nov 2017 18:39:47: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 18:39:47: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 18:39:47: #1 total tags in treatment: 1850895 INFO @ Fri, 10 Nov 2017 18:39:47: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:39:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 18:39:47: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 18:39:47: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 18:39:47: #1 total tags in treatment: 1850895 INFO @ Fri, 10 Nov 2017 18:39:47: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:39:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 18:39:47: #1 tags after filtering in treatment: 1850601 INFO @ Fri, 10 Nov 2017 18:39:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:39:47: #1 finished! INFO @ Fri, 10 Nov 2017 18:39:47: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:39:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:39:47: #1 tags after filtering in treatment: 1850601 INFO @ Fri, 10 Nov 2017 18:39:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:39:47: #1 finished! INFO @ Fri, 10 Nov 2017 18:39:47: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:39:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:39:47: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 18:39:47: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 18:39:47: #1 total tags in treatment: 1850895 INFO @ Fri, 10 Nov 2017 18:39:47: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:39:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 18:39:47: #1 tags after filtering in treatment: 1850601 INFO @ Fri, 10 Nov 2017 18:39:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:39:47: #1 finished! INFO @ Fri, 10 Nov 2017 18:39:47: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:39:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:39:54: #2 number of paired peaks: 96714 INFO @ Fri, 10 Nov 2017 18:39:54: start model_add_line... INFO @ Fri, 10 Nov 2017 18:39:54: start X-correlation... INFO @ Fri, 10 Nov 2017 18:39:54: end of X-cor INFO @ Fri, 10 Nov 2017 18:39:54: #2 finished! INFO @ Fri, 10 Nov 2017 18:39:54: #2 predicted fragment length is 298 bps INFO @ Fri, 10 Nov 2017 18:39:54: #2 alternative fragment length(s) may be 298 bps INFO @ Fri, 10 Nov 2017 18:39:54: #2.2 Generate R script for model : SRX695945.10_model.r INFO @ Fri, 10 Nov 2017 18:39:54: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:39:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:39:54: #2 number of paired peaks: 96714 INFO @ Fri, 10 Nov 2017 18:39:54: start model_add_line... INFO @ Fri, 10 Nov 2017 18:39:54: start X-correlation... INFO @ Fri, 10 Nov 2017 18:39:54: end of X-cor INFO @ Fri, 10 Nov 2017 18:39:54: #2 finished! INFO @ Fri, 10 Nov 2017 18:39:54: #2 predicted fragment length is 298 bps INFO @ Fri, 10 Nov 2017 18:39:54: #2 alternative fragment length(s) may be 298 bps INFO @ Fri, 10 Nov 2017 18:39:54: #2.2 Generate R script for model : SRX695945.05_model.r INFO @ Fri, 10 Nov 2017 18:39:54: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:39:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:39:55: #2 number of paired peaks: 96714 INFO @ Fri, 10 Nov 2017 18:39:55: start model_add_line... INFO @ Fri, 10 Nov 2017 18:39:55: start X-correlation... INFO @ Fri, 10 Nov 2017 18:39:55: end of X-cor INFO @ Fri, 10 Nov 2017 18:39:55: #2 finished! INFO @ Fri, 10 Nov 2017 18:39:55: #2 predicted fragment length is 298 bps INFO @ Fri, 10 Nov 2017 18:39:55: #2 alternative fragment length(s) may be 298 bps INFO @ Fri, 10 Nov 2017 18:39:55: #2.2 Generate R script for model : SRX695945.20_model.r INFO @ Fri, 10 Nov 2017 18:39:55: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:39:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:39:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:39:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:40:01: #4 Write output xls file... SRX695945.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:40:01: #4 Write peak in narrowPeak format file... SRX695945.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:40:01: #4 Write summits bed file... SRX695945.10_summits.bed INFO @ Fri, 10 Nov 2017 18:40:01: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:40:01: #4 Write output xls file... SRX695945.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:40:01: #4 Write peak in narrowPeak format file... SRX695945.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:40:01: #4 Write summits bed file... SRX695945.05_summits.bed INFO @ Fri, 10 Nov 2017 18:40:01: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (34 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:40:02: #4 Write output xls file... SRX695945.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:40:02: #4 Write peak in narrowPeak format file... SRX695945.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:40:02: #4 Write summits bed file... SRX695945.20_summits.bed INFO @ Fri, 10 Nov 2017 18:40:02: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。