Job ID = 11240802 sra ファイルのダウンロード中... Completed: 273573K bytes transferred in 6 seconds (345597K 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 7897365 spots for /home/okishinya/chipatlas/results/dm3/SRX4798849/SRR7965220.sra Written 7897365 spots for /home/okishinya/chipatlas/results/dm3/SRX4798849/SRR7965220.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: 00:01:09 7897365 reads; of these: 7897365 (100.00%) were unpaired; of these: 5000822 (63.32%) aligned 0 times 2780205 (35.20%) aligned exactly 1 time 116338 (1.47%) aligned >1 times 36.68% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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_rmdupse_core] 785728 / 2896543 = 0.2713 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 @ Sun, 07 Oct 2018 20:42:54: # Command line: callpeak -t SRX4798849.bam -f BAM -g dm -n SRX4798849.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4798849.20 # format = BAM # ChIP-seq file = ['SRX4798849.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 @ Sun, 07 Oct 2018 20:42:54: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:42:54: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:42:54: # Command line: callpeak -t SRX4798849.bam -f BAM -g dm -n SRX4798849.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4798849.10 # format = BAM # ChIP-seq file = ['SRX4798849.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 @ Sun, 07 Oct 2018 20:42:54: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:42:54: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:42:54: # Command line: callpeak -t SRX4798849.bam -f BAM -g dm -n SRX4798849.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4798849.05 # format = BAM # ChIP-seq file = ['SRX4798849.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 @ Sun, 07 Oct 2018 20:42:54: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:42:54: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:43:02: 1000000 INFO @ Sun, 07 Oct 2018 20:43:02: 1000000 INFO @ Sun, 07 Oct 2018 20:43:02: 1000000 INFO @ Sun, 07 Oct 2018 20:43:09: 2000000 INFO @ Sun, 07 Oct 2018 20:43:10: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:43:10: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:43:10: #1 total tags in treatment: 2110815 INFO @ Sun, 07 Oct 2018 20:43:10: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:43:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:43:10: #1 tags after filtering in treatment: 2110815 INFO @ Sun, 07 Oct 2018 20:43:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:43:10: #1 finished! INFO @ Sun, 07 Oct 2018 20:43:10: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:43:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:43:10: 2000000 INFO @ Sun, 07 Oct 2018 20:43:10: 2000000 INFO @ Sun, 07 Oct 2018 20:43:10: #2 number of paired peaks: 6077 INFO @ Sun, 07 Oct 2018 20:43:10: start model_add_line... INFO @ Sun, 07 Oct 2018 20:43:11: start X-correlation... INFO @ Sun, 07 Oct 2018 20:43:11: end of X-cor INFO @ Sun, 07 Oct 2018 20:43:11: #2 finished! INFO @ Sun, 07 Oct 2018 20:43:11: #2 predicted fragment length is 148 bps INFO @ Sun, 07 Oct 2018 20:43:11: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 07 Oct 2018 20:43:11: #2.2 Generate R script for model : SRX4798849.20_model.r INFO @ Sun, 07 Oct 2018 20:43:11: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:43:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:43:11: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:43:11: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:43:11: #1 total tags in treatment: 2110815 INFO @ Sun, 07 Oct 2018 20:43:11: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:43:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:43:11: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:43:11: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:43:11: #1 total tags in treatment: 2110815 INFO @ Sun, 07 Oct 2018 20:43:11: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:43:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:43:11: #1 tags after filtering in treatment: 2110815 INFO @ Sun, 07 Oct 2018 20:43:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:43:11: #1 finished! INFO @ Sun, 07 Oct 2018 20:43:11: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:43:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:43:11: #1 tags after filtering in treatment: 2110815 INFO @ Sun, 07 Oct 2018 20:43:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:43:11: #1 finished! INFO @ Sun, 07 Oct 2018 20:43:11: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:43:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:43:11: #2 number of paired peaks: 6077 INFO @ Sun, 07 Oct 2018 20:43:11: start model_add_line... INFO @ Sun, 07 Oct 2018 20:43:11: #2 number of paired peaks: 6077 INFO @ Sun, 07 Oct 2018 20:43:11: start model_add_line... INFO @ Sun, 07 Oct 2018 20:43:11: start X-correlation... INFO @ Sun, 07 Oct 2018 20:43:11: end of X-cor INFO @ Sun, 07 Oct 2018 20:43:11: #2 finished! INFO @ Sun, 07 Oct 2018 20:43:11: #2 predicted fragment length is 148 bps INFO @ Sun, 07 Oct 2018 20:43:11: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 07 Oct 2018 20:43:11: #2.2 Generate R script for model : SRX4798849.05_model.r INFO @ Sun, 07 Oct 2018 20:43:11: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:43:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:43:11: start X-correlation... INFO @ Sun, 07 Oct 2018 20:43:11: end of X-cor INFO @ Sun, 07 Oct 2018 20:43:11: #2 finished! INFO @ Sun, 07 Oct 2018 20:43:11: #2 predicted fragment length is 148 bps INFO @ Sun, 07 Oct 2018 20:43:11: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 07 Oct 2018 20:43:11: #2.2 Generate R script for model : SRX4798849.10_model.r INFO @ Sun, 07 Oct 2018 20:43:11: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:43:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:43:17: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:43:18: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:43:18: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:43:20: #4 Write output xls file... SRX4798849.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:43:20: #4 Write peak in narrowPeak format file... SRX4798849.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:43:20: #4 Write summits bed file... SRX4798849.20_summits.bed INFO @ Sun, 07 Oct 2018 20:43:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2998 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:43:21: #4 Write output xls file... SRX4798849.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:43:21: #4 Write peak in narrowPeak format file... SRX4798849.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:43:21: #4 Write summits bed file... SRX4798849.10_summits.bed INFO @ Sun, 07 Oct 2018 20:43:21: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4932 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:43:22: #4 Write output xls file... SRX4798849.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:43:22: #4 Write peak in narrowPeak format file... SRX4798849.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:43:22: #4 Write summits bed file... SRX4798849.05_summits.bed INFO @ Sun, 07 Oct 2018 20:43:22: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7351 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。