Job ID = 11240795 sra ファイルのダウンロード中... Completed: 208765K bytes transferred in 6 seconds (281087K 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 6367813 spots for /home/okishinya/chipatlas/results/dm3/SRX4798833/SRR7965236.sra Written 6367813 spots for /home/okishinya/chipatlas/results/dm3/SRX4798833/SRR7965236.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: 00:01:56 6367813 reads; of these: 6367813 (100.00%) were unpaired; of these: 732138 (11.50%) aligned 0 times 4757846 (74.72%) aligned exactly 1 time 877829 (13.79%) aligned >1 times 88.50% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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] 706785 / 5635675 = 0.1254 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 20:43:34: # Command line: callpeak -t SRX4798833.bam -f BAM -g dm -n SRX4798833.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4798833.20 # format = BAM # ChIP-seq file = ['SRX4798833.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 20:43:34: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:43:34: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:43:34: # Command line: callpeak -t SRX4798833.bam -f BAM -g dm -n SRX4798833.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4798833.05 # format = BAM # ChIP-seq file = ['SRX4798833.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 20:43:34: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:43:34: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:43:34: # Command line: callpeak -t SRX4798833.bam -f BAM -g dm -n SRX4798833.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4798833.10 # format = BAM # ChIP-seq file = ['SRX4798833.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 20:43:34: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:43:34: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:43:41: 1000000 INFO @ Sun, 07 Oct 2018 20:43:41: 1000000 INFO @ Sun, 07 Oct 2018 20:43:41: 1000000 INFO @ Sun, 07 Oct 2018 20:43:48: 2000000 INFO @ Sun, 07 Oct 2018 20:43:48: 2000000 INFO @ Sun, 07 Oct 2018 20:43:48: 2000000 INFO @ Sun, 07 Oct 2018 20:43:56: 3000000 INFO @ Sun, 07 Oct 2018 20:43:56: 3000000 INFO @ Sun, 07 Oct 2018 20:43:56: 3000000 INFO @ Sun, 07 Oct 2018 20:44:04: 4000000 INFO @ Sun, 07 Oct 2018 20:44:04: 4000000 INFO @ Sun, 07 Oct 2018 20:44:04: 4000000 INFO @ Sun, 07 Oct 2018 20:44:11: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:44:11: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:44:11: #1 total tags in treatment: 4928890 INFO @ Sun, 07 Oct 2018 20:44:11: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:44:11: #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 20:44:11: #1 tags after filtering in treatment: 4928890 INFO @ Sun, 07 Oct 2018 20:44:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:44:11: #1 finished! INFO @ Sun, 07 Oct 2018 20:44:11: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:44:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:44:11: #2 number of paired peaks: 1938 INFO @ Sun, 07 Oct 2018 20:44:11: start model_add_line... INFO @ Sun, 07 Oct 2018 20:44:11: start X-correlation... INFO @ Sun, 07 Oct 2018 20:44:11: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:44:11: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:44:11: #1 total tags in treatment: 4928890 INFO @ Sun, 07 Oct 2018 20:44:11: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:44:11: #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 20:44:11: end of X-cor INFO @ Sun, 07 Oct 2018 20:44:11: #2 finished! INFO @ Sun, 07 Oct 2018 20:44:11: #2 predicted fragment length is 147 bps INFO @ Sun, 07 Oct 2018 20:44:11: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 07 Oct 2018 20:44:11: #2.2 Generate R script for model : SRX4798833.10_model.r INFO @ Sun, 07 Oct 2018 20:44:11: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:44:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:44:12: #1 tags after filtering in treatment: 4928890 INFO @ Sun, 07 Oct 2018 20:44:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:44:12: #1 finished! INFO @ Sun, 07 Oct 2018 20:44:12: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:44:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:44:12: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:44:12: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:44:12: #1 total tags in treatment: 4928890 INFO @ Sun, 07 Oct 2018 20:44:12: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:44:12: #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 20:44:12: #1 tags after filtering in treatment: 4928890 INFO @ Sun, 07 Oct 2018 20:44:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:44:12: #1 finished! INFO @ Sun, 07 Oct 2018 20:44:12: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:44:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:44:12: #2 number of paired peaks: 1938 INFO @ Sun, 07 Oct 2018 20:44:12: start model_add_line... INFO @ Sun, 07 Oct 2018 20:44:12: start X-correlation... INFO @ Sun, 07 Oct 2018 20:44:12: end of X-cor INFO @ Sun, 07 Oct 2018 20:44:12: #2 finished! INFO @ Sun, 07 Oct 2018 20:44:12: #2 predicted fragment length is 147 bps INFO @ Sun, 07 Oct 2018 20:44:12: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 07 Oct 2018 20:44:12: #2.2 Generate R script for model : SRX4798833.20_model.r INFO @ Sun, 07 Oct 2018 20:44:12: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:44:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:44:12: #2 number of paired peaks: 1938 INFO @ Sun, 07 Oct 2018 20:44:12: start model_add_line... INFO @ Sun, 07 Oct 2018 20:44:13: start X-correlation... INFO @ Sun, 07 Oct 2018 20:44:13: end of X-cor INFO @ Sun, 07 Oct 2018 20:44:13: #2 finished! INFO @ Sun, 07 Oct 2018 20:44:13: #2 predicted fragment length is 147 bps INFO @ Sun, 07 Oct 2018 20:44:13: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 07 Oct 2018 20:44:13: #2.2 Generate R script for model : SRX4798833.05_model.r INFO @ Sun, 07 Oct 2018 20:44:13: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:44:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:44:24: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:44:25: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:44:25: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:44:30: #4 Write output xls file... SRX4798833.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:44:30: #4 Write peak in narrowPeak format file... SRX4798833.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:44:30: #4 Write summits bed file... SRX4798833.10_summits.bed INFO @ Sun, 07 Oct 2018 20:44:30: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (617 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:44:32: #4 Write output xls file... SRX4798833.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:44:32: #4 Write peak in narrowPeak format file... SRX4798833.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:44:32: #4 Write summits bed file... SRX4798833.20_summits.bed INFO @ Sun, 07 Oct 2018 20:44:32: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:44:32: #4 Write output xls file... SRX4798833.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:44:32: #4 Write peak in narrowPeak format file... SRX4798833.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:44:32: #4 Write summits bed file... SRX4798833.05_summits.bed INFO @ Sun, 07 Oct 2018 20:44:32: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1892 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。