Job ID = 11293656 sra ファイルのダウンロード中... Completed: 188235K bytes transferred in 6 seconds (240781K 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 9087649 spots for /home/okishinya/chipatlas/results/dm3/SRX3873745/SRR6927810.sra Written 9087649 spots for /home/okishinya/chipatlas/results/dm3/SRX3873745/SRR6927810.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: 00:02:46 9087649 reads; of these: 9087649 (100.00%) were unpaired; of these: 511963 (5.63%) aligned 0 times 7130518 (78.46%) aligned exactly 1 time 1445168 (15.90%) aligned >1 times 94.37% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 1655771 / 8575686 = 0.1931 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, 04 Nov 2018 17:52:02: # Command line: callpeak -t SRX3873745.bam -f BAM -g dm -n SRX3873745.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3873745.10 # format = BAM # ChIP-seq file = ['SRX3873745.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, 04 Nov 2018 17:52:02: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:52:02: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:52:02: # Command line: callpeak -t SRX3873745.bam -f BAM -g dm -n SRX3873745.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3873745.20 # format = BAM # ChIP-seq file = ['SRX3873745.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, 04 Nov 2018 17:52:02: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:52:02: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:52:02: # Command line: callpeak -t SRX3873745.bam -f BAM -g dm -n SRX3873745.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3873745.05 # format = BAM # ChIP-seq file = ['SRX3873745.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, 04 Nov 2018 17:52:02: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:52:02: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:52:09: 1000000 INFO @ Sun, 04 Nov 2018 17:52:10: 1000000 INFO @ Sun, 04 Nov 2018 17:52:10: 1000000 INFO @ Sun, 04 Nov 2018 17:52:16: 2000000 INFO @ Sun, 04 Nov 2018 17:52:17: 2000000 INFO @ Sun, 04 Nov 2018 17:52:17: 2000000 INFO @ Sun, 04 Nov 2018 17:52:23: 3000000 INFO @ Sun, 04 Nov 2018 17:52:24: 3000000 INFO @ Sun, 04 Nov 2018 17:52:24: 3000000 INFO @ Sun, 04 Nov 2018 17:52:31: 4000000 INFO @ Sun, 04 Nov 2018 17:52:31: 4000000 INFO @ Sun, 04 Nov 2018 17:52:32: 4000000 INFO @ Sun, 04 Nov 2018 17:52:38: 5000000 INFO @ Sun, 04 Nov 2018 17:52:39: 5000000 INFO @ Sun, 04 Nov 2018 17:52:39: 5000000 INFO @ Sun, 04 Nov 2018 17:52:45: 6000000 INFO @ Sun, 04 Nov 2018 17:52:46: 6000000 INFO @ Sun, 04 Nov 2018 17:52:47: 6000000 INFO @ Sun, 04 Nov 2018 17:52:52: #1 tag size is determined as 50 bps INFO @ Sun, 04 Nov 2018 17:52:52: #1 tag size = 50 INFO @ Sun, 04 Nov 2018 17:52:52: #1 total tags in treatment: 6919915 INFO @ Sun, 04 Nov 2018 17:52:52: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:52:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:52:52: #1 tags after filtering in treatment: 6919915 INFO @ Sun, 04 Nov 2018 17:52:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:52:52: #1 finished! INFO @ Sun, 04 Nov 2018 17:52:52: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:52:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:52:52: #1 tag size is determined as 50 bps INFO @ Sun, 04 Nov 2018 17:52:52: #1 tag size = 50 INFO @ Sun, 04 Nov 2018 17:52:52: #1 total tags in treatment: 6919915 INFO @ Sun, 04 Nov 2018 17:52:52: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:52:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:52:52: #1 tags after filtering in treatment: 6919915 INFO @ Sun, 04 Nov 2018 17:52:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:52:52: #1 finished! INFO @ Sun, 04 Nov 2018 17:52:52: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:52:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:52:53: #2 number of paired peaks: 4766 INFO @ Sun, 04 Nov 2018 17:52:53: start model_add_line... INFO @ Sun, 04 Nov 2018 17:52:53: start X-correlation... INFO @ Sun, 04 Nov 2018 17:52:53: end of X-cor INFO @ Sun, 04 Nov 2018 17:52:53: #2 finished! INFO @ Sun, 04 Nov 2018 17:52:53: #2 predicted fragment length is 177 bps INFO @ Sun, 04 Nov 2018 17:52:53: #2 alternative fragment length(s) may be 177 bps INFO @ Sun, 04 Nov 2018 17:52:53: #2.2 Generate R script for model : SRX3873745.05_model.r INFO @ Sun, 04 Nov 2018 17:52:53: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:52:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:52:53: #2 number of paired peaks: 4766 INFO @ Sun, 04 Nov 2018 17:52:53: start model_add_line... INFO @ Sun, 04 Nov 2018 17:52:53: #1 tag size is determined as 50 bps INFO @ Sun, 04 Nov 2018 17:52:53: #1 tag size = 50 INFO @ Sun, 04 Nov 2018 17:52:53: #1 total tags in treatment: 6919915 INFO @ Sun, 04 Nov 2018 17:52:53: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:52:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:52:53: start X-correlation... INFO @ Sun, 04 Nov 2018 17:52:53: end of X-cor INFO @ Sun, 04 Nov 2018 17:52:53: #2 finished! INFO @ Sun, 04 Nov 2018 17:52:53: #2 predicted fragment length is 177 bps INFO @ Sun, 04 Nov 2018 17:52:53: #2 alternative fragment length(s) may be 177 bps INFO @ Sun, 04 Nov 2018 17:52:53: #2.2 Generate R script for model : SRX3873745.10_model.r INFO @ Sun, 04 Nov 2018 17:52:53: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:52:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:52:54: #1 tags after filtering in treatment: 6919915 INFO @ Sun, 04 Nov 2018 17:52:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:52:54: #1 finished! INFO @ Sun, 04 Nov 2018 17:52:54: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:52:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:52:54: #2 number of paired peaks: 4766 INFO @ Sun, 04 Nov 2018 17:52:54: start model_add_line... INFO @ Sun, 04 Nov 2018 17:52:55: start X-correlation... INFO @ Sun, 04 Nov 2018 17:52:55: end of X-cor INFO @ Sun, 04 Nov 2018 17:52:55: #2 finished! INFO @ Sun, 04 Nov 2018 17:52:55: #2 predicted fragment length is 177 bps INFO @ Sun, 04 Nov 2018 17:52:55: #2 alternative fragment length(s) may be 177 bps INFO @ Sun, 04 Nov 2018 17:52:55: #2.2 Generate R script for model : SRX3873745.20_model.r INFO @ Sun, 04 Nov 2018 17:52:55: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:52:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:53:13: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:53:14: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:53:14: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:53:23: #4 Write output xls file... SRX3873745.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:53:23: #4 Write peak in narrowPeak format file... SRX3873745.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:53:23: #4 Write summits bed file... SRX3873745.10_summits.bed INFO @ Sun, 04 Nov 2018 17:53:23: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5849 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:53:24: #4 Write output xls file... SRX3873745.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:53:24: #4 Write peak in narrowPeak format file... SRX3873745.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:53:24: #4 Write summits bed file... SRX3873745.20_summits.bed INFO @ Sun, 04 Nov 2018 17:53:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3823 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:53:25: #4 Write output xls file... SRX3873745.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:53:25: #4 Write peak in narrowPeak format file... SRX3873745.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:53:25: #4 Write summits bed file... SRX3873745.05_summits.bed INFO @ Sun, 04 Nov 2018 17:53:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8018 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。