Job ID = 11293658 sra ファイルのダウンロード中... Completed: 138315K bytes transferred in 5 seconds (197999K 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 6636856 spots for /home/okishinya/chipatlas/results/dm3/SRX3873747/SRR6927812.sra Written 6636856 spots for /home/okishinya/chipatlas/results/dm3/SRX3873747/SRR6927812.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: 00:00:01 Multiseed full-index search: 00:01:55 6636856 reads; of these: 6636856 (100.00%) were unpaired; of these: 810645 (12.21%) aligned 0 times 4805482 (72.41%) aligned exactly 1 time 1020729 (15.38%) aligned >1 times 87.79% 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] 1118849 / 5826211 = 0.1920 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 17:50:17: # Command line: callpeak -t SRX3873747.bam -f BAM -g dm -n SRX3873747.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3873747.05 # format = BAM # ChIP-seq file = ['SRX3873747.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 17:50:17: # Command line: callpeak -t SRX3873747.bam -f BAM -g dm -n SRX3873747.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3873747.10 # format = BAM # ChIP-seq file = ['SRX3873747.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 17:50:17: # Command line: callpeak -t SRX3873747.bam -f BAM -g dm -n SRX3873747.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3873747.20 # format = BAM # ChIP-seq file = ['SRX3873747.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 17:50:17: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:50:17: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:50:17: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:50:17: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:50:17: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:50:17: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:50:23: 1000000 INFO @ Sun, 04 Nov 2018 17:50:23: 1000000 INFO @ Sun, 04 Nov 2018 17:50:23: 1000000 INFO @ Sun, 04 Nov 2018 17:50:29: 2000000 INFO @ Sun, 04 Nov 2018 17:50:30: 2000000 INFO @ Sun, 04 Nov 2018 17:50:30: 2000000 INFO @ Sun, 04 Nov 2018 17:50:36: 3000000 INFO @ Sun, 04 Nov 2018 17:50:37: 3000000 INFO @ Sun, 04 Nov 2018 17:50:37: 3000000 INFO @ Sun, 04 Nov 2018 17:50:42: 4000000 INFO @ Sun, 04 Nov 2018 17:50:44: 4000000 INFO @ Sun, 04 Nov 2018 17:50:44: 4000000 INFO @ Sun, 04 Nov 2018 17:50:47: #1 tag size is determined as 49 bps INFO @ Sun, 04 Nov 2018 17:50:47: #1 tag size = 49 INFO @ Sun, 04 Nov 2018 17:50:47: #1 total tags in treatment: 4707362 INFO @ Sun, 04 Nov 2018 17:50:47: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:50:47: #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 17:50:47: #1 tags after filtering in treatment: 4707362 INFO @ Sun, 04 Nov 2018 17:50:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:50:47: #1 finished! INFO @ Sun, 04 Nov 2018 17:50:47: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:50:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:50:48: #2 number of paired peaks: 3867 INFO @ Sun, 04 Nov 2018 17:50:48: start model_add_line... INFO @ Sun, 04 Nov 2018 17:50:48: start X-correlation... INFO @ Sun, 04 Nov 2018 17:50:48: end of X-cor INFO @ Sun, 04 Nov 2018 17:50:48: #2 finished! INFO @ Sun, 04 Nov 2018 17:50:48: #2 predicted fragment length is 165 bps INFO @ Sun, 04 Nov 2018 17:50:48: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 04 Nov 2018 17:50:48: #2.2 Generate R script for model : SRX3873747.20_model.r INFO @ Sun, 04 Nov 2018 17:50:48: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:50:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:50:48: #1 tag size is determined as 49 bps INFO @ Sun, 04 Nov 2018 17:50:48: #1 tag size = 49 INFO @ Sun, 04 Nov 2018 17:50:48: #1 total tags in treatment: 4707362 INFO @ Sun, 04 Nov 2018 17:50:48: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:50:48: #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 17:50:48: #1 tags after filtering in treatment: 4707362 INFO @ Sun, 04 Nov 2018 17:50:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:50:48: #1 finished! INFO @ Sun, 04 Nov 2018 17:50:48: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:50:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:50:49: #1 tag size is determined as 49 bps INFO @ Sun, 04 Nov 2018 17:50:49: #1 tag size = 49 INFO @ Sun, 04 Nov 2018 17:50:49: #1 total tags in treatment: 4707362 INFO @ Sun, 04 Nov 2018 17:50:49: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:50:49: #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 17:50:49: #1 tags after filtering in treatment: 4707362 INFO @ Sun, 04 Nov 2018 17:50:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:50:49: #1 finished! INFO @ Sun, 04 Nov 2018 17:50:49: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:50:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:50:49: #2 number of paired peaks: 3867 INFO @ Sun, 04 Nov 2018 17:50:49: start model_add_line... INFO @ Sun, 04 Nov 2018 17:50:49: start X-correlation... INFO @ Sun, 04 Nov 2018 17:50:49: end of X-cor INFO @ Sun, 04 Nov 2018 17:50:49: #2 finished! INFO @ Sun, 04 Nov 2018 17:50:49: #2 predicted fragment length is 165 bps INFO @ Sun, 04 Nov 2018 17:50:49: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 04 Nov 2018 17:50:49: #2.2 Generate R script for model : SRX3873747.05_model.r INFO @ Sun, 04 Nov 2018 17:50:49: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:50:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:50:49: #2 number of paired peaks: 3867 INFO @ Sun, 04 Nov 2018 17:50:49: start model_add_line... INFO @ Sun, 04 Nov 2018 17:50:49: start X-correlation... INFO @ Sun, 04 Nov 2018 17:50:49: end of X-cor INFO @ Sun, 04 Nov 2018 17:50:49: #2 finished! INFO @ Sun, 04 Nov 2018 17:50:49: #2 predicted fragment length is 165 bps INFO @ Sun, 04 Nov 2018 17:50:49: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 04 Nov 2018 17:50:49: #2.2 Generate R script for model : SRX3873747.10_model.r INFO @ Sun, 04 Nov 2018 17:50:49: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:50:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:51:02: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:51:03: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:51:03: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:51:09: #4 Write output xls file... SRX3873747.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:51:09: #4 Write peak in narrowPeak format file... SRX3873747.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:51:09: #4 Write summits bed file... SRX3873747.20_summits.bed INFO @ Sun, 04 Nov 2018 17:51:09: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2352 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:51:10: #4 Write output xls file... SRX3873747.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:51:10: #4 Write peak in narrowPeak format file... SRX3873747.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:51:10: #4 Write summits bed file... SRX3873747.10_summits.bed INFO @ Sun, 04 Nov 2018 17:51:10: Done! INFO @ Sun, 04 Nov 2018 17:51:10: #4 Write output xls file... SRX3873747.05_peaks.xls pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3818 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:51:10: #4 Write peak in narrowPeak format file... SRX3873747.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:51:10: #4 Write summits bed file... SRX3873747.05_summits.bed INFO @ Sun, 04 Nov 2018 17:51:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5718 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。