Job ID = 11171294 sra ファイルのダウンロード中... Completed: 1267518K bytes transferred in 39 seconds (264697K 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 40878894 spots for /home/okishinya/chipatlas/results/dm3/SRX3032296/SRR5863986.sra Written 40878894 spots for /home/okishinya/chipatlas/results/dm3/SRX3032296/SRR5863986.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: 00:04:58 40878894 reads; of these: 40878894 (100.00%) were unpaired; of these: 38392427 (93.92%) aligned 0 times 2402014 (5.88%) aligned exactly 1 time 84453 (0.21%) aligned >1 times 6.08% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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] 1736194 / 2486467 = 0.6983 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 @ Sat, 08 Sep 2018 13:38:49: # Command line: callpeak -t SRX3032296.bam -f BAM -g dm -n SRX3032296.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3032296.20 # format = BAM # ChIP-seq file = ['SRX3032296.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 @ Sat, 08 Sep 2018 13:38:49: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:38:49: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:38:49: # Command line: callpeak -t SRX3032296.bam -f BAM -g dm -n SRX3032296.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3032296.10 # format = BAM # ChIP-seq file = ['SRX3032296.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 @ Sat, 08 Sep 2018 13:38:49: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:38:49: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:38:49: # Command line: callpeak -t SRX3032296.bam -f BAM -g dm -n SRX3032296.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3032296.05 # format = BAM # ChIP-seq file = ['SRX3032296.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 @ Sat, 08 Sep 2018 13:38:49: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:38:49: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:38:55: #1 tag size is determined as 74 bps INFO @ Sat, 08 Sep 2018 13:38:55: #1 tag size is determined as 74 bps INFO @ Sat, 08 Sep 2018 13:38:55: #1 tag size = 74 INFO @ Sat, 08 Sep 2018 13:38:55: #1 tag size = 74 INFO @ Sat, 08 Sep 2018 13:38:55: #1 total tags in treatment: 750273 INFO @ Sat, 08 Sep 2018 13:38:55: #1 total tags in treatment: 750273 INFO @ Sat, 08 Sep 2018 13:38:55: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:38:55: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:38:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:38:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:38:55: #1 tags after filtering in treatment: 750273 INFO @ Sat, 08 Sep 2018 13:38:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:38:55: #1 tags after filtering in treatment: 750273 INFO @ Sat, 08 Sep 2018 13:38:55: #1 finished! INFO @ Sat, 08 Sep 2018 13:38:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:38:55: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:38:55: #1 finished! INFO @ Sat, 08 Sep 2018 13:38:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:38:55: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:38:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:38:55: #1 tag size is determined as 74 bps INFO @ Sat, 08 Sep 2018 13:38:55: #1 tag size = 74 INFO @ Sat, 08 Sep 2018 13:38:55: #1 total tags in treatment: 750273 INFO @ Sat, 08 Sep 2018 13:38:55: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:38:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:38:55: #1 tags after filtering in treatment: 750273 INFO @ Sat, 08 Sep 2018 13:38:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:38:55: #1 finished! INFO @ Sat, 08 Sep 2018 13:38:55: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:38:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:38:55: #2 number of paired peaks: 6602 INFO @ Sat, 08 Sep 2018 13:38:55: start model_add_line... INFO @ Sat, 08 Sep 2018 13:38:55: start X-correlation... INFO @ Sat, 08 Sep 2018 13:38:55: end of X-cor INFO @ Sat, 08 Sep 2018 13:38:55: #2 finished! INFO @ Sat, 08 Sep 2018 13:38:55: #2 predicted fragment length is 221 bps INFO @ Sat, 08 Sep 2018 13:38:55: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 08 Sep 2018 13:38:55: #2.2 Generate R script for model : SRX3032296.10_model.r INFO @ Sat, 08 Sep 2018 13:38:55: #2 number of paired peaks: 6602 INFO @ Sat, 08 Sep 2018 13:38:55: start model_add_line... INFO @ Sat, 08 Sep 2018 13:38:55: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:38:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:38:55: start X-correlation... INFO @ Sat, 08 Sep 2018 13:38:55: end of X-cor INFO @ Sat, 08 Sep 2018 13:38:55: #2 finished! INFO @ Sat, 08 Sep 2018 13:38:55: #2 predicted fragment length is 221 bps INFO @ Sat, 08 Sep 2018 13:38:55: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 08 Sep 2018 13:38:55: #2.2 Generate R script for model : SRX3032296.05_model.r INFO @ Sat, 08 Sep 2018 13:38:55: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:38:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:38:55: #2 number of paired peaks: 6602 INFO @ Sat, 08 Sep 2018 13:38:55: start model_add_line... INFO @ Sat, 08 Sep 2018 13:38:55: start X-correlation... INFO @ Sat, 08 Sep 2018 13:38:55: end of X-cor INFO @ Sat, 08 Sep 2018 13:38:55: #2 finished! INFO @ Sat, 08 Sep 2018 13:38:55: #2 predicted fragment length is 221 bps INFO @ Sat, 08 Sep 2018 13:38:55: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 08 Sep 2018 13:38:55: #2.2 Generate R script for model : SRX3032296.20_model.r INFO @ Sat, 08 Sep 2018 13:38:55: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:38:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:38:57: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:38:57: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:38:57: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:38:58: #4 Write output xls file... SRX3032296.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:38:58: #4 Write peak in narrowPeak format file... SRX3032296.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:38:58: #4 Write summits bed file... SRX3032296.10_summits.bed INFO @ Sat, 08 Sep 2018 13:38:58: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1904 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:38:58: #4 Write output xls file... SRX3032296.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:38:58: #4 Write peak in narrowPeak format file... SRX3032296.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:38:58: #4 Write summits bed file... SRX3032296.20_summits.bed INFO @ Sat, 08 Sep 2018 13:38:58: Done! INFO @ Sat, 08 Sep 2018 13:38:58: #4 Write output xls file... SRX3032296.05_peaks.xls pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (803 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:38:58: #4 Write peak in narrowPeak format file... SRX3032296.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:38:58: #4 Write summits bed file... SRX3032296.05_summits.bed INFO @ Sat, 08 Sep 2018 13:38:58: Done! pass1 - making usageList (11 chroms): 7 millis pass2 - checking and writing primary data (3293 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。