Job ID = 11293652 sra ファイルのダウンロード中... Completed: 199105K bytes transferred in 7 seconds (215831K 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 9594732 spots for /home/okishinya/chipatlas/results/dm3/SRX3873733/SRR6927798.sra Written 9594732 spots for /home/okishinya/chipatlas/results/dm3/SRX3873733/SRR6927798.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: 00:02:51 9594732 reads; of these: 9594732 (100.00%) were unpaired; of these: 580291 (6.05%) aligned 0 times 7446366 (77.61%) aligned exactly 1 time 1568075 (16.34%) aligned >1 times 93.95% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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] 1621161 / 9014441 = 0.1798 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 17:52:20: # Command line: callpeak -t SRX3873733.bam -f BAM -g dm -n SRX3873733.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3873733.05 # format = BAM # ChIP-seq file = ['SRX3873733.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 17:52:20: # Command line: callpeak -t SRX3873733.bam -f BAM -g dm -n SRX3873733.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3873733.20 # format = BAM # ChIP-seq file = ['SRX3873733.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 17:52:20: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:52:20: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:52:20: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:52:20: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:52:20: # Command line: callpeak -t SRX3873733.bam -f BAM -g dm -n SRX3873733.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3873733.10 # format = BAM # ChIP-seq file = ['SRX3873733.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 17:52:20: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:52:20: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:52:27: 1000000 INFO @ Sun, 04 Nov 2018 17:52:27: 1000000 INFO @ Sun, 04 Nov 2018 17:52:27: 1000000 INFO @ Sun, 04 Nov 2018 17:52:34: 2000000 INFO @ Sun, 04 Nov 2018 17:52:34: 2000000 INFO @ Sun, 04 Nov 2018 17:52:34: 2000000 INFO @ Sun, 04 Nov 2018 17:52:41: 3000000 INFO @ Sun, 04 Nov 2018 17:52:41: 3000000 INFO @ Sun, 04 Nov 2018 17:52:41: 3000000 INFO @ Sun, 04 Nov 2018 17:52:47: 4000000 INFO @ Sun, 04 Nov 2018 17:52:48: 4000000 INFO @ Sun, 04 Nov 2018 17:52:48: 4000000 INFO @ Sun, 04 Nov 2018 17:52:54: 5000000 INFO @ Sun, 04 Nov 2018 17:52:55: 5000000 INFO @ Sun, 04 Nov 2018 17:52:55: 5000000 INFO @ Sun, 04 Nov 2018 17:53:01: 6000000 INFO @ Sun, 04 Nov 2018 17:53:02: 6000000 INFO @ Sun, 04 Nov 2018 17:53:03: 6000000 INFO @ Sun, 04 Nov 2018 17:53:08: 7000000 INFO @ Sun, 04 Nov 2018 17:53:09: 7000000 INFO @ Sun, 04 Nov 2018 17:53:10: 7000000 INFO @ Sun, 04 Nov 2018 17:53:11: #1 tag size is determined as 50 bps INFO @ Sun, 04 Nov 2018 17:53:11: #1 tag size = 50 INFO @ Sun, 04 Nov 2018 17:53:11: #1 total tags in treatment: 7393280 INFO @ Sun, 04 Nov 2018 17:53:11: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:53:11: #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 17:53:11: #1 tags after filtering in treatment: 7393280 INFO @ Sun, 04 Nov 2018 17:53:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:53:11: #1 finished! INFO @ Sun, 04 Nov 2018 17:53:11: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:53:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:53:12: #2 number of paired peaks: 4522 INFO @ Sun, 04 Nov 2018 17:53:12: start model_add_line... INFO @ Sun, 04 Nov 2018 17:53:12: #1 tag size is determined as 50 bps INFO @ Sun, 04 Nov 2018 17:53:12: #1 tag size = 50 INFO @ Sun, 04 Nov 2018 17:53:12: #1 total tags in treatment: 7393280 INFO @ Sun, 04 Nov 2018 17:53:12: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:53:12: #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 17:53:12: start X-correlation... INFO @ Sun, 04 Nov 2018 17:53:12: #1 tags after filtering in treatment: 7393280 INFO @ Sun, 04 Nov 2018 17:53:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:53:12: #1 finished! INFO @ Sun, 04 Nov 2018 17:53:12: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:53:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:53:12: end of X-cor INFO @ Sun, 04 Nov 2018 17:53:12: #2 finished! INFO @ Sun, 04 Nov 2018 17:53:12: #2 predicted fragment length is 186 bps INFO @ Sun, 04 Nov 2018 17:53:12: #2 alternative fragment length(s) may be 186 bps INFO @ Sun, 04 Nov 2018 17:53:12: #2.2 Generate R script for model : SRX3873733.05_model.r INFO @ Sun, 04 Nov 2018 17:53:12: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:53:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:53:13: #1 tag size is determined as 50 bps INFO @ Sun, 04 Nov 2018 17:53:13: #1 tag size = 50 INFO @ Sun, 04 Nov 2018 17:53:13: #1 total tags in treatment: 7393280 INFO @ Sun, 04 Nov 2018 17:53:13: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:53:13: #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 17:53:13: #2 number of paired peaks: 4522 INFO @ Sun, 04 Nov 2018 17:53:13: start model_add_line... INFO @ Sun, 04 Nov 2018 17:53:13: #1 tags after filtering in treatment: 7393280 INFO @ Sun, 04 Nov 2018 17:53:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:53:13: #1 finished! INFO @ Sun, 04 Nov 2018 17:53:13: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:53:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:53:13: start X-correlation... INFO @ Sun, 04 Nov 2018 17:53:13: end of X-cor INFO @ Sun, 04 Nov 2018 17:53:13: #2 finished! INFO @ Sun, 04 Nov 2018 17:53:13: #2 predicted fragment length is 186 bps INFO @ Sun, 04 Nov 2018 17:53:13: #2 alternative fragment length(s) may be 186 bps INFO @ Sun, 04 Nov 2018 17:53:13: #2.2 Generate R script for model : SRX3873733.20_model.r INFO @ Sun, 04 Nov 2018 17:53:13: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:53:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:53:14: #2 number of paired peaks: 4522 INFO @ Sun, 04 Nov 2018 17:53:14: start model_add_line... INFO @ Sun, 04 Nov 2018 17:53:14: start X-correlation... INFO @ Sun, 04 Nov 2018 17:53:14: end of X-cor INFO @ Sun, 04 Nov 2018 17:53:14: #2 finished! INFO @ Sun, 04 Nov 2018 17:53:14: #2 predicted fragment length is 186 bps INFO @ Sun, 04 Nov 2018 17:53:14: #2 alternative fragment length(s) may be 186 bps INFO @ Sun, 04 Nov 2018 17:53:14: #2.2 Generate R script for model : SRX3873733.10_model.r INFO @ Sun, 04 Nov 2018 17:53:14: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:53:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:53:33: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:53:34: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:53:36: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:53:45: #4 Write output xls file... SRX3873733.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:53:45: #4 Write peak in narrowPeak format file... SRX3873733.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:53:45: #4 Write summits bed file... SRX3873733.20_summits.bed INFO @ Sun, 04 Nov 2018 17:53:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3802 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:53:46: #4 Write output xls file... SRX3873733.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:53:46: #4 Write peak in narrowPeak format file... SRX3873733.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:53:46: #4 Write summits bed file... SRX3873733.05_summits.bed INFO @ Sun, 04 Nov 2018 17:53:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8167 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:53:49: #4 Write output xls file... SRX3873733.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:53:49: #4 Write peak in narrowPeak format file... SRX3873733.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:53:49: #4 Write summits bed file... SRX3873733.10_summits.bed INFO @ Sun, 04 Nov 2018 17:53:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6008 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。