Job ID = 9157972 sra ファイルのダウンロード中... Completed: 70375K bytes transferred in 3 seconds (147011K bits/sec), in 1 file, 2 directories. 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... Written 5542137 spots for /home/okishinya/chipatlas/results/dm3/SRX2748311/SRR5460298.sra Written 5542137 spots total 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: 00:01:20 5542137 reads; of these: 5542137 (100.00%) were unpaired; of these: 552465 (9.97%) aligned 0 times 3942772 (71.14%) aligned exactly 1 time 1046900 (18.89%) aligned >1 times 90.03% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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] 1794579 / 4989672 = 0.3597 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 @ Tue, 27 Jun 2017 14:18:06: # Command line: callpeak -t SRX2748311.bam -f BAM -g dm -n SRX2748311.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2748311.10 # format = BAM # ChIP-seq file = ['SRX2748311.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 @ Tue, 27 Jun 2017 14:18:06: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:18:06: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:18:06: # Command line: callpeak -t SRX2748311.bam -f BAM -g dm -n SRX2748311.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2748311.20 # format = BAM # ChIP-seq file = ['SRX2748311.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 @ Tue, 27 Jun 2017 14:18:06: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:18:06: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:18:06: # Command line: callpeak -t SRX2748311.bam -f BAM -g dm -n SRX2748311.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2748311.05 # format = BAM # ChIP-seq file = ['SRX2748311.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 @ Tue, 27 Jun 2017 14:18:06: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:18:06: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:18:13: 1000000 INFO @ Tue, 27 Jun 2017 14:18:13: 1000000 INFO @ Tue, 27 Jun 2017 14:18:13: 1000000 INFO @ Tue, 27 Jun 2017 14:18:19: 2000000 INFO @ Tue, 27 Jun 2017 14:18:20: 2000000 INFO @ Tue, 27 Jun 2017 14:18:20: 2000000 INFO @ Tue, 27 Jun 2017 14:18:27: 3000000 INFO @ Tue, 27 Jun 2017 14:18:28: 3000000 INFO @ Tue, 27 Jun 2017 14:18:28: 3000000 INFO @ Tue, 27 Jun 2017 14:18:28: #1 tag size is determined as 25 bps INFO @ Tue, 27 Jun 2017 14:18:28: #1 tag size = 25 INFO @ Tue, 27 Jun 2017 14:18:28: #1 total tags in treatment: 3195093 INFO @ Tue, 27 Jun 2017 14:18:28: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:18:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:18:28: #1 tags after filtering in treatment: 3195093 INFO @ Tue, 27 Jun 2017 14:18:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:18:28: #1 finished! INFO @ Tue, 27 Jun 2017 14:18:28: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:18:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:18:28: #2 number of paired peaks: 1235 INFO @ Tue, 27 Jun 2017 14:18:28: start model_add_line... INFO @ Tue, 27 Jun 2017 14:18:28: start X-correlation... INFO @ Tue, 27 Jun 2017 14:18:28: end of X-cor INFO @ Tue, 27 Jun 2017 14:18:28: #2 finished! INFO @ Tue, 27 Jun 2017 14:18:28: #2 predicted fragment length is 105 bps INFO @ Tue, 27 Jun 2017 14:18:28: #2 alternative fragment length(s) may be 105 bps INFO @ Tue, 27 Jun 2017 14:18:28: #2.2 Generate R script for model : SRX2748311.05_model.r INFO @ Tue, 27 Jun 2017 14:18:28: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:18:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:18:29: #1 tag size is determined as 25 bps INFO @ Tue, 27 Jun 2017 14:18:29: #1 tag size is determined as 25 bps INFO @ Tue, 27 Jun 2017 14:18:29: #1 tag size = 25 INFO @ Tue, 27 Jun 2017 14:18:29: #1 tag size = 25 INFO @ Tue, 27 Jun 2017 14:18:29: #1 total tags in treatment: 3195093 INFO @ Tue, 27 Jun 2017 14:18:29: #1 total tags in treatment: 3195093 INFO @ Tue, 27 Jun 2017 14:18:29: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:18:29: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:18:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:18:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:18:29: #1 tags after filtering in treatment: 3195093 INFO @ Tue, 27 Jun 2017 14:18:29: #1 tags after filtering in treatment: 3195093 INFO @ Tue, 27 Jun 2017 14:18:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:18:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:18:29: #1 finished! INFO @ Tue, 27 Jun 2017 14:18:29: #1 finished! INFO @ Tue, 27 Jun 2017 14:18:29: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:18:29: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:18:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:18:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:18:29: #2 number of paired peaks: 1235 INFO @ Tue, 27 Jun 2017 14:18:29: start model_add_line... INFO @ Tue, 27 Jun 2017 14:18:29: #2 number of paired peaks: 1235 INFO @ Tue, 27 Jun 2017 14:18:29: start model_add_line... INFO @ Tue, 27 Jun 2017 14:18:29: start X-correlation... INFO @ Tue, 27 Jun 2017 14:18:29: end of X-cor INFO @ Tue, 27 Jun 2017 14:18:29: #2 finished! INFO @ Tue, 27 Jun 2017 14:18:29: #2 predicted fragment length is 105 bps INFO @ Tue, 27 Jun 2017 14:18:29: #2 alternative fragment length(s) may be 105 bps INFO @ Tue, 27 Jun 2017 14:18:29: #2.2 Generate R script for model : SRX2748311.20_model.r INFO @ Tue, 27 Jun 2017 14:18:29: start X-correlation... INFO @ Tue, 27 Jun 2017 14:18:29: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:18:29: end of X-cor INFO @ Tue, 27 Jun 2017 14:18:29: #2 finished! INFO @ Tue, 27 Jun 2017 14:18:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:18:29: #2 predicted fragment length is 105 bps INFO @ Tue, 27 Jun 2017 14:18:29: #2 alternative fragment length(s) may be 105 bps INFO @ Tue, 27 Jun 2017 14:18:29: #2.2 Generate R script for model : SRX2748311.10_model.r INFO @ Tue, 27 Jun 2017 14:18:29: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:18:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:18:36: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:18:38: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:18:38: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:18:41: #4 Write output xls file... SRX2748311.05_peaks.xls INFO @ Tue, 27 Jun 2017 14:18:41: #4 Write peak in narrowPeak format file... SRX2748311.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:18:41: #4 Write summits bed file... SRX2748311.05_summits.bed INFO @ Tue, 27 Jun 2017 14:18:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3129 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:18:42: #4 Write output xls file... SRX2748311.10_peaks.xls INFO @ Tue, 27 Jun 2017 14:18:42: #4 Write peak in narrowPeak format file... SRX2748311.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:18:42: #4 Write summits bed file... SRX2748311.10_summits.bed INFO @ Tue, 27 Jun 2017 14:18:42: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1504 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:18:43: #4 Write output xls file... SRX2748311.20_peaks.xls INFO @ Tue, 27 Jun 2017 14:18:43: #4 Write peak in narrowPeak format file... SRX2748311.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:18:43: #4 Write summits bed file... SRX2748311.20_summits.bed INFO @ Tue, 27 Jun 2017 14:18:43: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (514 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。