Job ID = 9157412 sra ファイルのダウンロード中... Completed: 326049K bytes transferred in 5 seconds (480633K 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 11715770 spots for /home/okishinya/chipatlas/results/ce10/SRX208778/SRR628912.sra Written 11715770 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:35 11715770 reads; of these: 11715770 (100.00%) were unpaired; of these: 6224256 (53.13%) aligned 0 times 4213892 (35.97%) aligned exactly 1 time 1277622 (10.91%) aligned >1 times 46.87% overall alignment rate Time searching: 00:01:36 Overall time: 00:01:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1746254 / 5491514 = 0.3180 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 11:52:01: # Command line: callpeak -t SRX208778.bam -f BAM -g ce -n SRX208778.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208778.20 # format = BAM # ChIP-seq file = ['SRX208778.bam'] # control file = None # effective genome size = 9.00e+07 # 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 11:52:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:52:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:52:01: # Command line: callpeak -t SRX208778.bam -f BAM -g ce -n SRX208778.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208778.05 # format = BAM # ChIP-seq file = ['SRX208778.bam'] # control file = None # effective genome size = 9.00e+07 # 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 11:52:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:52:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:52:01: # Command line: callpeak -t SRX208778.bam -f BAM -g ce -n SRX208778.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208778.10 # format = BAM # ChIP-seq file = ['SRX208778.bam'] # control file = None # effective genome size = 9.00e+07 # 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 11:52:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:52:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:52:10: 1000000 INFO @ Tue, 27 Jun 2017 11:52:10: 1000000 INFO @ Tue, 27 Jun 2017 11:52:10: 1000000 INFO @ Tue, 27 Jun 2017 11:52:19: 2000000 INFO @ Tue, 27 Jun 2017 11:52:19: 2000000 INFO @ Tue, 27 Jun 2017 11:52:19: 2000000 INFO @ Tue, 27 Jun 2017 11:52:28: 3000000 INFO @ Tue, 27 Jun 2017 11:52:28: 3000000 INFO @ Tue, 27 Jun 2017 11:52:28: 3000000 INFO @ Tue, 27 Jun 2017 11:52:35: #1 tag size is determined as 37 bps INFO @ Tue, 27 Jun 2017 11:52:35: #1 tag size = 37 INFO @ Tue, 27 Jun 2017 11:52:35: #1 total tags in treatment: 3745260 INFO @ Tue, 27 Jun 2017 11:52:35: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:52:35: #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 11:52:35: #1 tags after filtering in treatment: 3745260 INFO @ Tue, 27 Jun 2017 11:52:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:52:35: #1 finished! INFO @ Tue, 27 Jun 2017 11:52:35: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:52:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:52:35: #1 tag size is determined as 37 bps INFO @ Tue, 27 Jun 2017 11:52:35: #1 tag size = 37 INFO @ Tue, 27 Jun 2017 11:52:35: #1 total tags in treatment: 3745260 INFO @ Tue, 27 Jun 2017 11:52:35: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:52:35: #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 11:52:35: #1 tags after filtering in treatment: 3745260 INFO @ Tue, 27 Jun 2017 11:52:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:52:35: #1 finished! INFO @ Tue, 27 Jun 2017 11:52:35: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:52:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:52:36: #2 number of paired peaks: 1413 INFO @ Tue, 27 Jun 2017 11:52:36: start model_add_line... INFO @ Tue, 27 Jun 2017 11:52:36: start X-correlation... INFO @ Tue, 27 Jun 2017 11:52:36: end of X-cor INFO @ Tue, 27 Jun 2017 11:52:36: #2 finished! INFO @ Tue, 27 Jun 2017 11:52:36: #2 predicted fragment length is 174 bps INFO @ Tue, 27 Jun 2017 11:52:36: #2 alternative fragment length(s) may be 174 bps INFO @ Tue, 27 Jun 2017 11:52:36: #2.2 Generate R script for model : SRX208778.20_model.r INFO @ Tue, 27 Jun 2017 11:52:36: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:52:36: #2 number of paired peaks: 1413 INFO @ Tue, 27 Jun 2017 11:52:36: start model_add_line... INFO @ Tue, 27 Jun 2017 11:52:36: #1 tag size is determined as 37 bps INFO @ Tue, 27 Jun 2017 11:52:36: #1 tag size = 37 INFO @ Tue, 27 Jun 2017 11:52:36: #1 total tags in treatment: 3745260 INFO @ Tue, 27 Jun 2017 11:52:36: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:52:36: #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 11:52:36: start X-correlation... INFO @ Tue, 27 Jun 2017 11:52:36: end of X-cor INFO @ Tue, 27 Jun 2017 11:52:36: #2 finished! INFO @ Tue, 27 Jun 2017 11:52:36: #2 predicted fragment length is 174 bps INFO @ Tue, 27 Jun 2017 11:52:36: #2 alternative fragment length(s) may be 174 bps INFO @ Tue, 27 Jun 2017 11:52:36: #2.2 Generate R script for model : SRX208778.10_model.r INFO @ Tue, 27 Jun 2017 11:52:36: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:52:36: #1 tags after filtering in treatment: 3745260 INFO @ Tue, 27 Jun 2017 11:52:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:52:36: #1 finished! INFO @ Tue, 27 Jun 2017 11:52:36: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:52:36: #2 number of paired peaks: 1413 INFO @ Tue, 27 Jun 2017 11:52:36: start model_add_line... INFO @ Tue, 27 Jun 2017 11:52:36: start X-correlation... INFO @ Tue, 27 Jun 2017 11:52:36: end of X-cor INFO @ Tue, 27 Jun 2017 11:52:36: #2 finished! INFO @ Tue, 27 Jun 2017 11:52:36: #2 predicted fragment length is 174 bps INFO @ Tue, 27 Jun 2017 11:52:36: #2 alternative fragment length(s) may be 174 bps INFO @ Tue, 27 Jun 2017 11:52:36: #2.2 Generate R script for model : SRX208778.05_model.r INFO @ Tue, 27 Jun 2017 11:52:36: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:52:47: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:52:48: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:52:48: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:52:53: #4 Write output xls file... SRX208778.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:52:53: #4 Write peak in narrowPeak format file... SRX208778.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:52:53: #4 Write summits bed file... SRX208778.20_summits.bed INFO @ Tue, 27 Jun 2017 11:52:53: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1158 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:52:53: #4 Write output xls file... SRX208778.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:52:53: #4 Write peak in narrowPeak format file... SRX208778.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:52:53: #4 Write summits bed file... SRX208778.10_summits.bed INFO @ Tue, 27 Jun 2017 11:52:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1681 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:52:53: #4 Write output xls file... SRX208778.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:52:53: #4 Write peak in narrowPeak format file... SRX208778.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:52:54: #4 Write summits bed file... SRX208778.05_summits.bed INFO @ Tue, 27 Jun 2017 11:52:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2417 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。