Job ID = 11632621 sra ファイルのダウンロード中... Completed: 450268K bytes transferred in 8 seconds (454608K 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 17909387 spots for /home/okishinya/chipatlas/results/rn6/ERX1844923/ERR1780369.sra Written 17909387 spots for /home/okishinya/chipatlas/results/rn6/ERX1844923/ERR1780369.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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:06:48 17909387 reads; of these: 17909387 (100.00%) were unpaired; of these: 2201691 (12.29%) aligned 0 times 12007806 (67.05%) aligned exactly 1 time 3699890 (20.66%) aligned >1 times 87.71% overall alignment rate Time searching: 00:06:52 Overall time: 00:06:52 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 12785360 / 15707696 = 0.8140 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 @ Fri, 15 Feb 2019 06:08:12: # Command line: callpeak -t ERX1844923.bam -f BAM -g 2.15e9 -n ERX1844923.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1844923.10 # format = BAM # ChIP-seq file = ['ERX1844923.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 15 Feb 2019 06:08:12: # Command line: callpeak -t ERX1844923.bam -f BAM -g 2.15e9 -n ERX1844923.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1844923.05 # format = BAM # ChIP-seq file = ['ERX1844923.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 15 Feb 2019 06:08:12: # Command line: callpeak -t ERX1844923.bam -f BAM -g 2.15e9 -n ERX1844923.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1844923.20 # format = BAM # ChIP-seq file = ['ERX1844923.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 15 Feb 2019 06:08:12: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:08:12: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:08:12: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:08:12: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:08:12: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:08:12: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:08:18: 1000000 INFO @ Fri, 15 Feb 2019 06:08:19: 1000000 INFO @ Fri, 15 Feb 2019 06:08:19: 1000000 INFO @ Fri, 15 Feb 2019 06:08:24: 2000000 INFO @ Fri, 15 Feb 2019 06:08:25: 2000000 INFO @ Fri, 15 Feb 2019 06:08:25: 2000000 INFO @ Fri, 15 Feb 2019 06:08:30: #1 tag size is determined as 36 bps INFO @ Fri, 15 Feb 2019 06:08:30: #1 tag size = 36 INFO @ Fri, 15 Feb 2019 06:08:30: #1 total tags in treatment: 2922336 INFO @ Fri, 15 Feb 2019 06:08:30: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:08:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:08:31: #1 tags after filtering in treatment: 2922056 INFO @ Fri, 15 Feb 2019 06:08:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:08:31: #1 finished! INFO @ Fri, 15 Feb 2019 06:08:31: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:08:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:08:31: #1 tag size is determined as 36 bps INFO @ Fri, 15 Feb 2019 06:08:31: #1 tag size = 36 INFO @ Fri, 15 Feb 2019 06:08:31: #1 total tags in treatment: 2922336 INFO @ Fri, 15 Feb 2019 06:08:31: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:08:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:08:31: #1 tag size is determined as 36 bps INFO @ Fri, 15 Feb 2019 06:08:31: #1 tag size = 36 INFO @ Fri, 15 Feb 2019 06:08:31: #1 total tags in treatment: 2922336 INFO @ Fri, 15 Feb 2019 06:08:31: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:08:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:08:31: #1 tags after filtering in treatment: 2922056 INFO @ Fri, 15 Feb 2019 06:08:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:08:31: #1 finished! INFO @ Fri, 15 Feb 2019 06:08:31: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:08:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:08:31: #1 tags after filtering in treatment: 2922056 INFO @ Fri, 15 Feb 2019 06:08:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:08:31: #1 finished! INFO @ Fri, 15 Feb 2019 06:08:31: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:08:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:08:35: #2 number of paired peaks: 102528 INFO @ Fri, 15 Feb 2019 06:08:35: start model_add_line... INFO @ Fri, 15 Feb 2019 06:08:35: start X-correlation... INFO @ Fri, 15 Feb 2019 06:08:35: end of X-cor INFO @ Fri, 15 Feb 2019 06:08:35: #2 finished! INFO @ Fri, 15 Feb 2019 06:08:35: #2 predicted fragment length is 99 bps INFO @ Fri, 15 Feb 2019 06:08:35: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 15 Feb 2019 06:08:35: #2.2 Generate R script for model : ERX1844923.05_model.r INFO @ Fri, 15 Feb 2019 06:08:35: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:08:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:08:36: #2 number of paired peaks: 102528 INFO @ Fri, 15 Feb 2019 06:08:36: start model_add_line... INFO @ Fri, 15 Feb 2019 06:08:36: start X-correlation... INFO @ Fri, 15 Feb 2019 06:08:36: end of X-cor INFO @ Fri, 15 Feb 2019 06:08:36: #2 finished! INFO @ Fri, 15 Feb 2019 06:08:36: #2 predicted fragment length is 99 bps INFO @ Fri, 15 Feb 2019 06:08:36: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 15 Feb 2019 06:08:36: #2.2 Generate R script for model : ERX1844923.10_model.r INFO @ Fri, 15 Feb 2019 06:08:36: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:08:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:08:36: #2 number of paired peaks: 102528 INFO @ Fri, 15 Feb 2019 06:08:36: start model_add_line... INFO @ Fri, 15 Feb 2019 06:08:36: start X-correlation... INFO @ Fri, 15 Feb 2019 06:08:36: end of X-cor INFO @ Fri, 15 Feb 2019 06:08:36: #2 finished! INFO @ Fri, 15 Feb 2019 06:08:36: #2 predicted fragment length is 99 bps INFO @ Fri, 15 Feb 2019 06:08:36: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 15 Feb 2019 06:08:36: #2.2 Generate R script for model : ERX1844923.20_model.r INFO @ Fri, 15 Feb 2019 06:08:36: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:08:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:08:43: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:08:43: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:08:43: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:08:47: #4 Write output xls file... ERX1844923.10_peaks.xls INFO @ Fri, 15 Feb 2019 06:08:47: #4 Write peak in narrowPeak format file... ERX1844923.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:08:47: #4 Write summits bed file... ERX1844923.10_summits.bed INFO @ Fri, 15 Feb 2019 06:08:47: Done! INFO @ Fri, 15 Feb 2019 06:08:47: #4 Write output xls file... ERX1844923.20_peaks.xls INFO @ Fri, 15 Feb 2019 06:08:47: #4 Write peak in narrowPeak format file... ERX1844923.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:08:47: #4 Write summits bed file... ERX1844923.20_summits.bed INFO @ Fri, 15 Feb 2019 06:08:47: Done! INFO @ Fri, 15 Feb 2019 06:08:48: #4 Write output xls file... ERX1844923.05_peaks.xls INFO @ Fri, 15 Feb 2019 06:08:48: #4 Write peak in narrowPeak format file... ERX1844923.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:08:48: #4 Write summits bed file... ERX1844923.05_summits.bed INFO @ Fri, 15 Feb 2019 06:08:48: Done! pass1 - making usageList (25 chroms): 5 millis pass1 - making usageList (34 chroms): 6 millis pass2 - checking and writing primary data (152 records, 4 fields): 8 millis pass2 - checking and writing primary data (578 records, 4 fields): 8 millis CompletedMACS2peakCalling CompletedMACS2peakCalling pass1 - making usageList (51 chroms): 3 millis pass2 - checking and writing primary data (2076 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。