Job ID = 10608875 sra ファイルのダウンロード中... Completed: 532016K bytes transferred in 13 seconds (318001K 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... Written 11971483 spots for /home/okishinya/chipatlas/results/rn6/SRX2727610/SRR5437673.sra Written 11971483 spots total 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: 00:17:39 11971483 reads; of these: 11971483 (100.00%) were unpaired; of these: 1613289 (13.48%) aligned 0 times 8498775 (70.99%) aligned exactly 1 time 1859419 (15.53%) aligned >1 times 86.52% overall alignment rate Time searching: 00:17:43 Overall time: 00:17:43 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_sort_core] merging from 8 files... [bam_rmdupse_core] 750754 / 10358194 = 0.0725 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 @ Thu, 03 May 2018 22:39:06: # Command line: callpeak -t SRX2727610.bam -f BAM -g 2.15e9 -n SRX2727610.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2727610.05 # format = BAM # ChIP-seq file = ['SRX2727610.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 @ Thu, 03 May 2018 22:39:06: #1 read tag files... INFO @ Thu, 03 May 2018 22:39:06: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:39:06: # Command line: callpeak -t SRX2727610.bam -f BAM -g 2.15e9 -n SRX2727610.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2727610.20 # format = BAM # ChIP-seq file = ['SRX2727610.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 @ Thu, 03 May 2018 22:39:06: #1 read tag files... INFO @ Thu, 03 May 2018 22:39:06: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:39:06: # Command line: callpeak -t SRX2727610.bam -f BAM -g 2.15e9 -n SRX2727610.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2727610.10 # format = BAM # ChIP-seq file = ['SRX2727610.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 @ Thu, 03 May 2018 22:39:06: #1 read tag files... INFO @ Thu, 03 May 2018 22:39:06: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:39:16: 1000000 INFO @ Thu, 03 May 2018 22:39:16: 1000000 INFO @ Thu, 03 May 2018 22:39:16: 1000000 INFO @ Thu, 03 May 2018 22:39:25: 2000000 INFO @ Thu, 03 May 2018 22:39:26: 2000000 INFO @ Thu, 03 May 2018 22:39:26: 2000000 INFO @ Thu, 03 May 2018 22:39:34: 3000000 INFO @ Thu, 03 May 2018 22:39:36: 3000000 INFO @ Thu, 03 May 2018 22:39:36: 3000000 INFO @ Thu, 03 May 2018 22:39:44: 4000000 INFO @ Thu, 03 May 2018 22:39:46: 4000000 INFO @ Thu, 03 May 2018 22:39:46: 4000000 INFO @ Thu, 03 May 2018 22:39:53: 5000000 INFO @ Thu, 03 May 2018 22:39:56: 5000000 INFO @ Thu, 03 May 2018 22:39:56: 5000000 INFO @ Thu, 03 May 2018 22:40:03: 6000000 INFO @ Thu, 03 May 2018 22:40:06: 6000000 INFO @ Thu, 03 May 2018 22:40:06: 6000000 INFO @ Thu, 03 May 2018 22:40:13: 7000000 INFO @ Thu, 03 May 2018 22:40:17: 7000000 INFO @ Thu, 03 May 2018 22:40:17: 7000000 INFO @ Thu, 03 May 2018 22:40:22: 8000000 INFO @ Thu, 03 May 2018 22:40:28: 8000000 INFO @ Thu, 03 May 2018 22:40:28: 8000000 INFO @ Thu, 03 May 2018 22:40:32: 9000000 INFO @ Thu, 03 May 2018 22:40:38: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:40:38: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:40:38: #1 total tags in treatment: 9607440 INFO @ Thu, 03 May 2018 22:40:38: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:40:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:40:38: 9000000 INFO @ Thu, 03 May 2018 22:40:38: 9000000 INFO @ Thu, 03 May 2018 22:40:39: #1 tags after filtering in treatment: 9607179 INFO @ Thu, 03 May 2018 22:40:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:40:39: #1 finished! INFO @ Thu, 03 May 2018 22:40:39: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:40:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:40:41: #2 number of paired peaks: 54200 INFO @ Thu, 03 May 2018 22:40:41: start model_add_line... INFO @ Thu, 03 May 2018 22:40:41: start X-correlation... INFO @ Thu, 03 May 2018 22:40:41: end of X-cor INFO @ Thu, 03 May 2018 22:40:41: #2 finished! INFO @ Thu, 03 May 2018 22:40:41: #2 predicted fragment length is 208 bps INFO @ Thu, 03 May 2018 22:40:41: #2 alternative fragment length(s) may be 208 bps INFO @ Thu, 03 May 2018 22:40:41: #2.2 Generate R script for model : SRX2727610.10_model.r INFO @ Thu, 03 May 2018 22:40:41: #3 Call peaks... INFO @ Thu, 03 May 2018 22:40:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:40:45: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:40:45: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:40:45: #1 total tags in treatment: 9607440 INFO @ Thu, 03 May 2018 22:40:45: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:40:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:40:45: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:40:45: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:40:45: #1 total tags in treatment: 9607440 INFO @ Thu, 03 May 2018 22:40:45: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:40:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:40:45: #1 tags after filtering in treatment: 9607179 INFO @ Thu, 03 May 2018 22:40:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:40:45: #1 finished! INFO @ Thu, 03 May 2018 22:40:45: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:40:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:40:45: #1 tags after filtering in treatment: 9607179 INFO @ Thu, 03 May 2018 22:40:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:40:45: #1 finished! INFO @ Thu, 03 May 2018 22:40:45: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:40:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:40:48: #2 number of paired peaks: 54200 INFO @ Thu, 03 May 2018 22:40:48: start model_add_line... INFO @ Thu, 03 May 2018 22:40:48: #2 number of paired peaks: 54200 INFO @ Thu, 03 May 2018 22:40:48: start model_add_line... INFO @ Thu, 03 May 2018 22:40:48: start X-correlation... INFO @ Thu, 03 May 2018 22:40:48: end of X-cor INFO @ Thu, 03 May 2018 22:40:48: #2 finished! INFO @ Thu, 03 May 2018 22:40:48: #2 predicted fragment length is 208 bps INFO @ Thu, 03 May 2018 22:40:48: #2 alternative fragment length(s) may be 208 bps INFO @ Thu, 03 May 2018 22:40:48: #2.2 Generate R script for model : SRX2727610.05_model.r INFO @ Thu, 03 May 2018 22:40:48: #3 Call peaks... INFO @ Thu, 03 May 2018 22:40:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:40:48: start X-correlation... INFO @ Thu, 03 May 2018 22:40:48: end of X-cor INFO @ Thu, 03 May 2018 22:40:48: #2 finished! INFO @ Thu, 03 May 2018 22:40:48: #2 predicted fragment length is 208 bps INFO @ Thu, 03 May 2018 22:40:48: #2 alternative fragment length(s) may be 208 bps INFO @ Thu, 03 May 2018 22:40:48: #2.2 Generate R script for model : SRX2727610.20_model.r INFO @ Thu, 03 May 2018 22:40:48: #3 Call peaks... INFO @ Thu, 03 May 2018 22:40:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:41:05: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:41:12: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:41:14: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:41:20: #4 Write output xls file... SRX2727610.10_peaks.xls INFO @ Thu, 03 May 2018 22:41:20: #4 Write peak in narrowPeak format file... SRX2727610.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:41:20: #4 Write summits bed file... SRX2727610.10_summits.bed INFO @ Thu, 03 May 2018 22:41:20: Done! pass1 - making usageList (57 chroms): 3 millis pass2 - checking and writing primary data (10727 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:41:28: #4 Write output xls file... SRX2727610.05_peaks.xls INFO @ Thu, 03 May 2018 22:41:28: #4 Write peak in narrowPeak format file... SRX2727610.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:41:28: #4 Write summits bed file... SRX2727610.05_summits.bed INFO @ Thu, 03 May 2018 22:41:28: Done! pass1 - making usageList (87 chroms): 4 millis pass2 - checking and writing primary data (19780 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:41:29: #4 Write output xls file... SRX2727610.20_peaks.xls INFO @ Thu, 03 May 2018 22:41:29: #4 Write peak in narrowPeak format file... SRX2727610.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:41:29: #4 Write summits bed file... SRX2727610.20_summits.bed INFO @ Thu, 03 May 2018 22:41:29: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (3694 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。