Job ID = 11632694 sra ファイルのダウンロード中... Completed: 1974355K bytes transferred in 20 seconds (772210K 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 77018316 spots for /home/okishinya/chipatlas/results/rn6/SRX3782453/SRR6826271.sra Written 77018316 spots for /home/okishinya/chipatlas/results/rn6/SRX3782453/SRR6826271.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:36:25 77018316 reads; of these: 77018316 (100.00%) were unpaired; of these: 22899236 (29.73%) aligned 0 times 43206681 (56.10%) aligned exactly 1 time 10912399 (14.17%) aligned >1 times 70.27% overall alignment rate Time searching: 00:36:27 Overall time: 00:36:27 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 20 files... [bam_rmdupse_core] 44175253 / 54119080 = 0.8163 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 07:13:44: # Command line: callpeak -t SRX3782453.bam -f BAM -g 2.15e9 -n SRX3782453.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782453.10 # format = BAM # ChIP-seq file = ['SRX3782453.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 07:13:44: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:13:44: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:13:44: # Command line: callpeak -t SRX3782453.bam -f BAM -g 2.15e9 -n SRX3782453.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782453.20 # format = BAM # ChIP-seq file = ['SRX3782453.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 07:13:44: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:13:44: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:13:44: # Command line: callpeak -t SRX3782453.bam -f BAM -g 2.15e9 -n SRX3782453.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782453.05 # format = BAM # ChIP-seq file = ['SRX3782453.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 07:13:44: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:13:44: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:13:51: 1000000 INFO @ Fri, 15 Feb 2019 07:13:52: 1000000 INFO @ Fri, 15 Feb 2019 07:13:52: 1000000 INFO @ Fri, 15 Feb 2019 07:13:57: 2000000 INFO @ Fri, 15 Feb 2019 07:14:00: 2000000 INFO @ Fri, 15 Feb 2019 07:14:00: 2000000 INFO @ Fri, 15 Feb 2019 07:14:03: 3000000 INFO @ Fri, 15 Feb 2019 07:14:08: 3000000 INFO @ Fri, 15 Feb 2019 07:14:08: 3000000 INFO @ Fri, 15 Feb 2019 07:14:10: 4000000 INFO @ Fri, 15 Feb 2019 07:14:15: 4000000 INFO @ Fri, 15 Feb 2019 07:14:15: 4000000 INFO @ Fri, 15 Feb 2019 07:14:16: 5000000 INFO @ Fri, 15 Feb 2019 07:14:22: 5000000 INFO @ Fri, 15 Feb 2019 07:14:22: 5000000 INFO @ Fri, 15 Feb 2019 07:14:22: 6000000 INFO @ Fri, 15 Feb 2019 07:14:29: 7000000 INFO @ Fri, 15 Feb 2019 07:14:29: 6000000 INFO @ Fri, 15 Feb 2019 07:14:29: 6000000 INFO @ Fri, 15 Feb 2019 07:14:35: 8000000 INFO @ Fri, 15 Feb 2019 07:14:36: 7000000 INFO @ Fri, 15 Feb 2019 07:14:36: 7000000 INFO @ Fri, 15 Feb 2019 07:14:41: 9000000 INFO @ Fri, 15 Feb 2019 07:14:42: 8000000 INFO @ Fri, 15 Feb 2019 07:14:42: 8000000 INFO @ Fri, 15 Feb 2019 07:14:47: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 07:14:47: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 07:14:47: #1 total tags in treatment: 9943827 INFO @ Fri, 15 Feb 2019 07:14:47: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:14:47: #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 07:14:48: #1 tags after filtering in treatment: 9943654 INFO @ Fri, 15 Feb 2019 07:14:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:14:48: #1 finished! INFO @ Fri, 15 Feb 2019 07:14:48: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:14:49: 9000000 INFO @ Fri, 15 Feb 2019 07:14:49: 9000000 INFO @ Fri, 15 Feb 2019 07:14:51: #2 number of paired peaks: 53089 INFO @ Fri, 15 Feb 2019 07:14:51: start model_add_line... INFO @ Fri, 15 Feb 2019 07:14:51: start X-correlation... INFO @ Fri, 15 Feb 2019 07:14:51: end of X-cor INFO @ Fri, 15 Feb 2019 07:14:51: #2 finished! INFO @ Fri, 15 Feb 2019 07:14:51: #2 predicted fragment length is 115 bps INFO @ Fri, 15 Feb 2019 07:14:51: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 15 Feb 2019 07:14:51: #2.2 Generate R script for model : SRX3782453.10_model.r INFO @ Fri, 15 Feb 2019 07:14:51: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:14:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:14:55: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 07:14:55: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 07:14:55: #1 total tags in treatment: 9943827 INFO @ Fri, 15 Feb 2019 07:14:55: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 07:14:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:14:55: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 07:14:55: #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 07:14:55: #1 total tags in treatment: 9943827 INFO @ Fri, 15 Feb 2019 07:14:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:14:55: #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 07:14:55: #1 tags after filtering in treatment: 9943654 INFO @ Fri, 15 Feb 2019 07:14:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:14:55: #1 finished! INFO @ Fri, 15 Feb 2019 07:14:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:14:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:14:55: #1 tags after filtering in treatment: 9943654 INFO @ Fri, 15 Feb 2019 07:14:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:14:55: #1 finished! INFO @ Fri, 15 Feb 2019 07:14:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:14:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:14:58: #2 number of paired peaks: 53089 INFO @ Fri, 15 Feb 2019 07:14:58: start model_add_line... INFO @ Fri, 15 Feb 2019 07:14:58: #2 number of paired peaks: 53089 INFO @ Fri, 15 Feb 2019 07:14:58: start model_add_line... INFO @ Fri, 15 Feb 2019 07:14:59: start X-correlation... INFO @ Fri, 15 Feb 2019 07:14:59: end of X-cor INFO @ Fri, 15 Feb 2019 07:14:59: #2 finished! INFO @ Fri, 15 Feb 2019 07:14:59: #2 predicted fragment length is 115 bps INFO @ Fri, 15 Feb 2019 07:14:59: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 15 Feb 2019 07:14:59: #2.2 Generate R script for model : SRX3782453.05_model.r INFO @ Fri, 15 Feb 2019 07:14:59: start X-correlation... INFO @ Fri, 15 Feb 2019 07:14:59: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:14:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:14:59: end of X-cor INFO @ Fri, 15 Feb 2019 07:14:59: #2 finished! INFO @ Fri, 15 Feb 2019 07:14:59: #2 predicted fragment length is 115 bps INFO @ Fri, 15 Feb 2019 07:14:59: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 15 Feb 2019 07:14:59: #2.2 Generate R script for model : SRX3782453.20_model.r INFO @ Fri, 15 Feb 2019 07:14:59: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:14:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:15:16: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:15:22: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:15:23: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:15:31: #4 Write output xls file... SRX3782453.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:15:31: #4 Write peak in narrowPeak format file... SRX3782453.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:15:31: #4 Write summits bed file... SRX3782453.10_summits.bed INFO @ Fri, 15 Feb 2019 07:15:31: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (1460 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:15:37: #4 Write output xls file... SRX3782453.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:15:37: #4 Write peak in narrowPeak format file... SRX3782453.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:15:37: #4 Write summits bed file... SRX3782453.05_summits.bed INFO @ Fri, 15 Feb 2019 07:15:37: Done! pass1 - making usageList (104 chroms): 2 millis pass2 - checking and writing primary data (9382 records, 4 fields): 17 millis INFO @ Fri, 15 Feb 2019 07:15:37: #4 Write output xls file... SRX3782453.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:15:37: #4 Write peak in narrowPeak format file... SRX3782453.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:15:37: #4 Write summits bed file... SRX3782453.20_summits.bed INFO @ Fri, 15 Feb 2019 07:15:37: Done! CompletedMACS2peakCalling pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (409 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。