Job ID = 11632688 sra ファイルのダウンロード中... Completed: 1030521K bytes transferred in 12 seconds (698840K 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 40646559 spots for /home/okishinya/chipatlas/results/rn6/SRX3782447/SRR6826265.sra Written 40646559 spots for /home/okishinya/chipatlas/results/rn6/SRX3782447/SRR6826265.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: 00:00:02 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:19:55 40646559 reads; of these: 40646559 (100.00%) were unpaired; of these: 3887217 (9.56%) aligned 0 times 31074144 (76.45%) aligned exactly 1 time 5685198 (13.99%) aligned >1 times 90.44% overall alignment rate Time searching: 00:20:00 Overall time: 00:20:00 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 16 files... [bam_rmdupse_core] 17802407 / 36759342 = 0.4843 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 07:32:41: # Command line: callpeak -t SRX3782447.bam -f BAM -g 2.15e9 -n SRX3782447.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782447.05 # format = BAM # ChIP-seq file = ['SRX3782447.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 07:32:41: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:32:41: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:32:41: # Command line: callpeak -t SRX3782447.bam -f BAM -g 2.15e9 -n SRX3782447.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782447.10 # format = BAM # ChIP-seq file = ['SRX3782447.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 07:32:41: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:32:41: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:32:41: # Command line: callpeak -t SRX3782447.bam -f BAM -g 2.15e9 -n SRX3782447.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782447.20 # format = BAM # ChIP-seq file = ['SRX3782447.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 07:32:41: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:32:41: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:32:47: 1000000 INFO @ Fri, 15 Feb 2019 07:32:47: 1000000 INFO @ Fri, 15 Feb 2019 07:32:47: 1000000 INFO @ Fri, 15 Feb 2019 07:32:54: 2000000 INFO @ Fri, 15 Feb 2019 07:32:54: 2000000 INFO @ Fri, 15 Feb 2019 07:32:54: 2000000 INFO @ Fri, 15 Feb 2019 07:32:59: 3000000 INFO @ Fri, 15 Feb 2019 07:33:00: 3000000 INFO @ Fri, 15 Feb 2019 07:33:00: 3000000 INFO @ Fri, 15 Feb 2019 07:33:05: 4000000 INFO @ Fri, 15 Feb 2019 07:33:06: 4000000 INFO @ Fri, 15 Feb 2019 07:33:06: 4000000 INFO @ Fri, 15 Feb 2019 07:33:11: 5000000 INFO @ Fri, 15 Feb 2019 07:33:12: 5000000 INFO @ Fri, 15 Feb 2019 07:33:12: 5000000 INFO @ Fri, 15 Feb 2019 07:33:17: 6000000 INFO @ Fri, 15 Feb 2019 07:33:18: 6000000 INFO @ Fri, 15 Feb 2019 07:33:18: 6000000 INFO @ Fri, 15 Feb 2019 07:33:23: 7000000 INFO @ Fri, 15 Feb 2019 07:33:24: 7000000 INFO @ Fri, 15 Feb 2019 07:33:24: 7000000 INFO @ Fri, 15 Feb 2019 07:33:29: 8000000 INFO @ Fri, 15 Feb 2019 07:33:30: 8000000 INFO @ Fri, 15 Feb 2019 07:33:30: 8000000 INFO @ Fri, 15 Feb 2019 07:33:35: 9000000 INFO @ Fri, 15 Feb 2019 07:33:36: 9000000 INFO @ Fri, 15 Feb 2019 07:33:37: 9000000 INFO @ Fri, 15 Feb 2019 07:33:41: 10000000 INFO @ Fri, 15 Feb 2019 07:33:43: 10000000 INFO @ Fri, 15 Feb 2019 07:33:43: 10000000 INFO @ Fri, 15 Feb 2019 07:33:47: 11000000 INFO @ Fri, 15 Feb 2019 07:33:49: 11000000 INFO @ Fri, 15 Feb 2019 07:33:49: 11000000 INFO @ Fri, 15 Feb 2019 07:33:53: 12000000 INFO @ Fri, 15 Feb 2019 07:33:55: 12000000 INFO @ Fri, 15 Feb 2019 07:33:56: 12000000 INFO @ Fri, 15 Feb 2019 07:33:59: 13000000 INFO @ Fri, 15 Feb 2019 07:34:01: 13000000 INFO @ Fri, 15 Feb 2019 07:34:02: 13000000 INFO @ Fri, 15 Feb 2019 07:34:05: 14000000 INFO @ Fri, 15 Feb 2019 07:34:08: 14000000 INFO @ Fri, 15 Feb 2019 07:34:09: 14000000 INFO @ Fri, 15 Feb 2019 07:34:11: 15000000 INFO @ Fri, 15 Feb 2019 07:34:14: 15000000 INFO @ Fri, 15 Feb 2019 07:34:15: 15000000 INFO @ Fri, 15 Feb 2019 07:34:17: 16000000 INFO @ Fri, 15 Feb 2019 07:34:21: 16000000 INFO @ Fri, 15 Feb 2019 07:34:22: 16000000 INFO @ Fri, 15 Feb 2019 07:34:22: 17000000 INFO @ Fri, 15 Feb 2019 07:34:27: 17000000 INFO @ Fri, 15 Feb 2019 07:34:28: 17000000 INFO @ Fri, 15 Feb 2019 07:34:28: 18000000 INFO @ Fri, 15 Feb 2019 07:34:34: 18000000 INFO @ Fri, 15 Feb 2019 07:34:35: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 07:34:35: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 07:34:35: #1 total tags in treatment: 18956935 INFO @ Fri, 15 Feb 2019 07:34:35: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:34:35: #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 07:34:35: 18000000 INFO @ Fri, 15 Feb 2019 07:34:35: #1 tags after filtering in treatment: 18956746 INFO @ Fri, 15 Feb 2019 07:34:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:34:35: #1 finished! INFO @ Fri, 15 Feb 2019 07:34:35: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:34:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:34:40: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 07:34:40: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 07:34:40: #1 total tags in treatment: 18956935 INFO @ Fri, 15 Feb 2019 07:34:40: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:34:40: #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 07:34:40: #2 number of paired peaks: 106711 INFO @ Fri, 15 Feb 2019 07:34:40: start model_add_line... INFO @ Fri, 15 Feb 2019 07:34:41: start X-correlation... INFO @ Fri, 15 Feb 2019 07:34:41: end of X-cor INFO @ Fri, 15 Feb 2019 07:34:41: #2 finished! INFO @ Fri, 15 Feb 2019 07:34:41: #2 predicted fragment length is 180 bps INFO @ Fri, 15 Feb 2019 07:34:41: #2 alternative fragment length(s) may be 180 bps INFO @ Fri, 15 Feb 2019 07:34:41: #2.2 Generate R script for model : SRX3782447.05_model.r INFO @ Fri, 15 Feb 2019 07:34:41: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:34:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:34:41: #1 tags after filtering in treatment: 18956746 INFO @ Fri, 15 Feb 2019 07:34:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:34:41: #1 finished! INFO @ Fri, 15 Feb 2019 07:34:41: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:34:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:34:41: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 07:34:41: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 07:34:41: #1 total tags in treatment: 18956935 INFO @ Fri, 15 Feb 2019 07:34:41: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:34:41: #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 07:34:42: #1 tags after filtering in treatment: 18956746 INFO @ Fri, 15 Feb 2019 07:34:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:34:42: #1 finished! INFO @ Fri, 15 Feb 2019 07:34:42: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:34:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:34:46: #2 number of paired peaks: 106711 INFO @ Fri, 15 Feb 2019 07:34:46: start model_add_line... INFO @ Fri, 15 Feb 2019 07:34:47: start X-correlation... INFO @ Fri, 15 Feb 2019 07:34:47: end of X-cor INFO @ Fri, 15 Feb 2019 07:34:47: #2 finished! INFO @ Fri, 15 Feb 2019 07:34:47: #2 predicted fragment length is 180 bps INFO @ Fri, 15 Feb 2019 07:34:47: #2 alternative fragment length(s) may be 180 bps INFO @ Fri, 15 Feb 2019 07:34:47: #2.2 Generate R script for model : SRX3782447.20_model.r INFO @ Fri, 15 Feb 2019 07:34:47: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:34:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:34:47: #2 number of paired peaks: 106711 INFO @ Fri, 15 Feb 2019 07:34:47: start model_add_line... INFO @ Fri, 15 Feb 2019 07:34:48: start X-correlation... INFO @ Fri, 15 Feb 2019 07:34:48: end of X-cor INFO @ Fri, 15 Feb 2019 07:34:48: #2 finished! INFO @ Fri, 15 Feb 2019 07:34:48: #2 predicted fragment length is 180 bps INFO @ Fri, 15 Feb 2019 07:34:48: #2 alternative fragment length(s) may be 180 bps INFO @ Fri, 15 Feb 2019 07:34:48: #2.2 Generate R script for model : SRX3782447.10_model.r INFO @ Fri, 15 Feb 2019 07:34:48: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:34:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:35:34: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:35:34: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:35:38: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:36:05: #4 Write output xls file... SRX3782447.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:36:06: #4 Write peak in narrowPeak format file... SRX3782447.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:36:06: #4 Write summits bed file... SRX3782447.05_summits.bed INFO @ Fri, 15 Feb 2019 07:36:06: Done! pass1 - making usageList (106 chroms): 8 millis pass2 - checking and writing primary data (28388 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:36:07: #4 Write output xls file... SRX3782447.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:36:07: #4 Write peak in narrowPeak format file... SRX3782447.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:36:07: #4 Write summits bed file... SRX3782447.20_summits.bed INFO @ Fri, 15 Feb 2019 07:36:07: Done! pass1 - making usageList (34 chroms): 4 millis pass2 - checking and writing primary data (1183 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:36:08: #4 Write output xls file... SRX3782447.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:36:08: #4 Write peak in narrowPeak format file... SRX3782447.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:36:08: #4 Write summits bed file... SRX3782447.10_summits.bed INFO @ Fri, 15 Feb 2019 07:36:08: Done! pass1 - making usageList (74 chroms): 5 millis pass2 - checking and writing primary data (10504 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。