Job ID = 10194786 sra ファイルのダウンロード中... Completed: 364198K bytes transferred in 5 seconds (544181K 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 15888362 spots for /home/okishinya/chipatlas/results/rn6/SRX1774918/SRR3544952.sra Written 15888362 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: 00:00:00 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:35 15888362 reads; of these: 15888362 (100.00%) were unpaired; of these: 1175550 (7.40%) aligned 0 times 11295727 (71.09%) aligned exactly 1 time 3417085 (21.51%) aligned >1 times 92.60% overall alignment rate Time searching: 00:11:38 Overall time: 00:11:38 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] 1782187 / 14712812 = 0.1211 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, 10 Nov 2017 17:22:26: # Command line: callpeak -t SRX1774918.bam -f BAM -g 2.15e9 -n SRX1774918.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1774918.20 # format = BAM # ChIP-seq file = ['SRX1774918.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, 10 Nov 2017 17:22:26: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:22:26: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:22:26: # Command line: callpeak -t SRX1774918.bam -f BAM -g 2.15e9 -n SRX1774918.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1774918.10 # format = BAM # ChIP-seq file = ['SRX1774918.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, 10 Nov 2017 17:22:26: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:22:26: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:22:26: # Command line: callpeak -t SRX1774918.bam -f BAM -g 2.15e9 -n SRX1774918.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1774918.05 # format = BAM # ChIP-seq file = ['SRX1774918.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, 10 Nov 2017 17:22:26: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:22:26: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:22:33: 1000000 INFO @ Fri, 10 Nov 2017 17:22:33: 1000000 INFO @ Fri, 10 Nov 2017 17:22:33: 1000000 INFO @ Fri, 10 Nov 2017 17:22:39: 2000000 INFO @ Fri, 10 Nov 2017 17:22:40: 2000000 INFO @ Fri, 10 Nov 2017 17:22:40: 2000000 INFO @ Fri, 10 Nov 2017 17:22:46: 3000000 INFO @ Fri, 10 Nov 2017 17:22:46: 3000000 INFO @ Fri, 10 Nov 2017 17:22:46: 3000000 INFO @ Fri, 10 Nov 2017 17:22:52: 4000000 INFO @ Fri, 10 Nov 2017 17:22:53: 4000000 INFO @ Fri, 10 Nov 2017 17:22:53: 4000000 INFO @ Fri, 10 Nov 2017 17:22:58: 5000000 INFO @ Fri, 10 Nov 2017 17:22:59: 5000000 INFO @ Fri, 10 Nov 2017 17:23:00: 5000000 INFO @ Fri, 10 Nov 2017 17:23:04: 6000000 INFO @ Fri, 10 Nov 2017 17:23:06: 6000000 INFO @ Fri, 10 Nov 2017 17:23:07: 6000000 INFO @ Fri, 10 Nov 2017 17:23:11: 7000000 INFO @ Fri, 10 Nov 2017 17:23:13: 7000000 INFO @ Fri, 10 Nov 2017 17:23:14: 7000000 INFO @ Fri, 10 Nov 2017 17:23:17: 8000000 INFO @ Fri, 10 Nov 2017 17:23:20: 8000000 INFO @ Fri, 10 Nov 2017 17:23:21: 8000000 INFO @ Fri, 10 Nov 2017 17:23:23: 9000000 INFO @ Fri, 10 Nov 2017 17:23:26: 9000000 INFO @ Fri, 10 Nov 2017 17:23:28: 9000000 INFO @ Fri, 10 Nov 2017 17:23:30: 10000000 INFO @ Fri, 10 Nov 2017 17:23:33: 10000000 INFO @ Fri, 10 Nov 2017 17:23:35: 10000000 INFO @ Fri, 10 Nov 2017 17:23:36: 11000000 INFO @ Fri, 10 Nov 2017 17:23:39: 11000000 INFO @ Fri, 10 Nov 2017 17:23:42: 11000000 INFO @ Fri, 10 Nov 2017 17:23:44: 12000000 INFO @ Fri, 10 Nov 2017 17:23:46: 12000000 INFO @ Fri, 10 Nov 2017 17:23:49: 12000000 INFO @ Fri, 10 Nov 2017 17:23:51: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:23:51: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:23:51: #1 total tags in treatment: 12930625 INFO @ Fri, 10 Nov 2017 17:23:51: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:23:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:23:51: #1 tags after filtering in treatment: 12930421 INFO @ Fri, 10 Nov 2017 17:23:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:23:51: #1 finished! INFO @ Fri, 10 Nov 2017 17:23:51: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:23:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:23:52: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:23:52: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:23:52: #1 total tags in treatment: 12930625 INFO @ Fri, 10 Nov 2017 17:23:52: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:23:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:23:53: #1 tags after filtering in treatment: 12930421 INFO @ Fri, 10 Nov 2017 17:23:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:23:53: #1 finished! INFO @ Fri, 10 Nov 2017 17:23:53: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:23:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:23:53: #2 number of paired peaks: 11797 INFO @ Fri, 10 Nov 2017 17:23:53: start model_add_line... INFO @ Fri, 10 Nov 2017 17:23:53: start X-correlation... INFO @ Fri, 10 Nov 2017 17:23:53: end of X-cor INFO @ Fri, 10 Nov 2017 17:23:53: #2 finished! INFO @ Fri, 10 Nov 2017 17:23:53: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Nov 2017 17:23:53: #2 alternative fragment length(s) may be 54,155 bps INFO @ Fri, 10 Nov 2017 17:23:53: #2.2 Generate R script for model : SRX1774918.05_model.r INFO @ Fri, 10 Nov 2017 17:23:53: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:23:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:23:54: #2 number of paired peaks: 11797 INFO @ Fri, 10 Nov 2017 17:23:54: start model_add_line... INFO @ Fri, 10 Nov 2017 17:23:55: start X-correlation... INFO @ Fri, 10 Nov 2017 17:23:55: end of X-cor INFO @ Fri, 10 Nov 2017 17:23:55: #2 finished! INFO @ Fri, 10 Nov 2017 17:23:55: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Nov 2017 17:23:55: #2 alternative fragment length(s) may be 54,155 bps INFO @ Fri, 10 Nov 2017 17:23:55: #2.2 Generate R script for model : SRX1774918.20_model.r INFO @ Fri, 10 Nov 2017 17:23:55: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:23:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:23:55: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:23:55: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:23:55: #1 total tags in treatment: 12930625 INFO @ Fri, 10 Nov 2017 17:23:55: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:23:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:23:55: #1 tags after filtering in treatment: 12930421 INFO @ Fri, 10 Nov 2017 17:23:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:23:55: #1 finished! INFO @ Fri, 10 Nov 2017 17:23:55: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:23:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:23:57: #2 number of paired peaks: 11797 INFO @ Fri, 10 Nov 2017 17:23:57: start model_add_line... INFO @ Fri, 10 Nov 2017 17:23:57: start X-correlation... INFO @ Fri, 10 Nov 2017 17:23:57: end of X-cor INFO @ Fri, 10 Nov 2017 17:23:57: #2 finished! INFO @ Fri, 10 Nov 2017 17:23:57: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Nov 2017 17:23:57: #2 alternative fragment length(s) may be 54,155 bps INFO @ Fri, 10 Nov 2017 17:23:57: #2.2 Generate R script for model : SRX1774918.10_model.r INFO @ Fri, 10 Nov 2017 17:23:57: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:23:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:24:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:24:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:24:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:24:45: #4 Write output xls file... SRX1774918.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:24:45: #4 Write peak in narrowPeak format file... SRX1774918.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:24:45: #4 Write summits bed file... SRX1774918.20_summits.bed INFO @ Fri, 10 Nov 2017 17:24:45: Done! pass1 - making usageList (19 chroms): 0 millis pass2 - checking and writing primary data (154 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:24:47: #4 Write output xls file... SRX1774918.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:24:47: #4 Write peak in narrowPeak format file... SRX1774918.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:24:47: #4 Write summits bed file... SRX1774918.05_summits.bed INFO @ Fri, 10 Nov 2017 17:24:47: Done! pass1 - making usageList (32 chroms): 0 millis pass2 - checking and writing primary data (481 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:24:50: #4 Write output xls file... SRX1774918.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:24:50: #4 Write peak in narrowPeak format file... SRX1774918.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:24:50: #4 Write summits bed file... SRX1774918.10_summits.bed INFO @ Fri, 10 Nov 2017 17:24:50: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (286 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。