Job ID = 10194944 sra ファイルのダウンロード中... Completed: 704696K bytes transferred in 13 seconds (440807K 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 18631904 spots for /home/okishinya/chipatlas/results/rn6/SRX2568197/SRR5264109.sra Written 18631904 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:47:23 18631904 reads; of these: 18631904 (100.00%) were unpaired; of these: 753931 (4.05%) aligned 0 times 15846722 (85.05%) aligned exactly 1 time 2031251 (10.90%) aligned >1 times 95.95% overall alignment rate Time searching: 00:47:27 Overall time: 00:47:27 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 8 files... [bam_rmdupse_core] 1124852 / 17877973 = 0.0629 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 @ Sat, 11 Nov 2017 00:58:11: # Command line: callpeak -t SRX2568197.bam -f BAM -g 2.15e9 -n SRX2568197.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2568197.10 # format = BAM # ChIP-seq file = ['SRX2568197.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 @ Sat, 11 Nov 2017 00:58:11: # Command line: callpeak -t SRX2568197.bam -f BAM -g 2.15e9 -n SRX2568197.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2568197.20 # format = BAM # ChIP-seq file = ['SRX2568197.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 @ Sat, 11 Nov 2017 00:58:11: # Command line: callpeak -t SRX2568197.bam -f BAM -g 2.15e9 -n SRX2568197.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2568197.05 # format = BAM # ChIP-seq file = ['SRX2568197.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 @ Sat, 11 Nov 2017 00:58:11: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:58:11: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:58:11: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:58:11: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:58:11: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:58:11: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:58:19: 1000000 INFO @ Sat, 11 Nov 2017 00:58:22: 1000000 INFO @ Sat, 11 Nov 2017 00:58:22: 1000000 INFO @ Sat, 11 Nov 2017 00:58:27: 2000000 INFO @ Sat, 11 Nov 2017 00:58:33: 2000000 INFO @ Sat, 11 Nov 2017 00:58:35: 2000000 INFO @ Sat, 11 Nov 2017 00:58:35: 3000000 INFO @ Sat, 11 Nov 2017 00:58:43: 4000000 INFO @ Sat, 11 Nov 2017 00:58:44: 3000000 INFO @ Sat, 11 Nov 2017 00:58:47: 3000000 INFO @ Sat, 11 Nov 2017 00:58:51: 5000000 INFO @ Sat, 11 Nov 2017 00:58:56: 4000000 INFO @ Sat, 11 Nov 2017 00:58:59: 6000000 INFO @ Sat, 11 Nov 2017 00:58:59: 4000000 INFO @ Sat, 11 Nov 2017 00:59:07: 7000000 INFO @ Sat, 11 Nov 2017 00:59:08: 5000000 INFO @ Sat, 11 Nov 2017 00:59:12: 5000000 INFO @ Sat, 11 Nov 2017 00:59:15: 8000000 INFO @ Sat, 11 Nov 2017 00:59:18: 6000000 INFO @ Sat, 11 Nov 2017 00:59:23: 9000000 INFO @ Sat, 11 Nov 2017 00:59:24: 6000000 INFO @ Sat, 11 Nov 2017 00:59:30: 7000000 INFO @ Sat, 11 Nov 2017 00:59:31: 10000000 INFO @ Sat, 11 Nov 2017 00:59:35: 7000000 INFO @ Sat, 11 Nov 2017 00:59:38: 11000000 INFO @ Sat, 11 Nov 2017 00:59:41: 8000000 INFO @ Sat, 11 Nov 2017 00:59:46: 12000000 INFO @ Sat, 11 Nov 2017 00:59:47: 8000000 INFO @ Sat, 11 Nov 2017 00:59:52: 9000000 INFO @ Sat, 11 Nov 2017 00:59:54: 13000000 INFO @ Sat, 11 Nov 2017 00:59:59: 9000000 INFO @ Sat, 11 Nov 2017 01:00:02: 14000000 INFO @ Sat, 11 Nov 2017 01:00:03: 10000000 INFO @ Sat, 11 Nov 2017 01:00:10: 10000000 INFO @ Sat, 11 Nov 2017 01:00:10: 15000000 INFO @ Sat, 11 Nov 2017 01:00:14: 11000000 INFO @ Sat, 11 Nov 2017 01:00:18: 16000000 INFO @ Sat, 11 Nov 2017 01:00:18: 11000000 INFO @ Sat, 11 Nov 2017 01:00:24: 12000000 INFO @ Sat, 11 Nov 2017 01:00:25: #1 tag size is determined as 75 bps INFO @ Sat, 11 Nov 2017 01:00:25: #1 tag size = 75 INFO @ Sat, 11 Nov 2017 01:00:25: #1 total tags in treatment: 16753121 INFO @ Sat, 11 Nov 2017 01:00:25: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:00:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:00:25: #1 tags after filtering in treatment: 16752866 INFO @ Sat, 11 Nov 2017 01:00:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:00:25: #1 finished! INFO @ Sat, 11 Nov 2017 01:00:25: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:00:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:00:26: 12000000 INFO @ Sat, 11 Nov 2017 01:00:31: #2 number of paired peaks: 93127 INFO @ Sat, 11 Nov 2017 01:00:31: start model_add_line... INFO @ Sat, 11 Nov 2017 01:00:32: start X-correlation... INFO @ Sat, 11 Nov 2017 01:00:32: end of X-cor INFO @ Sat, 11 Nov 2017 01:00:32: #2 finished! INFO @ Sat, 11 Nov 2017 01:00:32: #2 predicted fragment length is 182 bps INFO @ Sat, 11 Nov 2017 01:00:32: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 11 Nov 2017 01:00:32: #2.2 Generate R script for model : SRX2568197.10_model.r INFO @ Sat, 11 Nov 2017 01:00:32: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:00:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:00:34: 13000000 INFO @ Sat, 11 Nov 2017 01:00:35: 13000000 INFO @ Sat, 11 Nov 2017 01:00:42: 14000000 INFO @ Sat, 11 Nov 2017 01:00:45: 14000000 INFO @ Sat, 11 Nov 2017 01:00:50: 15000000 INFO @ Sat, 11 Nov 2017 01:00:55: 15000000 INFO @ Sat, 11 Nov 2017 01:00:58: 16000000 INFO @ Sat, 11 Nov 2017 01:01:05: #1 tag size is determined as 75 bps INFO @ Sat, 11 Nov 2017 01:01:05: #1 tag size = 75 INFO @ Sat, 11 Nov 2017 01:01:05: #1 total tags in treatment: 16753121 INFO @ Sat, 11 Nov 2017 01:01:05: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:01:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:01:06: #1 tags after filtering in treatment: 16752866 INFO @ Sat, 11 Nov 2017 01:01:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:01:06: #1 finished! INFO @ Sat, 11 Nov 2017 01:01:06: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:01:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:01:06: 16000000 INFO @ Sat, 11 Nov 2017 01:01:12: #2 number of paired peaks: 93127 INFO @ Sat, 11 Nov 2017 01:01:12: start model_add_line... INFO @ Sat, 11 Nov 2017 01:01:12: start X-correlation... INFO @ Sat, 11 Nov 2017 01:01:12: end of X-cor INFO @ Sat, 11 Nov 2017 01:01:12: #2 finished! INFO @ Sat, 11 Nov 2017 01:01:12: #2 predicted fragment length is 182 bps INFO @ Sat, 11 Nov 2017 01:01:12: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 11 Nov 2017 01:01:12: #2.2 Generate R script for model : SRX2568197.20_model.r INFO @ Sat, 11 Nov 2017 01:01:12: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:01:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:01:14: #1 tag size is determined as 75 bps INFO @ Sat, 11 Nov 2017 01:01:14: #1 tag size = 75 INFO @ Sat, 11 Nov 2017 01:01:14: #1 total tags in treatment: 16753121 INFO @ Sat, 11 Nov 2017 01:01:14: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:01:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:01:14: #1 tags after filtering in treatment: 16752866 INFO @ Sat, 11 Nov 2017 01:01:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:01:14: #1 finished! INFO @ Sat, 11 Nov 2017 01:01:14: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:01:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:01:20: #2 number of paired peaks: 93127 INFO @ Sat, 11 Nov 2017 01:01:20: start model_add_line... INFO @ Sat, 11 Nov 2017 01:01:21: start X-correlation... INFO @ Sat, 11 Nov 2017 01:01:21: end of X-cor INFO @ Sat, 11 Nov 2017 01:01:21: #2 finished! INFO @ Sat, 11 Nov 2017 01:01:21: #2 predicted fragment length is 182 bps INFO @ Sat, 11 Nov 2017 01:01:21: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 11 Nov 2017 01:01:21: #2.2 Generate R script for model : SRX2568197.05_model.r INFO @ Sat, 11 Nov 2017 01:01:21: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:01:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:01:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:02:03: #4 Write output xls file... SRX2568197.10_peaks.xls INFO @ Sat, 11 Nov 2017 01:02:03: #4 Write peak in narrowPeak format file... SRX2568197.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:02:03: #4 Write summits bed file... SRX2568197.10_summits.bed INFO @ Sat, 11 Nov 2017 01:02:03: Done! pass1 - making usageList (92 chroms): 7 millis pass2 - checking and writing primary data (26471 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:02:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:02:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:02:41: #4 Write output xls file... SRX2568197.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:02:42: #4 Write peak in narrowPeak format file... SRX2568197.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:02:42: #4 Write summits bed file... SRX2568197.20_summits.bed INFO @ Sat, 11 Nov 2017 01:02:42: Done! pass1 - making usageList (54 chroms): 4 millis pass2 - checking and writing primary data (13226 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:02:52: #4 Write output xls file... SRX2568197.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:02:53: #4 Write peak in narrowPeak format file... SRX2568197.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:02:53: #4 Write summits bed file... SRX2568197.05_summits.bed INFO @ Sat, 11 Nov 2017 01:02:53: Done! pass1 - making usageList (111 chroms): 10 millis pass2 - checking and writing primary data (40111 records, 4 fields): 65 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。