Job ID = 10194914 sra ファイルのダウンロード中... Completed: 88325K bytes transferred in 6 seconds (114650K bits/sec), in 1 file. Completed: 86177K bytes transferred in 8 seconds (87303K bits/sec), in 1 file. Completed: 145216K bytes transferred in 11 seconds (102554K bits/sec), in 1 file. Completed: 142345K bytes transferred in 10 seconds (107023K bits/sec), in 1 file. Completed: 142665K bytes transferred in 10 seconds (108511K bits/sec), in 1 file. Completed: 140239K bytes transferred in 6 seconds (164902K 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 2004265 spots for /home/okishinya/chipatlas/results/rn6/SRX2202909/SRR4319999.sra Written 2004265 spots total Written 2063336 spots for /home/okishinya/chipatlas/results/rn6/SRX2202909/SRR4319998.sra Written 2063336 spots total Written 3069585 spots for /home/okishinya/chipatlas/results/rn6/SRX2202909/SRR4320001.sra Written 3069585 spots total Written 3098830 spots for /home/okishinya/chipatlas/results/rn6/SRX2202909/SRR4320002.sra Written 3050215 spots for /home/okishinya/chipatlas/results/rn6/SRX2202909/SRR4320003.sra Written 3098830 spots total Written 3050215 spots total Written 3151654 spots for /home/okishinya/chipatlas/results/rn6/SRX2202909/SRR4320000.sra Written 3151654 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 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: 00:00:02 Multiseed full-index search: 00:31:46 16437885 reads; of these: 16437885 (100.00%) were unpaired; of these: 1158145 (7.05%) aligned 0 times 10568811 (64.30%) aligned exactly 1 time 4710929 (28.66%) aligned >1 times 92.95% overall alignment rate Time searching: 00:31:51 Overall time: 00:31:51 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] 1087860 / 15279740 = 0.0712 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 23:21:11: # Command line: callpeak -t SRX2202909.bam -f BAM -g 2.15e9 -n SRX2202909.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202909.05 # format = BAM # ChIP-seq file = ['SRX2202909.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 23:21:11: # Command line: callpeak -t SRX2202909.bam -f BAM -g 2.15e9 -n SRX2202909.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202909.10 # format = BAM # ChIP-seq file = ['SRX2202909.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 23:21:11: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:21:11: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:21:11: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:21:11: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:21:11: # Command line: callpeak -t SRX2202909.bam -f BAM -g 2.15e9 -n SRX2202909.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202909.20 # format = BAM # ChIP-seq file = ['SRX2202909.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 23:21:11: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:21:11: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:21:32: 1000000 INFO @ Fri, 10 Nov 2017 23:21:32: 1000000 INFO @ Fri, 10 Nov 2017 23:21:33: 1000000 INFO @ Fri, 10 Nov 2017 23:21:50: 2000000 INFO @ Fri, 10 Nov 2017 23:21:53: 2000000 INFO @ Fri, 10 Nov 2017 23:21:54: 2000000 INFO @ Fri, 10 Nov 2017 23:22:09: 3000000 INFO @ Fri, 10 Nov 2017 23:22:13: 3000000 INFO @ Fri, 10 Nov 2017 23:22:15: 3000000 INFO @ Fri, 10 Nov 2017 23:22:28: 4000000 INFO @ Fri, 10 Nov 2017 23:22:33: 4000000 INFO @ Fri, 10 Nov 2017 23:22:38: 4000000 INFO @ Fri, 10 Nov 2017 23:22:51: 5000000 INFO @ Fri, 10 Nov 2017 23:22:53: 5000000 INFO @ Fri, 10 Nov 2017 23:22:58: 5000000 INFO @ Fri, 10 Nov 2017 23:23:13: 6000000 INFO @ Fri, 10 Nov 2017 23:23:13: 6000000 INFO @ Fri, 10 Nov 2017 23:23:19: 6000000 INFO @ Fri, 10 Nov 2017 23:23:32: 7000000 INFO @ Fri, 10 Nov 2017 23:23:35: 7000000 INFO @ Fri, 10 Nov 2017 23:23:40: 7000000 INFO @ Fri, 10 Nov 2017 23:23:51: 8000000 INFO @ Fri, 10 Nov 2017 23:23:57: 8000000 INFO @ Fri, 10 Nov 2017 23:24:02: 8000000 INFO @ Fri, 10 Nov 2017 23:24:10: 9000000 INFO @ Fri, 10 Nov 2017 23:24:17: 9000000 INFO @ Fri, 10 Nov 2017 23:24:24: 9000000 INFO @ Fri, 10 Nov 2017 23:24:31: 10000000 INFO @ Fri, 10 Nov 2017 23:24:38: 10000000 INFO @ Fri, 10 Nov 2017 23:24:46: 10000000 INFO @ Fri, 10 Nov 2017 23:24:51: 11000000 INFO @ Fri, 10 Nov 2017 23:24:59: 11000000 INFO @ Fri, 10 Nov 2017 23:25:08: 11000000 INFO @ Fri, 10 Nov 2017 23:25:12: 12000000 INFO @ Fri, 10 Nov 2017 23:25:20: 12000000 INFO @ Fri, 10 Nov 2017 23:25:29: 12000000 INFO @ Fri, 10 Nov 2017 23:25:34: 13000000 INFO @ Fri, 10 Nov 2017 23:25:43: 13000000 INFO @ Fri, 10 Nov 2017 23:25:51: 13000000 INFO @ Fri, 10 Nov 2017 23:25:55: 14000000 INFO @ Fri, 10 Nov 2017 23:25:59: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:25:59: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:25:59: #1 total tags in treatment: 14191880 INFO @ Fri, 10 Nov 2017 23:25:59: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:25:59: #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 23:26:00: #1 tags after filtering in treatment: 14191713 INFO @ Fri, 10 Nov 2017 23:26:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:26:00: #1 finished! INFO @ Fri, 10 Nov 2017 23:26:00: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:26:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:26:03: #2 number of paired peaks: 24540 INFO @ Fri, 10 Nov 2017 23:26:03: start model_add_line... INFO @ Fri, 10 Nov 2017 23:26:03: start X-correlation... INFO @ Fri, 10 Nov 2017 23:26:03: end of X-cor INFO @ Fri, 10 Nov 2017 23:26:03: #2 finished! INFO @ Fri, 10 Nov 2017 23:26:03: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Nov 2017 23:26:03: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Nov 2017 23:26:03: #2.2 Generate R script for model : SRX2202909.05_model.r INFO @ Fri, 10 Nov 2017 23:26:03: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:26:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:26:04: 14000000 INFO @ Fri, 10 Nov 2017 23:26:08: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:26:08: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:26:08: #1 total tags in treatment: 14191880 INFO @ Fri, 10 Nov 2017 23:26:08: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:26:08: #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 23:26:09: #1 tags after filtering in treatment: 14191713 INFO @ Fri, 10 Nov 2017 23:26:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:26:09: #1 finished! INFO @ Fri, 10 Nov 2017 23:26:09: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:26:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:26:12: #2 number of paired peaks: 24540 INFO @ Fri, 10 Nov 2017 23:26:12: start model_add_line... INFO @ Fri, 10 Nov 2017 23:26:12: start X-correlation... INFO @ Fri, 10 Nov 2017 23:26:12: end of X-cor INFO @ Fri, 10 Nov 2017 23:26:12: #2 finished! INFO @ Fri, 10 Nov 2017 23:26:12: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Nov 2017 23:26:12: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Nov 2017 23:26:12: #2.2 Generate R script for model : SRX2202909.10_model.r INFO @ Fri, 10 Nov 2017 23:26:12: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:26:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:26:12: 14000000 INFO @ Fri, 10 Nov 2017 23:26:16: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:26:16: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:26:16: #1 total tags in treatment: 14191880 INFO @ Fri, 10 Nov 2017 23:26:16: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:26:16: #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 23:26:17: #1 tags after filtering in treatment: 14191713 INFO @ Fri, 10 Nov 2017 23:26:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:26:17: #1 finished! INFO @ Fri, 10 Nov 2017 23:26:17: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:26:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:26:20: #2 number of paired peaks: 24540 INFO @ Fri, 10 Nov 2017 23:26:20: start model_add_line... INFO @ Fri, 10 Nov 2017 23:26:20: start X-correlation... INFO @ Fri, 10 Nov 2017 23:26:20: end of X-cor INFO @ Fri, 10 Nov 2017 23:26:20: #2 finished! INFO @ Fri, 10 Nov 2017 23:26:20: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Nov 2017 23:26:20: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Nov 2017 23:26:20: #2.2 Generate R script for model : SRX2202909.20_model.r INFO @ Fri, 10 Nov 2017 23:26:20: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:26:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:26:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:27:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:27:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:27:16: #4 Write output xls file... SRX2202909.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:27:16: #4 Write peak in narrowPeak format file... SRX2202909.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:27:16: #4 Write summits bed file... SRX2202909.05_summits.bed INFO @ Fri, 10 Nov 2017 23:27:16: Done! pass1 - making usageList (58 chroms): 3 millis pass2 - checking and writing primary data (7589 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:27:33: #4 Write output xls file... SRX2202909.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:27:33: #4 Write peak in narrowPeak format file... SRX2202909.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:27:33: #4 Write summits bed file... SRX2202909.10_summits.bed INFO @ Fri, 10 Nov 2017 23:27:33: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (1892 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:27:34: #4 Write output xls file... SRX2202909.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:27:34: #4 Write peak in narrowPeak format file... SRX2202909.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:27:34: #4 Write summits bed file... SRX2202909.20_summits.bed INFO @ Fri, 10 Nov 2017 23:27:34: Done! pass1 - making usageList (31 chroms): 2 millis pass2 - checking and writing primary data (399 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。