Job ID = 10194877 sra ファイルのダウンロード中... Completed: 158084K bytes transferred in 8 seconds (145300K bits/sec), in 1 file. Completed: 158797K bytes transferred in 9 seconds (135482K bits/sec), in 1 file. Completed: 150895K bytes transferred in 8 seconds (151831K bits/sec), in 1 file. Completed: 148754K bytes transferred in 7 seconds (170140K bits/sec), in 1 file. Completed: 175776K bytes transferred in 8 seconds (166365K bits/sec), in 1 file. Completed: 178006K bytes transferred in 7 seconds (193991K 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 3350957 spots for /home/okishinya/chipatlas/results/rn6/SRX2202872/SRR4319779.sra Written 3350957 spots total Written 3390996 spots for /home/okishinya/chipatlas/results/rn6/SRX2202872/SRR4319778.sra Written 3390996 spots total Written 3541911 spots for /home/okishinya/chipatlas/results/rn6/SRX2202872/SRR4319776.sra Written 3541911 spots total Written 3546026 spots for /home/okishinya/chipatlas/results/rn6/SRX2202872/SRR4319777.sra Written 3546026 spots total Written 3849269 spots for /home/okishinya/chipatlas/results/rn6/SRX2202872/SRR4319780.sra Written 3849269 spots total Written 3883583 spots for /home/okishinya/chipatlas/results/rn6/SRX2202872/SRR4319781.sra Written 3883583 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:15:18 21562742 reads; of these: 21562742 (100.00%) were unpaired; of these: 759763 (3.52%) aligned 0 times 16290275 (75.55%) aligned exactly 1 time 4512704 (20.93%) aligned >1 times 96.48% overall alignment rate Time searching: 00:15:21 Overall time: 00:15:21 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 12 files... [bam_rmdupse_core] 1887368 / 20802979 = 0.0907 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 17:51:08: # Command line: callpeak -t SRX2202872.bam -f BAM -g 2.15e9 -n SRX2202872.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202872.05 # format = BAM # ChIP-seq file = ['SRX2202872.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 17:51:08: # Command line: callpeak -t SRX2202872.bam -f BAM -g 2.15e9 -n SRX2202872.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202872.20 # format = BAM # ChIP-seq file = ['SRX2202872.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 17:51:08: # Command line: callpeak -t SRX2202872.bam -f BAM -g 2.15e9 -n SRX2202872.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202872.10 # format = BAM # ChIP-seq file = ['SRX2202872.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 17:51:08: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:51:08: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:51:08: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:51:08: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:51:08: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:51:08: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:51:15: 1000000 INFO @ Fri, 10 Nov 2017 17:51:15: 1000000 INFO @ Fri, 10 Nov 2017 17:51:16: 1000000 INFO @ Fri, 10 Nov 2017 17:51:23: 2000000 INFO @ Fri, 10 Nov 2017 17:51:23: 2000000 INFO @ Fri, 10 Nov 2017 17:51:23: 2000000 INFO @ Fri, 10 Nov 2017 17:51:30: 3000000 INFO @ Fri, 10 Nov 2017 17:51:30: 3000000 INFO @ Fri, 10 Nov 2017 17:51:32: 3000000 INFO @ Fri, 10 Nov 2017 17:51:38: 4000000 INFO @ Fri, 10 Nov 2017 17:51:38: 4000000 INFO @ Fri, 10 Nov 2017 17:51:40: 4000000 INFO @ Fri, 10 Nov 2017 17:51:46: 5000000 INFO @ Fri, 10 Nov 2017 17:51:46: 5000000 INFO @ Fri, 10 Nov 2017 17:51:48: 5000000 INFO @ Fri, 10 Nov 2017 17:51:54: 6000000 INFO @ Fri, 10 Nov 2017 17:51:54: 6000000 INFO @ Fri, 10 Nov 2017 17:51:57: 6000000 INFO @ Fri, 10 Nov 2017 17:52:01: 7000000 INFO @ Fri, 10 Nov 2017 17:52:01: 7000000 INFO @ Fri, 10 Nov 2017 17:52:05: 7000000 INFO @ Fri, 10 Nov 2017 17:52:09: 8000000 INFO @ Fri, 10 Nov 2017 17:52:09: 8000000 INFO @ Fri, 10 Nov 2017 17:52:13: 8000000 INFO @ Fri, 10 Nov 2017 17:52:17: 9000000 INFO @ Fri, 10 Nov 2017 17:52:17: 9000000 INFO @ Fri, 10 Nov 2017 17:52:21: 9000000 INFO @ Fri, 10 Nov 2017 17:52:24: 10000000 INFO @ Fri, 10 Nov 2017 17:52:24: 10000000 INFO @ Fri, 10 Nov 2017 17:52:30: 10000000 INFO @ Fri, 10 Nov 2017 17:52:32: 11000000 INFO @ Fri, 10 Nov 2017 17:52:32: 11000000 INFO @ Fri, 10 Nov 2017 17:52:38: 11000000 INFO @ Fri, 10 Nov 2017 17:52:40: 12000000 INFO @ Fri, 10 Nov 2017 17:52:40: 12000000 INFO @ Fri, 10 Nov 2017 17:52:46: 12000000 INFO @ Fri, 10 Nov 2017 17:52:47: 13000000 INFO @ Fri, 10 Nov 2017 17:52:47: 13000000 INFO @ Fri, 10 Nov 2017 17:52:55: 13000000 INFO @ Fri, 10 Nov 2017 17:52:55: 14000000 INFO @ Fri, 10 Nov 2017 17:52:55: 14000000 INFO @ Fri, 10 Nov 2017 17:53:02: 15000000 INFO @ Fri, 10 Nov 2017 17:53:02: 15000000 INFO @ Fri, 10 Nov 2017 17:53:03: 14000000 INFO @ Fri, 10 Nov 2017 17:53:10: 16000000 INFO @ Fri, 10 Nov 2017 17:53:10: 16000000 INFO @ Fri, 10 Nov 2017 17:53:11: 15000000 INFO @ Fri, 10 Nov 2017 17:53:17: 17000000 INFO @ Fri, 10 Nov 2017 17:53:17: 17000000 INFO @ Fri, 10 Nov 2017 17:53:19: 16000000 INFO @ Fri, 10 Nov 2017 17:53:25: 18000000 INFO @ Fri, 10 Nov 2017 17:53:25: 18000000 INFO @ Fri, 10 Nov 2017 17:53:27: 17000000 INFO @ Fri, 10 Nov 2017 17:53:32: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:53:32: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:53:32: #1 total tags in treatment: 18915611 INFO @ Fri, 10 Nov 2017 17:53:32: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:53:32: #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 17:53:32: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:53:32: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:53:32: #1 total tags in treatment: 18915611 INFO @ Fri, 10 Nov 2017 17:53:32: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:53:32: #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 17:53:33: #1 tags after filtering in treatment: 18915441 INFO @ Fri, 10 Nov 2017 17:53:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:53:33: #1 finished! INFO @ Fri, 10 Nov 2017 17:53:33: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:53:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:53:33: #1 tags after filtering in treatment: 18915441 INFO @ Fri, 10 Nov 2017 17:53:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:53:33: #1 finished! INFO @ Fri, 10 Nov 2017 17:53:33: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:53:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:53:34: 18000000 INFO @ Fri, 10 Nov 2017 17:53:36: #2 number of paired peaks: 47801 INFO @ Fri, 10 Nov 2017 17:53:36: start model_add_line... INFO @ Fri, 10 Nov 2017 17:53:36: #2 number of paired peaks: 47801 INFO @ Fri, 10 Nov 2017 17:53:36: start model_add_line... INFO @ Fri, 10 Nov 2017 17:53:36: start X-correlation... INFO @ Fri, 10 Nov 2017 17:53:36: end of X-cor INFO @ Fri, 10 Nov 2017 17:53:36: #2 finished! INFO @ Fri, 10 Nov 2017 17:53:36: #2 predicted fragment length is 160 bps INFO @ Fri, 10 Nov 2017 17:53:36: #2 alternative fragment length(s) may be 160 bps INFO @ Fri, 10 Nov 2017 17:53:36: #2.2 Generate R script for model : SRX2202872.05_model.r INFO @ Fri, 10 Nov 2017 17:53:36: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:53:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:53:37: start X-correlation... INFO @ Fri, 10 Nov 2017 17:53:37: end of X-cor INFO @ Fri, 10 Nov 2017 17:53:37: #2 finished! INFO @ Fri, 10 Nov 2017 17:53:37: #2 predicted fragment length is 160 bps INFO @ Fri, 10 Nov 2017 17:53:37: #2 alternative fragment length(s) may be 160 bps INFO @ Fri, 10 Nov 2017 17:53:37: #2.2 Generate R script for model : SRX2202872.20_model.r INFO @ Fri, 10 Nov 2017 17:53:37: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:53:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:53:41: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:53:41: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:53:41: #1 total tags in treatment: 18915611 INFO @ Fri, 10 Nov 2017 17:53:41: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:53:41: #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 17:53:42: #1 tags after filtering in treatment: 18915441 INFO @ Fri, 10 Nov 2017 17:53:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:53:42: #1 finished! INFO @ Fri, 10 Nov 2017 17:53:42: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:53:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:53:45: #2 number of paired peaks: 47801 INFO @ Fri, 10 Nov 2017 17:53:45: start model_add_line... INFO @ Fri, 10 Nov 2017 17:53:45: start X-correlation... INFO @ Fri, 10 Nov 2017 17:53:45: end of X-cor INFO @ Fri, 10 Nov 2017 17:53:45: #2 finished! INFO @ Fri, 10 Nov 2017 17:53:45: #2 predicted fragment length is 160 bps INFO @ Fri, 10 Nov 2017 17:53:45: #2 alternative fragment length(s) may be 160 bps INFO @ Fri, 10 Nov 2017 17:53:45: #2.2 Generate R script for model : SRX2202872.10_model.r INFO @ Fri, 10 Nov 2017 17:53:45: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:53:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:54:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:54:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:54:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:54:50: #4 Write output xls file... SRX2202872.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:54:50: #4 Write peak in narrowPeak format file... SRX2202872.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:54:50: #4 Write summits bed file... SRX2202872.20_summits.bed INFO @ Fri, 10 Nov 2017 17:54:50: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (1730 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:54:53: #4 Write output xls file... SRX2202872.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:54:53: #4 Write peak in narrowPeak format file... SRX2202872.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:54:54: #4 Write summits bed file... SRX2202872.05_summits.bed INFO @ Fri, 10 Nov 2017 17:54:54: Done! pass1 - making usageList (83 chroms): 3 millis pass2 - checking and writing primary data (16106 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:54:59: #4 Write output xls file... SRX2202872.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:54:59: #4 Write peak in narrowPeak format file... SRX2202872.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:54:59: #4 Write summits bed file... SRX2202872.10_summits.bed INFO @ Fri, 10 Nov 2017 17:54:59: Done! pass1 - making usageList (59 chroms): 2 millis pass2 - checking and writing primary data (8050 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。