Job ID = 10194888 sra ファイルのダウンロード中... Completed: 231528K bytes transferred in 7 seconds (238208K bits/sec), in 1 file. Completed: 231577K bytes transferred in 7 seconds (241870K bits/sec), in 1 file. Completed: 219550K bytes transferred in 10 seconds (179576K bits/sec), in 1 file. Completed: 216763K bytes transferred in 8 seconds (203261K bits/sec), in 1 file. Completed: 273796K bytes transferred in 8 seconds (260291K bits/sec), in 1 file. Completed: 275395K bytes transferred in 11 seconds (200312K 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 4893470 spots for /home/okishinya/chipatlas/results/rn6/SRX2202883/SRR4319845.sra Written 4893470 spots total Written 4945422 spots for /home/okishinya/chipatlas/results/rn6/SRX2202883/SRR4319844.sra Written 4945422 spots total Written 5202623 spots for /home/okishinya/chipatlas/results/rn6/SRX2202883/SRR4319842.sra Written 5202623 spots total Written 5184653 spots for /home/okishinya/chipatlas/results/rn6/SRX2202883/SRR4319843.sra Written 5184653 spots total Written 6034839 spots for /home/okishinya/chipatlas/results/rn6/SRX2202883/SRR4319846.sra Written 6034839 spots total Written 6048454 spots for /home/okishinya/chipatlas/results/rn6/SRX2202883/SRR4319847.sra Written 6048454 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:23:51 32309461 reads; of these: 32309461 (100.00%) were unpaired; of these: 2381585 (7.37%) aligned 0 times 22366601 (69.23%) aligned exactly 1 time 7561275 (23.40%) aligned >1 times 92.63% overall alignment rate Time searching: 00:23:53 Overall time: 00:23:53 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] 7266121 / 29927876 = 0.2428 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 18:23:44: # Command line: callpeak -t SRX2202883.bam -f BAM -g 2.15e9 -n SRX2202883.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202883.20 # format = BAM # ChIP-seq file = ['SRX2202883.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 18:23:44: # Command line: callpeak -t SRX2202883.bam -f BAM -g 2.15e9 -n SRX2202883.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202883.05 # format = BAM # ChIP-seq file = ['SRX2202883.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 18:23:44: # Command line: callpeak -t SRX2202883.bam -f BAM -g 2.15e9 -n SRX2202883.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202883.10 # format = BAM # ChIP-seq file = ['SRX2202883.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 18:23:44: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:23:44: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:23:44: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:23:44: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:23:44: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:23:44: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:23:52: 1000000 INFO @ Fri, 10 Nov 2017 18:23:52: 1000000 INFO @ Fri, 10 Nov 2017 18:23:52: 1000000 INFO @ Fri, 10 Nov 2017 18:23:59: 2000000 INFO @ Fri, 10 Nov 2017 18:23:59: 2000000 INFO @ Fri, 10 Nov 2017 18:23:59: 2000000 INFO @ Fri, 10 Nov 2017 18:24:05: 3000000 INFO @ Fri, 10 Nov 2017 18:24:07: 3000000 INFO @ Fri, 10 Nov 2017 18:24:07: 3000000 INFO @ Fri, 10 Nov 2017 18:24:12: 4000000 INFO @ Fri, 10 Nov 2017 18:24:14: 4000000 INFO @ Fri, 10 Nov 2017 18:24:14: 4000000 INFO @ Fri, 10 Nov 2017 18:24:19: 5000000 INFO @ Fri, 10 Nov 2017 18:24:22: 5000000 INFO @ Fri, 10 Nov 2017 18:24:22: 5000000 INFO @ Fri, 10 Nov 2017 18:24:27: 6000000 INFO @ Fri, 10 Nov 2017 18:24:29: 6000000 INFO @ Fri, 10 Nov 2017 18:24:29: 6000000 INFO @ Fri, 10 Nov 2017 18:24:35: 7000000 INFO @ Fri, 10 Nov 2017 18:24:36: 7000000 INFO @ Fri, 10 Nov 2017 18:24:37: 7000000 INFO @ Fri, 10 Nov 2017 18:24:42: 8000000 INFO @ Fri, 10 Nov 2017 18:24:43: 8000000 INFO @ Fri, 10 Nov 2017 18:24:44: 8000000 INFO @ Fri, 10 Nov 2017 18:24:50: 9000000 INFO @ Fri, 10 Nov 2017 18:24:52: 9000000 INFO @ Fri, 10 Nov 2017 18:24:53: 9000000 INFO @ Fri, 10 Nov 2017 18:24:59: 10000000 INFO @ Fri, 10 Nov 2017 18:25:00: 10000000 INFO @ Fri, 10 Nov 2017 18:25:01: 10000000 INFO @ Fri, 10 Nov 2017 18:25:06: 11000000 INFO @ Fri, 10 Nov 2017 18:25:07: 11000000 INFO @ Fri, 10 Nov 2017 18:25:08: 11000000 INFO @ Fri, 10 Nov 2017 18:25:14: 12000000 INFO @ Fri, 10 Nov 2017 18:25:15: 12000000 INFO @ Fri, 10 Nov 2017 18:25:16: 12000000 INFO @ Fri, 10 Nov 2017 18:25:22: 13000000 INFO @ Fri, 10 Nov 2017 18:25:22: 13000000 INFO @ Fri, 10 Nov 2017 18:25:24: 13000000 INFO @ Fri, 10 Nov 2017 18:25:29: 14000000 INFO @ Fri, 10 Nov 2017 18:25:30: 14000000 INFO @ Fri, 10 Nov 2017 18:25:31: 14000000 INFO @ Fri, 10 Nov 2017 18:25:36: 15000000 INFO @ Fri, 10 Nov 2017 18:25:37: 15000000 INFO @ Fri, 10 Nov 2017 18:25:38: 15000000 INFO @ Fri, 10 Nov 2017 18:25:43: 16000000 INFO @ Fri, 10 Nov 2017 18:25:45: 16000000 INFO @ Fri, 10 Nov 2017 18:25:45: 16000000 INFO @ Fri, 10 Nov 2017 18:25:50: 17000000 INFO @ Fri, 10 Nov 2017 18:25:52: 17000000 INFO @ Fri, 10 Nov 2017 18:25:53: 17000000 INFO @ Fri, 10 Nov 2017 18:25:57: 18000000 INFO @ Fri, 10 Nov 2017 18:26:00: 18000000 INFO @ Fri, 10 Nov 2017 18:26:01: 18000000 INFO @ Fri, 10 Nov 2017 18:26:04: 19000000 INFO @ Fri, 10 Nov 2017 18:26:08: 19000000 INFO @ Fri, 10 Nov 2017 18:26:08: 19000000 INFO @ Fri, 10 Nov 2017 18:26:10: 20000000 INFO @ Fri, 10 Nov 2017 18:26:16: 20000000 INFO @ Fri, 10 Nov 2017 18:26:16: 20000000 INFO @ Fri, 10 Nov 2017 18:26:17: 21000000 INFO @ Fri, 10 Nov 2017 18:26:23: 21000000 INFO @ Fri, 10 Nov 2017 18:26:24: 21000000 INFO @ Fri, 10 Nov 2017 18:26:24: 22000000 INFO @ Fri, 10 Nov 2017 18:26:29: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:26:29: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:26:29: #1 total tags in treatment: 22661755 INFO @ Fri, 10 Nov 2017 18:26:29: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:26:29: #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 18:26:30: #1 tags after filtering in treatment: 22661638 INFO @ Fri, 10 Nov 2017 18:26:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:26:30: #1 finished! INFO @ Fri, 10 Nov 2017 18:26:30: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:26:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:26:31: 22000000 INFO @ Fri, 10 Nov 2017 18:26:31: 22000000 INFO @ Fri, 10 Nov 2017 18:26:32: #2 number of paired peaks: 23547 INFO @ Fri, 10 Nov 2017 18:26:32: start model_add_line... INFO @ Fri, 10 Nov 2017 18:26:33: start X-correlation... INFO @ Fri, 10 Nov 2017 18:26:33: end of X-cor INFO @ Fri, 10 Nov 2017 18:26:33: #2 finished! INFO @ Fri, 10 Nov 2017 18:26:33: #2 predicted fragment length is 125 bps INFO @ Fri, 10 Nov 2017 18:26:33: #2 alternative fragment length(s) may be 125 bps INFO @ Fri, 10 Nov 2017 18:26:33: #2.2 Generate R script for model : SRX2202883.10_model.r INFO @ Fri, 10 Nov 2017 18:26:33: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:26:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:26:36: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:26:36: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:26:36: #1 total tags in treatment: 22661755 INFO @ Fri, 10 Nov 2017 18:26:36: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:26:36: #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 18:26:36: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:26:36: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:26:36: #1 total tags in treatment: 22661755 INFO @ Fri, 10 Nov 2017 18:26:36: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:26:36: #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 18:26:37: #1 tags after filtering in treatment: 22661638 INFO @ Fri, 10 Nov 2017 18:26:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:26:37: #1 finished! INFO @ Fri, 10 Nov 2017 18:26:37: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:26:37: #1 tags after filtering in treatment: 22661638 INFO @ Fri, 10 Nov 2017 18:26:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:26:37: #1 finished! INFO @ Fri, 10 Nov 2017 18:26:37: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:26:40: #2 number of paired peaks: 23547 INFO @ Fri, 10 Nov 2017 18:26:40: start model_add_line... INFO @ Fri, 10 Nov 2017 18:26:40: #2 number of paired peaks: 23547 INFO @ Fri, 10 Nov 2017 18:26:40: start model_add_line... INFO @ Fri, 10 Nov 2017 18:26:40: start X-correlation... INFO @ Fri, 10 Nov 2017 18:26:40: end of X-cor INFO @ Fri, 10 Nov 2017 18:26:40: #2 finished! INFO @ Fri, 10 Nov 2017 18:26:40: #2 predicted fragment length is 125 bps INFO @ Fri, 10 Nov 2017 18:26:40: #2 alternative fragment length(s) may be 125 bps INFO @ Fri, 10 Nov 2017 18:26:40: #2.2 Generate R script for model : SRX2202883.20_model.r INFO @ Fri, 10 Nov 2017 18:26:40: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:26:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:26:40: start X-correlation... INFO @ Fri, 10 Nov 2017 18:26:40: end of X-cor INFO @ Fri, 10 Nov 2017 18:26:40: #2 finished! INFO @ Fri, 10 Nov 2017 18:26:40: #2 predicted fragment length is 125 bps INFO @ Fri, 10 Nov 2017 18:26:40: #2 alternative fragment length(s) may be 125 bps INFO @ Fri, 10 Nov 2017 18:26:40: #2.2 Generate R script for model : SRX2202883.05_model.r INFO @ Fri, 10 Nov 2017 18:26:40: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:26:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:27:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:27:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:27:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:28:00: #4 Write output xls file... SRX2202883.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:28:00: #4 Write peak in narrowPeak format file... SRX2202883.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:28:00: #4 Write summits bed file... SRX2202883.10_summits.bed INFO @ Fri, 10 Nov 2017 18:28:00: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1281 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:28:07: #4 Write output xls file... SRX2202883.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:28:07: #4 Write peak in narrowPeak format file... SRX2202883.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:28:07: #4 Write summits bed file... SRX2202883.20_summits.bed INFO @ Fri, 10 Nov 2017 18:28:07: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (383 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:28:10: #4 Write output xls file... SRX2202883.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:28:10: #4 Write peak in narrowPeak format file... SRX2202883.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:28:10: #4 Write summits bed file... SRX2202883.05_summits.bed INFO @ Fri, 10 Nov 2017 18:28:10: Done! pass1 - making usageList (66 chroms): 2 millis pass2 - checking and writing primary data (6304 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。