Job ID = 10194923 sra ファイルのダウンロード中... Completed: 152460K bytes transferred in 9 seconds (136833K bits/sec), in 1 file. Completed: 149109K bytes transferred in 10 seconds (113946K bits/sec), in 1 file. Completed: 250181K bytes transferred in 18 seconds (112253K bits/sec), in 1 file. Completed: 246512K bytes transferred in 17 seconds (116334K bits/sec), in 1 file. Completed: 245278K bytes transferred in 15 seconds (126551K bits/sec), in 1 file. Completed: 242010K bytes transferred in 14 seconds (136018K 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 3492485 spots for /home/okishinya/chipatlas/results/rn6/SRX2202918/SRR4320053.sra Written 3492485 spots total Written 3585828 spots for /home/okishinya/chipatlas/results/rn6/SRX2202918/SRR4320052.sra Written 3585828 spots total Written 5292238 spots for /home/okishinya/chipatlas/results/rn6/SRX2202918/SRR4320057.sra Written 5292238 spots total Written 5344177 spots for /home/okishinya/chipatlas/results/rn6/SRX2202918/SRR4320055.sra Written 5344177 spots total Written 5461196 spots for /home/okishinya/chipatlas/results/rn6/SRX2202918/SRR4320054.sra Written 5461196 spots total Written 5356276 spots for /home/okishinya/chipatlas/results/rn6/SRX2202918/SRR4320056.sra Written 5356276 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: 00:00:01 Multiseed full-index search: 00:50:59 28532200 reads; of these: 28532200 (100.00%) were unpaired; of these: 927359 (3.25%) aligned 0 times 19415660 (68.05%) aligned exactly 1 time 8189181 (28.70%) aligned >1 times 96.75% overall alignment rate Time searching: 00:51:03 Overall time: 00:51:03 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] 4296913 / 27604841 = 0.1557 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 00:17:54: # Command line: callpeak -t SRX2202918.bam -f BAM -g 2.15e9 -n SRX2202918.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202918.10 # format = BAM # ChIP-seq file = ['SRX2202918.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 00:17:54: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:17:54: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:17:54: # Command line: callpeak -t SRX2202918.bam -f BAM -g 2.15e9 -n SRX2202918.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202918.05 # format = BAM # ChIP-seq file = ['SRX2202918.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 00:17:54: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:17:54: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:17:54: # Command line: callpeak -t SRX2202918.bam -f BAM -g 2.15e9 -n SRX2202918.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202918.20 # format = BAM # ChIP-seq file = ['SRX2202918.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 00:17:54: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:17:54: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:18:05: 1000000 INFO @ Sat, 11 Nov 2017 00:18:05: 1000000 INFO @ Sat, 11 Nov 2017 00:18:09: 1000000 INFO @ Sat, 11 Nov 2017 00:18:15: 2000000 INFO @ Sat, 11 Nov 2017 00:18:16: 2000000 INFO @ Sat, 11 Nov 2017 00:18:24: 2000000 INFO @ Sat, 11 Nov 2017 00:18:24: 3000000 INFO @ Sat, 11 Nov 2017 00:18:27: 3000000 INFO @ Sat, 11 Nov 2017 00:18:35: 4000000 INFO @ Sat, 11 Nov 2017 00:18:39: 4000000 INFO @ Sat, 11 Nov 2017 00:18:39: 3000000 INFO @ Sat, 11 Nov 2017 00:18:44: 5000000 INFO @ Sat, 11 Nov 2017 00:18:50: 5000000 INFO @ Sat, 11 Nov 2017 00:18:53: 4000000 INFO @ Sat, 11 Nov 2017 00:18:54: 6000000 INFO @ Sat, 11 Nov 2017 00:19:01: 6000000 INFO @ Sat, 11 Nov 2017 00:19:04: 7000000 INFO @ Sat, 11 Nov 2017 00:19:05: 5000000 INFO @ Sat, 11 Nov 2017 00:19:12: 7000000 INFO @ Sat, 11 Nov 2017 00:19:13: 8000000 INFO @ Sat, 11 Nov 2017 00:19:17: 6000000 INFO @ Sat, 11 Nov 2017 00:19:23: 9000000 INFO @ Sat, 11 Nov 2017 00:19:24: 8000000 INFO @ Sat, 11 Nov 2017 00:19:29: 7000000 INFO @ Sat, 11 Nov 2017 00:19:32: 10000000 INFO @ Sat, 11 Nov 2017 00:19:35: 9000000 INFO @ Sat, 11 Nov 2017 00:19:41: 8000000 INFO @ Sat, 11 Nov 2017 00:19:42: 11000000 INFO @ Sat, 11 Nov 2017 00:19:47: 10000000 INFO @ Sat, 11 Nov 2017 00:19:51: 12000000 INFO @ Sat, 11 Nov 2017 00:19:54: 9000000 INFO @ Sat, 11 Nov 2017 00:20:00: 13000000 INFO @ Sat, 11 Nov 2017 00:20:00: 11000000 INFO @ Sat, 11 Nov 2017 00:20:09: 14000000 INFO @ Sat, 11 Nov 2017 00:20:09: 10000000 INFO @ Sat, 11 Nov 2017 00:20:15: 12000000 INFO @ Sat, 11 Nov 2017 00:20:17: 15000000 INFO @ Sat, 11 Nov 2017 00:20:22: 11000000 INFO @ Sat, 11 Nov 2017 00:20:26: 16000000 INFO @ Sat, 11 Nov 2017 00:20:29: 13000000 INFO @ Sat, 11 Nov 2017 00:20:34: 12000000 INFO @ Sat, 11 Nov 2017 00:20:35: 17000000 INFO @ Sat, 11 Nov 2017 00:20:43: 14000000 INFO @ Sat, 11 Nov 2017 00:20:44: 18000000 INFO @ Sat, 11 Nov 2017 00:20:48: 13000000 INFO @ Sat, 11 Nov 2017 00:20:52: 19000000 INFO @ Sat, 11 Nov 2017 00:20:58: 15000000 INFO @ Sat, 11 Nov 2017 00:21:01: 14000000 INFO @ Sat, 11 Nov 2017 00:21:01: 20000000 INFO @ Sat, 11 Nov 2017 00:21:10: 21000000 INFO @ Sat, 11 Nov 2017 00:21:12: 16000000 INFO @ Sat, 11 Nov 2017 00:21:14: 15000000 INFO @ Sat, 11 Nov 2017 00:21:19: 22000000 INFO @ Sat, 11 Nov 2017 00:21:26: 17000000 INFO @ Sat, 11 Nov 2017 00:21:26: 16000000 INFO @ Sat, 11 Nov 2017 00:21:28: 23000000 INFO @ Sat, 11 Nov 2017 00:21:31: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:21:31: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:21:31: #1 total tags in treatment: 23307928 INFO @ Sat, 11 Nov 2017 00:21:31: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:21:31: #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 00:21:32: #1 tags after filtering in treatment: 23307792 INFO @ Sat, 11 Nov 2017 00:21:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:21:32: #1 finished! INFO @ Sat, 11 Nov 2017 00:21:32: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:21:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:21:36: #2 number of paired peaks: 22469 INFO @ Sat, 11 Nov 2017 00:21:36: start model_add_line... INFO @ Sat, 11 Nov 2017 00:21:36: start X-correlation... INFO @ Sat, 11 Nov 2017 00:21:36: end of X-cor INFO @ Sat, 11 Nov 2017 00:21:36: #2 finished! INFO @ Sat, 11 Nov 2017 00:21:36: #2 predicted fragment length is 110 bps INFO @ Sat, 11 Nov 2017 00:21:36: #2 alternative fragment length(s) may be 110 bps INFO @ Sat, 11 Nov 2017 00:21:36: #2.2 Generate R script for model : SRX2202918.20_model.r INFO @ Sat, 11 Nov 2017 00:21:36: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:21:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:21:40: 17000000 INFO @ Sat, 11 Nov 2017 00:21:40: 18000000 INFO @ Sat, 11 Nov 2017 00:21:52: 18000000 INFO @ Sat, 11 Nov 2017 00:21:54: 19000000 INFO @ Sat, 11 Nov 2017 00:22:05: 19000000 INFO @ Sat, 11 Nov 2017 00:22:09: 20000000 INFO @ Sat, 11 Nov 2017 00:22:18: 20000000 INFO @ Sat, 11 Nov 2017 00:22:23: 21000000 INFO @ Sat, 11 Nov 2017 00:22:30: 21000000 INFO @ Sat, 11 Nov 2017 00:22:37: 22000000 INFO @ Sat, 11 Nov 2017 00:22:43: 22000000 INFO @ Sat, 11 Nov 2017 00:22:51: 23000000 INFO @ Sat, 11 Nov 2017 00:22:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:22:55: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:22:55: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:22:55: #1 total tags in treatment: 23307928 INFO @ Sat, 11 Nov 2017 00:22:55: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:22:55: #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 00:22:55: 23000000 INFO @ Sat, 11 Nov 2017 00:22:56: #1 tags after filtering in treatment: 23307792 INFO @ Sat, 11 Nov 2017 00:22:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:22:56: #1 finished! INFO @ Sat, 11 Nov 2017 00:22:56: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:22:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:22:59: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:22:59: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:22:59: #1 total tags in treatment: 23307928 INFO @ Sat, 11 Nov 2017 00:22:59: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:22:59: #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 00:23:00: #2 number of paired peaks: 22469 INFO @ Sat, 11 Nov 2017 00:23:00: start model_add_line... INFO @ Sat, 11 Nov 2017 00:23:00: #1 tags after filtering in treatment: 23307792 INFO @ Sat, 11 Nov 2017 00:23:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:23:00: #1 finished! INFO @ Sat, 11 Nov 2017 00:23:00: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:23:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:23:01: start X-correlation... INFO @ Sat, 11 Nov 2017 00:23:01: end of X-cor INFO @ Sat, 11 Nov 2017 00:23:01: #2 finished! INFO @ Sat, 11 Nov 2017 00:23:01: #2 predicted fragment length is 110 bps INFO @ Sat, 11 Nov 2017 00:23:01: #2 alternative fragment length(s) may be 110 bps INFO @ Sat, 11 Nov 2017 00:23:01: #2.2 Generate R script for model : SRX2202918.05_model.r INFO @ Sat, 11 Nov 2017 00:23:01: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:23:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:23:04: #2 number of paired peaks: 22469 INFO @ Sat, 11 Nov 2017 00:23:04: start model_add_line... INFO @ Sat, 11 Nov 2017 00:23:05: start X-correlation... INFO @ Sat, 11 Nov 2017 00:23:05: end of X-cor INFO @ Sat, 11 Nov 2017 00:23:05: #2 finished! INFO @ Sat, 11 Nov 2017 00:23:05: #2 predicted fragment length is 110 bps INFO @ Sat, 11 Nov 2017 00:23:05: #2 alternative fragment length(s) may be 110 bps INFO @ Sat, 11 Nov 2017 00:23:05: #2.2 Generate R script for model : SRX2202918.10_model.r INFO @ Sat, 11 Nov 2017 00:23:05: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:23:33: #4 Write output xls file... SRX2202918.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:23:33: #4 Write peak in narrowPeak format file... SRX2202918.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:23:33: #4 Write summits bed file... SRX2202918.20_summits.bed INFO @ Sat, 11 Nov 2017 00:23:33: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (565 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:24:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:24:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:24:57: #4 Write output xls file... SRX2202918.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:24:57: #4 Write peak in narrowPeak format file... SRX2202918.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:24:57: #4 Write summits bed file... SRX2202918.05_summits.bed INFO @ Sat, 11 Nov 2017 00:24:58: Done! pass1 - making usageList (75 chroms): 4 millis pass2 - checking and writing primary data (11930 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:25:08: #4 Write output xls file... SRX2202918.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:25:08: #4 Write peak in narrowPeak format file... SRX2202918.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:25:08: #4 Write summits bed file... SRX2202918.10_summits.bed INFO @ Sat, 11 Nov 2017 00:25:08: Done! pass1 - making usageList (50 chroms): 2 millis pass2 - checking and writing primary data (4005 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。