Job ID = 10194927 sra ファイルのダウンロード中... Completed: 102193K bytes transferred in 7 seconds (118452K bits/sec), in 1 file. Completed: 99844K bytes transferred in 8 seconds (96995K bits/sec), in 1 file. Completed: 169038K bytes transferred in 9 seconds (146921K bits/sec), in 1 file. Completed: 165940K bytes transferred in 12 seconds (112552K bits/sec), in 1 file. Completed: 166168K bytes transferred in 8 seconds (153477K bits/sec), in 1 file. Completed: 163788K bytes transferred in 12 seconds (109402K 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 2399158 spots for /home/okishinya/chipatlas/results/rn6/SRX2202922/SRR4320076.sra Written 2399158 spots total Written 2334369 spots for /home/okishinya/chipatlas/results/rn6/SRX2202922/SRR4320077.sra Written 2334369 spots total Written 3567230 spots for /home/okishinya/chipatlas/results/rn6/SRX2202922/SRR4320081.sra Written 3567230 spots total Written 3612667 spots for /home/okishinya/chipatlas/results/rn6/SRX2202922/SRR4320080.sra Written 3612667 spots total Written 3584811 spots for /home/okishinya/chipatlas/results/rn6/SRX2202922/SRR4320079.sra Written 3584811 spots total Written 3674606 spots for /home/okishinya/chipatlas/results/rn6/SRX2202922/SRR4320078.sra Written 3674606 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: 00:36:07 19172841 reads; of these: 19172841 (100.00%) were unpaired; of these: 792520 (4.13%) aligned 0 times 12611478 (65.78%) aligned exactly 1 time 5768843 (30.09%) aligned >1 times 95.87% overall alignment rate Time searching: 00:36:11 Overall time: 00:36:11 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] 2256475 / 18380321 = 0.1228 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 00:10:53: # Command line: callpeak -t SRX2202922.bam -f BAM -g 2.15e9 -n SRX2202922.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202922.10 # format = BAM # ChIP-seq file = ['SRX2202922.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 00:10:53: # Command line: callpeak -t SRX2202922.bam -f BAM -g 2.15e9 -n SRX2202922.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202922.20 # format = BAM # ChIP-seq file = ['SRX2202922.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 00:10:53: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:10:53: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:10:53: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:10:53: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:10:53: # Command line: callpeak -t SRX2202922.bam -f BAM -g 2.15e9 -n SRX2202922.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202922.05 # format = BAM # ChIP-seq file = ['SRX2202922.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 00:10:53: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:10:53: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:11:13: 1000000 INFO @ Sat, 11 Nov 2017 00:11:13: 1000000 INFO @ Sat, 11 Nov 2017 00:11:15: 1000000 INFO @ Sat, 11 Nov 2017 00:11:35: 2000000 INFO @ Sat, 11 Nov 2017 00:11:36: 2000000 INFO @ Sat, 11 Nov 2017 00:11:36: 2000000 INFO @ Sat, 11 Nov 2017 00:11:56: 3000000 INFO @ Sat, 11 Nov 2017 00:11:57: 3000000 INFO @ Sat, 11 Nov 2017 00:12:02: 3000000 INFO @ Sat, 11 Nov 2017 00:12:17: 4000000 INFO @ Sat, 11 Nov 2017 00:12:17: 4000000 INFO @ Sat, 11 Nov 2017 00:12:28: 4000000 INFO @ Sat, 11 Nov 2017 00:12:37: 5000000 INFO @ Sat, 11 Nov 2017 00:12:39: 5000000 INFO @ Sat, 11 Nov 2017 00:12:53: 5000000 INFO @ Sat, 11 Nov 2017 00:12:57: 6000000 INFO @ Sat, 11 Nov 2017 00:13:02: 6000000 INFO @ Sat, 11 Nov 2017 00:13:17: 6000000 INFO @ Sat, 11 Nov 2017 00:13:18: 7000000 INFO @ Sat, 11 Nov 2017 00:13:25: 7000000 INFO @ Sat, 11 Nov 2017 00:13:39: 8000000 INFO @ Sat, 11 Nov 2017 00:13:41: 7000000 INFO @ Sat, 11 Nov 2017 00:13:48: 8000000 INFO @ Sat, 11 Nov 2017 00:13:59: 9000000 INFO @ Sat, 11 Nov 2017 00:14:04: 8000000 INFO @ Sat, 11 Nov 2017 00:14:11: 9000000 INFO @ Sat, 11 Nov 2017 00:14:20: 10000000 INFO @ Sat, 11 Nov 2017 00:14:28: 9000000 INFO @ Sat, 11 Nov 2017 00:14:33: 10000000 INFO @ Sat, 11 Nov 2017 00:14:40: 11000000 INFO @ Sat, 11 Nov 2017 00:14:52: 10000000 INFO @ Sat, 11 Nov 2017 00:14:55: 11000000 INFO @ Sat, 11 Nov 2017 00:15:01: 12000000 INFO @ Sat, 11 Nov 2017 00:15:16: 11000000 INFO @ Sat, 11 Nov 2017 00:15:18: 12000000 INFO @ Sat, 11 Nov 2017 00:15:20: 13000000 INFO @ Sat, 11 Nov 2017 00:15:40: 14000000 INFO @ Sat, 11 Nov 2017 00:15:41: 13000000 INFO @ Sat, 11 Nov 2017 00:15:41: 12000000 INFO @ Sat, 11 Nov 2017 00:15:59: 15000000 INFO @ Sat, 11 Nov 2017 00:16:04: 14000000 INFO @ Sat, 11 Nov 2017 00:16:07: 13000000 INFO @ Sat, 11 Nov 2017 00:16:19: 16000000 INFO @ Sat, 11 Nov 2017 00:16:21: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:16:21: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:16:21: #1 total tags in treatment: 16123846 INFO @ Sat, 11 Nov 2017 00:16:21: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:16:21: #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 00:16:22: #1 tags after filtering in treatment: 16123719 INFO @ Sat, 11 Nov 2017 00:16:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:16:22: #1 finished! INFO @ Sat, 11 Nov 2017 00:16:22: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:16:25: #2 number of paired peaks: 30375 INFO @ Sat, 11 Nov 2017 00:16:25: start model_add_line... INFO @ Sat, 11 Nov 2017 00:16:25: start X-correlation... INFO @ Sat, 11 Nov 2017 00:16:25: end of X-cor INFO @ Sat, 11 Nov 2017 00:16:25: #2 finished! INFO @ Sat, 11 Nov 2017 00:16:25: #2 predicted fragment length is 115 bps INFO @ Sat, 11 Nov 2017 00:16:25: #2 alternative fragment length(s) may be 115 bps INFO @ Sat, 11 Nov 2017 00:16:25: #2.2 Generate R script for model : SRX2202922.20_model.r INFO @ Sat, 11 Nov 2017 00:16:25: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:16:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:16:27: 15000000 INFO @ Sat, 11 Nov 2017 00:16:32: 14000000 INFO @ Sat, 11 Nov 2017 00:16:51: 16000000 INFO @ Sat, 11 Nov 2017 00:16:53: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:16:53: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:16:53: #1 total tags in treatment: 16123846 INFO @ Sat, 11 Nov 2017 00:16:53: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:16:53: #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 00:16:54: #1 tags after filtering in treatment: 16123719 INFO @ Sat, 11 Nov 2017 00:16:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:16:54: #1 finished! INFO @ Sat, 11 Nov 2017 00:16:54: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:16:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:16:57: 15000000 INFO @ Sat, 11 Nov 2017 00:16:57: #2 number of paired peaks: 30375 INFO @ Sat, 11 Nov 2017 00:16:57: start model_add_line... INFO @ Sat, 11 Nov 2017 00:16:58: start X-correlation... INFO @ Sat, 11 Nov 2017 00:16:58: end of X-cor INFO @ Sat, 11 Nov 2017 00:16:58: #2 finished! INFO @ Sat, 11 Nov 2017 00:16:58: #2 predicted fragment length is 115 bps INFO @ Sat, 11 Nov 2017 00:16:58: #2 alternative fragment length(s) may be 115 bps INFO @ Sat, 11 Nov 2017 00:16:58: #2.2 Generate R script for model : SRX2202922.10_model.r INFO @ Sat, 11 Nov 2017 00:16:58: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:16:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:17:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:17:24: 16000000 INFO @ Sat, 11 Nov 2017 00:17:26: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:17:26: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:17:26: #1 total tags in treatment: 16123846 INFO @ Sat, 11 Nov 2017 00:17:26: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:17:26: #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 00:17:27: #1 tags after filtering in treatment: 16123719 INFO @ Sat, 11 Nov 2017 00:17:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:17:27: #1 finished! INFO @ Sat, 11 Nov 2017 00:17:27: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:17:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:17:30: #2 number of paired peaks: 30375 INFO @ Sat, 11 Nov 2017 00:17:30: start model_add_line... INFO @ Sat, 11 Nov 2017 00:17:31: start X-correlation... INFO @ Sat, 11 Nov 2017 00:17:31: end of X-cor INFO @ Sat, 11 Nov 2017 00:17:31: #2 finished! INFO @ Sat, 11 Nov 2017 00:17:31: #2 predicted fragment length is 115 bps INFO @ Sat, 11 Nov 2017 00:17:31: #2 alternative fragment length(s) may be 115 bps INFO @ Sat, 11 Nov 2017 00:17:31: #2.2 Generate R script for model : SRX2202922.05_model.r INFO @ Sat, 11 Nov 2017 00:17:31: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:17:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:17:50: #4 Write output xls file... SRX2202922.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:17:50: #4 Write peak in narrowPeak format file... SRX2202922.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:17:50: #4 Write summits bed file... SRX2202922.20_summits.bed INFO @ Sat, 11 Nov 2017 00:17:50: Done! pass1 - making usageList (35 chroms): 2 millis pass2 - checking and writing primary data (477 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:17:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:18:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:18:26: #4 Write output xls file... SRX2202922.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:18:26: #4 Write peak in narrowPeak format file... SRX2202922.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:18:26: #4 Write summits bed file... SRX2202922.10_summits.bed INFO @ Sat, 11 Nov 2017 00:18:26: Done! pass1 - making usageList (52 chroms): 2 millis pass2 - checking and writing primary data (2744 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:18:57: #4 Write output xls file... SRX2202922.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:18:58: #4 Write peak in narrowPeak format file... SRX2202922.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:18:58: #4 Write summits bed file... SRX2202922.05_summits.bed INFO @ Sat, 11 Nov 2017 00:18:58: Done! pass1 - making usageList (73 chroms): 4 millis pass2 - checking and writing primary data (10529 records, 4 fields): 77 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。