Job ID = 11388783 sra ファイルのダウンロード中... Completed: 818453K bytes transferred in 13 seconds (501199K 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... Read 27070720 spots for /home/okishinya/chipatlas/results/rn6/SRX1453549/SRR2962625.sra Written 27070720 spots for /home/okishinya/chipatlas/results/rn6/SRX1453549/SRR2962625.sra 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 rm: cannot remove `[DSE]RR*.fastq': 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: 00:00:02 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:53:47 27070720 reads; of these: 27070720 (100.00%) were unpaired; of these: 872229 (3.22%) aligned 0 times 17909768 (66.16%) aligned exactly 1 time 8288723 (30.62%) aligned >1 times 96.78% overall alignment rate Time searching: 00:53:53 Overall time: 00:53:53 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 12 files... [bam_rmdupse_core] 2357699 / 26198491 = 0.0900 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 @ Wed, 12 Dec 2018 23:22:07: # Command line: callpeak -t SRX1453549.bam -f BAM -g 2.15e9 -n SRX1453549.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1453549.10 # format = BAM # ChIP-seq file = ['SRX1453549.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 @ Wed, 12 Dec 2018 23:22:07: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:22:07: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:22:07: # Command line: callpeak -t SRX1453549.bam -f BAM -g 2.15e9 -n SRX1453549.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1453549.20 # format = BAM # ChIP-seq file = ['SRX1453549.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 @ Wed, 12 Dec 2018 23:22:07: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:22:07: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:22:07: # Command line: callpeak -t SRX1453549.bam -f BAM -g 2.15e9 -n SRX1453549.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1453549.05 # format = BAM # ChIP-seq file = ['SRX1453549.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 @ Wed, 12 Dec 2018 23:22:07: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:22:07: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:22:25: 1000000 INFO @ Wed, 12 Dec 2018 23:22:28: 1000000 INFO @ Wed, 12 Dec 2018 23:22:29: 1000000 INFO @ Wed, 12 Dec 2018 23:22:46: 2000000 INFO @ Wed, 12 Dec 2018 23:22:48: 2000000 INFO @ Wed, 12 Dec 2018 23:22:49: 2000000 INFO @ Wed, 12 Dec 2018 23:23:07: 3000000 INFO @ Wed, 12 Dec 2018 23:23:08: 3000000 INFO @ Wed, 12 Dec 2018 23:23:10: 3000000 INFO @ Wed, 12 Dec 2018 23:23:27: 4000000 INFO @ Wed, 12 Dec 2018 23:23:28: 4000000 INFO @ Wed, 12 Dec 2018 23:23:28: 4000000 INFO @ Wed, 12 Dec 2018 23:23:48: 5000000 INFO @ Wed, 12 Dec 2018 23:23:49: 5000000 INFO @ Wed, 12 Dec 2018 23:23:51: 5000000 INFO @ Wed, 12 Dec 2018 23:24:09: 6000000 INFO @ Wed, 12 Dec 2018 23:24:09: 6000000 INFO @ Wed, 12 Dec 2018 23:24:14: 6000000 INFO @ Wed, 12 Dec 2018 23:24:30: 7000000 INFO @ Wed, 12 Dec 2018 23:24:30: 7000000 INFO @ Wed, 12 Dec 2018 23:24:38: 7000000 INFO @ Wed, 12 Dec 2018 23:24:46: 8000000 INFO @ Wed, 12 Dec 2018 23:24:51: 8000000 INFO @ Wed, 12 Dec 2018 23:25:00: 9000000 INFO @ Wed, 12 Dec 2018 23:25:01: 8000000 INFO @ Wed, 12 Dec 2018 23:25:11: 9000000 INFO @ Wed, 12 Dec 2018 23:25:15: 10000000 INFO @ Wed, 12 Dec 2018 23:25:24: 9000000 INFO @ Wed, 12 Dec 2018 23:25:29: 11000000 INFO @ Wed, 12 Dec 2018 23:25:29: 10000000 INFO @ Wed, 12 Dec 2018 23:25:44: 12000000 INFO @ Wed, 12 Dec 2018 23:25:47: 10000000 INFO @ Wed, 12 Dec 2018 23:25:50: 11000000 INFO @ Wed, 12 Dec 2018 23:25:57: 13000000 INFO @ Wed, 12 Dec 2018 23:26:08: 11000000 INFO @ Wed, 12 Dec 2018 23:26:10: 12000000 INFO @ Wed, 12 Dec 2018 23:26:11: 14000000 INFO @ Wed, 12 Dec 2018 23:26:24: 15000000 INFO @ Wed, 12 Dec 2018 23:26:29: 12000000 INFO @ Wed, 12 Dec 2018 23:26:31: 13000000 INFO @ Wed, 12 Dec 2018 23:26:38: 16000000 INFO @ Wed, 12 Dec 2018 23:26:50: 13000000 INFO @ Wed, 12 Dec 2018 23:26:51: 17000000 INFO @ Wed, 12 Dec 2018 23:26:52: 14000000 INFO @ Wed, 12 Dec 2018 23:27:07: 18000000 INFO @ Wed, 12 Dec 2018 23:27:11: 14000000 INFO @ Wed, 12 Dec 2018 23:27:13: 15000000 INFO @ Wed, 12 Dec 2018 23:27:29: 19000000 INFO @ Wed, 12 Dec 2018 23:27:34: 15000000 INFO @ Wed, 12 Dec 2018 23:27:35: 16000000 INFO @ Wed, 12 Dec 2018 23:27:51: 20000000 INFO @ Wed, 12 Dec 2018 23:27:55: 16000000 INFO @ Wed, 12 Dec 2018 23:27:57: 17000000 INFO @ Wed, 12 Dec 2018 23:28:13: 21000000 INFO @ Wed, 12 Dec 2018 23:28:17: 17000000 INFO @ Wed, 12 Dec 2018 23:28:18: 18000000 INFO @ Wed, 12 Dec 2018 23:28:34: 22000000 INFO @ Wed, 12 Dec 2018 23:28:38: 18000000 INFO @ Wed, 12 Dec 2018 23:28:40: 19000000 INFO @ Wed, 12 Dec 2018 23:28:55: 23000000 INFO @ Wed, 12 Dec 2018 23:28:59: 19000000 INFO @ Wed, 12 Dec 2018 23:29:01: 20000000 INFO @ Wed, 12 Dec 2018 23:29:13: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 23:29:13: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 23:29:13: #1 total tags in treatment: 23840792 INFO @ Wed, 12 Dec 2018 23:29:13: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:29:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:29:14: #1 tags after filtering in treatment: 23840672 INFO @ Wed, 12 Dec 2018 23:29:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:29:14: #1 finished! INFO @ Wed, 12 Dec 2018 23:29:14: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:29:17: #2 number of paired peaks: 7027 INFO @ Wed, 12 Dec 2018 23:29:17: start model_add_line... INFO @ Wed, 12 Dec 2018 23:29:17: start X-correlation... INFO @ Wed, 12 Dec 2018 23:29:17: end of X-cor INFO @ Wed, 12 Dec 2018 23:29:17: #2 finished! INFO @ Wed, 12 Dec 2018 23:29:17: #2 predicted fragment length is 53 bps INFO @ Wed, 12 Dec 2018 23:29:17: #2 alternative fragment length(s) may be 53 bps INFO @ Wed, 12 Dec 2018 23:29:17: #2.2 Generate R script for model : SRX1453549.05_model.r WARNING @ Wed, 12 Dec 2018 23:29:17: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:29:17: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Wed, 12 Dec 2018 23:29:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:29:17: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:29:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:29:20: 20000000 INFO @ Wed, 12 Dec 2018 23:29:20: 21000000 INFO @ Wed, 12 Dec 2018 23:29:39: 22000000 INFO @ Wed, 12 Dec 2018 23:29:40: 21000000 INFO @ Wed, 12 Dec 2018 23:29:58: 23000000 INFO @ Wed, 12 Dec 2018 23:30:00: 22000000 INFO @ Wed, 12 Dec 2018 23:30:16: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 23:30:16: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 23:30:16: #1 total tags in treatment: 23840792 INFO @ Wed, 12 Dec 2018 23:30:16: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:30:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:30:17: #1 tags after filtering in treatment: 23840672 INFO @ Wed, 12 Dec 2018 23:30:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:30:17: #1 finished! INFO @ Wed, 12 Dec 2018 23:30:17: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:30:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:30:20: #2 number of paired peaks: 7027 INFO @ Wed, 12 Dec 2018 23:30:20: start model_add_line... INFO @ Wed, 12 Dec 2018 23:30:20: 23000000 INFO @ Wed, 12 Dec 2018 23:30:20: start X-correlation... INFO @ Wed, 12 Dec 2018 23:30:20: end of X-cor INFO @ Wed, 12 Dec 2018 23:30:20: #2 finished! INFO @ Wed, 12 Dec 2018 23:30:20: #2 predicted fragment length is 53 bps INFO @ Wed, 12 Dec 2018 23:30:20: #2 alternative fragment length(s) may be 53 bps INFO @ Wed, 12 Dec 2018 23:30:20: #2.2 Generate R script for model : SRX1453549.10_model.r WARNING @ Wed, 12 Dec 2018 23:30:20: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:30:20: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Wed, 12 Dec 2018 23:30:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:30:20: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:30:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:30:30: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:30:37: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 23:30:37: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 23:30:37: #1 total tags in treatment: 23840792 INFO @ Wed, 12 Dec 2018 23:30:37: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:30:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:30:38: #1 tags after filtering in treatment: 23840672 INFO @ Wed, 12 Dec 2018 23:30:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:30:38: #1 finished! INFO @ Wed, 12 Dec 2018 23:30:38: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:30:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:30:41: #2 number of paired peaks: 7027 INFO @ Wed, 12 Dec 2018 23:30:41: start model_add_line... INFO @ Wed, 12 Dec 2018 23:30:42: start X-correlation... INFO @ Wed, 12 Dec 2018 23:30:42: end of X-cor INFO @ Wed, 12 Dec 2018 23:30:42: #2 finished! INFO @ Wed, 12 Dec 2018 23:30:42: #2 predicted fragment length is 53 bps INFO @ Wed, 12 Dec 2018 23:30:42: #2 alternative fragment length(s) may be 53 bps INFO @ Wed, 12 Dec 2018 23:30:42: #2.2 Generate R script for model : SRX1453549.20_model.r WARNING @ Wed, 12 Dec 2018 23:30:42: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:30:42: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Wed, 12 Dec 2018 23:30:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:30:42: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:30:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:31:14: #4 Write output xls file... SRX1453549.05_peaks.xls INFO @ Wed, 12 Dec 2018 23:31:15: #4 Write peak in narrowPeak format file... SRX1453549.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:31:15: #4 Write summits bed file... SRX1453549.05_summits.bed INFO @ Wed, 12 Dec 2018 23:31:15: Done! pass1 - making usageList (64 chroms): 5 millis pass2 - checking and writing primary data (2273 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:31:35: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:31:54: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:32:19: #4 Write output xls file... SRX1453549.10_peaks.xls INFO @ Wed, 12 Dec 2018 23:32:19: #4 Write peak in narrowPeak format file... SRX1453549.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:32:19: #4 Write summits bed file... SRX1453549.10_summits.bed INFO @ Wed, 12 Dec 2018 23:32:19: Done! pass1 - making usageList (47 chroms): 4 millis pass2 - checking and writing primary data (1199 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:32:38: #4 Write output xls file... SRX1453549.20_peaks.xls INFO @ Wed, 12 Dec 2018 23:32:38: #4 Write peak in narrowPeak format file... SRX1453549.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:32:38: #4 Write summits bed file... SRX1453549.20_summits.bed INFO @ Wed, 12 Dec 2018 23:32:38: Done! pass1 - making usageList (36 chroms): 5 millis pass2 - checking and writing primary data (570 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。