Job ID = 10194732 sra ファイルのダウンロード中... Completed: 901956K bytes transferred in 13 seconds (553723K bits/sec), in 1 file. Completed: 894187K bytes transferred in 13 seconds (539616K 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 16301990 spots for /home/okishinya/chipatlas/results/rn6/SRX1056328/SRR2060198.sra Written 16301990 spots total Written 16764224 spots for /home/okishinya/chipatlas/results/rn6/SRX1056328/SRR2060197.sra Written 16764224 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: 02:10:38 33066214 reads; of these: 33066214 (100.00%) were unpaired; of these: 2240530 (6.78%) aligned 0 times 22887392 (69.22%) aligned exactly 1 time 7938292 (24.01%) aligned >1 times 93.22% overall alignment rate Time searching: 02:10:41 Overall time: 02:10:41 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] 1667564 / 30825684 = 0.0541 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 22:17:50: # Command line: callpeak -t SRX1056328.bam -f BAM -g 2.15e9 -n SRX1056328.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056328.10 # format = BAM # ChIP-seq file = ['SRX1056328.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 22:17:50: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:17:50: # Command line: callpeak -t SRX1056328.bam -f BAM -g 2.15e9 -n SRX1056328.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056328.20 # format = BAM # ChIP-seq file = ['SRX1056328.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 22:17:50: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:17:50: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:17:50: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:17:50: # Command line: callpeak -t SRX1056328.bam -f BAM -g 2.15e9 -n SRX1056328.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056328.05 # format = BAM # ChIP-seq file = ['SRX1056328.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 22:17:50: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:17:50: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:18:09: 1000000 INFO @ Fri, 10 Nov 2017 22:18:13: 1000000 INFO @ Fri, 10 Nov 2017 22:18:13: 1000000 INFO @ Fri, 10 Nov 2017 22:18:27: 2000000 INFO @ Fri, 10 Nov 2017 22:18:32: 2000000 INFO @ Fri, 10 Nov 2017 22:18:36: 2000000 INFO @ Fri, 10 Nov 2017 22:18:44: 3000000 INFO @ Fri, 10 Nov 2017 22:18:51: 3000000 INFO @ Fri, 10 Nov 2017 22:18:53: 3000000 INFO @ Fri, 10 Nov 2017 22:19:01: 4000000 INFO @ Fri, 10 Nov 2017 22:19:08: 4000000 INFO @ Fri, 10 Nov 2017 22:19:12: 4000000 INFO @ Fri, 10 Nov 2017 22:19:18: 5000000 INFO @ Fri, 10 Nov 2017 22:19:22: 5000000 INFO @ Fri, 10 Nov 2017 22:19:32: 5000000 INFO @ Fri, 10 Nov 2017 22:19:34: 6000000 INFO @ Fri, 10 Nov 2017 22:19:37: 6000000 INFO @ Fri, 10 Nov 2017 22:19:51: 7000000 INFO @ Fri, 10 Nov 2017 22:19:51: 6000000 INFO @ Fri, 10 Nov 2017 22:19:52: 7000000 INFO @ Fri, 10 Nov 2017 22:20:08: 8000000 INFO @ Fri, 10 Nov 2017 22:20:09: 8000000 INFO @ Fri, 10 Nov 2017 22:20:11: 7000000 INFO @ Fri, 10 Nov 2017 22:20:24: 9000000 INFO @ Fri, 10 Nov 2017 22:20:25: 9000000 INFO @ Fri, 10 Nov 2017 22:20:30: 8000000 INFO @ Fri, 10 Nov 2017 22:20:40: 10000000 INFO @ Fri, 10 Nov 2017 22:20:41: 10000000 INFO @ Fri, 10 Nov 2017 22:20:50: 9000000 INFO @ Fri, 10 Nov 2017 22:20:55: 11000000 INFO @ Fri, 10 Nov 2017 22:20:57: 11000000 INFO @ Fri, 10 Nov 2017 22:21:09: 10000000 INFO @ Fri, 10 Nov 2017 22:21:10: 12000000 INFO @ Fri, 10 Nov 2017 22:21:14: 12000000 INFO @ Fri, 10 Nov 2017 22:21:25: 13000000 INFO @ Fri, 10 Nov 2017 22:21:27: 11000000 INFO @ Fri, 10 Nov 2017 22:21:33: 13000000 INFO @ Fri, 10 Nov 2017 22:21:41: 14000000 INFO @ Fri, 10 Nov 2017 22:21:46: 12000000 INFO @ Fri, 10 Nov 2017 22:21:53: 14000000 INFO @ Fri, 10 Nov 2017 22:21:56: 15000000 INFO @ Fri, 10 Nov 2017 22:22:08: 13000000 INFO @ Fri, 10 Nov 2017 22:22:12: 16000000 INFO @ Fri, 10 Nov 2017 22:22:17: 15000000 INFO @ Fri, 10 Nov 2017 22:22:27: 17000000 INFO @ Fri, 10 Nov 2017 22:22:32: 14000000 INFO @ Fri, 10 Nov 2017 22:22:41: 16000000 INFO @ Fri, 10 Nov 2017 22:22:43: 18000000 INFO @ Fri, 10 Nov 2017 22:22:56: 15000000 INFO @ Fri, 10 Nov 2017 22:23:03: 19000000 INFO @ Fri, 10 Nov 2017 22:23:06: 17000000 INFO @ Fri, 10 Nov 2017 22:23:20: 16000000 INFO @ Fri, 10 Nov 2017 22:23:22: 20000000 INFO @ Fri, 10 Nov 2017 22:23:28: 18000000 INFO @ Fri, 10 Nov 2017 22:23:39: 17000000 INFO @ Fri, 10 Nov 2017 22:23:40: 21000000 INFO @ Fri, 10 Nov 2017 22:23:48: 19000000 INFO @ Fri, 10 Nov 2017 22:23:59: 22000000 INFO @ Fri, 10 Nov 2017 22:24:00: 18000000 INFO @ Fri, 10 Nov 2017 22:24:07: 20000000 INFO @ Fri, 10 Nov 2017 22:24:17: 19000000 INFO @ Fri, 10 Nov 2017 22:24:18: 23000000 INFO @ Fri, 10 Nov 2017 22:24:27: 21000000 INFO @ Fri, 10 Nov 2017 22:24:34: 20000000 INFO @ Fri, 10 Nov 2017 22:24:37: 24000000 INFO @ Fri, 10 Nov 2017 22:24:44: 22000000 INFO @ Fri, 10 Nov 2017 22:24:51: 21000000 INFO @ Fri, 10 Nov 2017 22:24:55: 25000000 INFO @ Fri, 10 Nov 2017 22:25:02: 23000000 INFO @ Fri, 10 Nov 2017 22:25:09: 22000000 INFO @ Fri, 10 Nov 2017 22:25:14: 26000000 INFO @ Fri, 10 Nov 2017 22:25:20: 24000000 INFO @ Fri, 10 Nov 2017 22:25:25: 23000000 INFO @ Fri, 10 Nov 2017 22:25:31: 27000000 INFO @ Fri, 10 Nov 2017 22:25:37: 25000000 INFO @ Fri, 10 Nov 2017 22:25:41: 24000000 INFO @ Fri, 10 Nov 2017 22:25:49: 28000000 INFO @ Fri, 10 Nov 2017 22:25:56: 26000000 INFO @ Fri, 10 Nov 2017 22:25:58: 25000000 INFO @ Fri, 10 Nov 2017 22:26:08: 29000000 INFO @ Fri, 10 Nov 2017 22:26:12: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 22:26:12: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 22:26:12: #1 total tags in treatment: 29158120 INFO @ Fri, 10 Nov 2017 22:26:12: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:26:12: #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 22:26:13: 27000000 INFO @ Fri, 10 Nov 2017 22:26:13: #1 tags after filtering in treatment: 29158029 INFO @ Fri, 10 Nov 2017 22:26:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:26:13: #1 finished! INFO @ Fri, 10 Nov 2017 22:26:13: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:26:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:26:16: 26000000 INFO @ Fri, 10 Nov 2017 22:26:16: #2 number of paired peaks: 6528 INFO @ Fri, 10 Nov 2017 22:26:16: start model_add_line... INFO @ Fri, 10 Nov 2017 22:26:17: start X-correlation... INFO @ Fri, 10 Nov 2017 22:26:17: end of X-cor INFO @ Fri, 10 Nov 2017 22:26:17: #2 finished! INFO @ Fri, 10 Nov 2017 22:26:17: #2 predicted fragment length is 99 bps INFO @ Fri, 10 Nov 2017 22:26:17: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 10 Nov 2017 22:26:17: #2.2 Generate R script for model : SRX1056328.20_model.r WARNING @ Fri, 10 Nov 2017 22:26:17: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 22:26:17: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Fri, 10 Nov 2017 22:26:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 22:26:17: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:26:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:26:29: 28000000 INFO @ Fri, 10 Nov 2017 22:26:33: 27000000 INFO @ Fri, 10 Nov 2017 22:26:47: 29000000 INFO @ Fri, 10 Nov 2017 22:26:50: 28000000 INFO @ Fri, 10 Nov 2017 22:26:50: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 22:26:50: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 22:26:50: #1 total tags in treatment: 29158120 INFO @ Fri, 10 Nov 2017 22:26:50: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:26:50: #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 22:26:52: #1 tags after filtering in treatment: 29158029 INFO @ Fri, 10 Nov 2017 22:26:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:26:52: #1 finished! INFO @ Fri, 10 Nov 2017 22:26:52: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:26:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:26:55: #2 number of paired peaks: 6528 INFO @ Fri, 10 Nov 2017 22:26:55: start model_add_line... INFO @ Fri, 10 Nov 2017 22:26:56: start X-correlation... INFO @ Fri, 10 Nov 2017 22:26:56: end of X-cor INFO @ Fri, 10 Nov 2017 22:26:56: #2 finished! INFO @ Fri, 10 Nov 2017 22:26:56: #2 predicted fragment length is 99 bps INFO @ Fri, 10 Nov 2017 22:26:56: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 10 Nov 2017 22:26:56: #2.2 Generate R script for model : SRX1056328.10_model.r WARNING @ Fri, 10 Nov 2017 22:26:56: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 22:26:56: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Fri, 10 Nov 2017 22:26:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 22:26:56: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:26:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:27:07: 29000000 INFO @ Fri, 10 Nov 2017 22:27:10: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 22:27:10: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 22:27:10: #1 total tags in treatment: 29158120 INFO @ Fri, 10 Nov 2017 22:27:10: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:27:10: #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 22:27:11: #1 tags after filtering in treatment: 29158029 INFO @ Fri, 10 Nov 2017 22:27:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:27:11: #1 finished! INFO @ Fri, 10 Nov 2017 22:27:11: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:27:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:27:15: #2 number of paired peaks: 6528 INFO @ Fri, 10 Nov 2017 22:27:15: start model_add_line... INFO @ Fri, 10 Nov 2017 22:27:16: start X-correlation... INFO @ Fri, 10 Nov 2017 22:27:16: end of X-cor INFO @ Fri, 10 Nov 2017 22:27:16: #2 finished! INFO @ Fri, 10 Nov 2017 22:27:16: #2 predicted fragment length is 99 bps INFO @ Fri, 10 Nov 2017 22:27:16: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 10 Nov 2017 22:27:16: #2.2 Generate R script for model : SRX1056328.05_model.r WARNING @ Fri, 10 Nov 2017 22:27:16: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 22:27:16: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Fri, 10 Nov 2017 22:27:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 22:27:16: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:27:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:27:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:28:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:28:37: #4 Write output xls file... SRX1056328.20_peaks.xls INFO @ Fri, 10 Nov 2017 22:28:37: #4 Write peak in narrowPeak format file... SRX1056328.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:28:37: #4 Write summits bed file... SRX1056328.20_summits.bed INFO @ Fri, 10 Nov 2017 22:28:37: Done! pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (489 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:28:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:29:19: #4 Write output xls file... SRX1056328.10_peaks.xls INFO @ Fri, 10 Nov 2017 22:29:19: #4 Write peak in narrowPeak format file... SRX1056328.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:29:19: #4 Write summits bed file... SRX1056328.10_summits.bed INFO @ Fri, 10 Nov 2017 22:29:19: Done! pass1 - making usageList (46 chroms): 2 millis pass2 - checking and writing primary data (968 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:29:38: #4 Write output xls file... SRX1056328.05_peaks.xls INFO @ Fri, 10 Nov 2017 22:29:38: #4 Write peak in narrowPeak format file... SRX1056328.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:29:38: #4 Write summits bed file... SRX1056328.05_summits.bed INFO @ Fri, 10 Nov 2017 22:29:38: Done! pass1 - making usageList (56 chroms): 2 millis pass2 - checking and writing primary data (1778 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。