Job ID = 10195004 sra ファイルのダウンロード中... Completed: 875817K bytes transferred in 11 seconds (604141K 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 35608252 spots for /home/okishinya/chipatlas/results/rn6/SRX831354/SRR1743290.sra Written 35608252 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 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:09 35608252 reads; of these: 35608252 (100.00%) were unpaired; of these: 854222 (2.40%) aligned 0 times 25342528 (71.17%) aligned exactly 1 time 9411502 (26.43%) aligned >1 times 97.60% overall alignment rate Time searching: 00:14:11 Overall time: 00:14:11 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 12 files... [bam_rmdupse_core] 2709932 / 34754030 = 0.0780 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 19:23:20: # Command line: callpeak -t SRX831354.bam -f BAM -g 2.15e9 -n SRX831354.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX831354.20 # format = BAM # ChIP-seq file = ['SRX831354.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 19:23:20: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:23:20: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:23:20: # Command line: callpeak -t SRX831354.bam -f BAM -g 2.15e9 -n SRX831354.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX831354.05 # format = BAM # ChIP-seq file = ['SRX831354.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 19:23:20: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:23:20: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:23:20: # Command line: callpeak -t SRX831354.bam -f BAM -g 2.15e9 -n SRX831354.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX831354.10 # format = BAM # ChIP-seq file = ['SRX831354.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 19:23:20: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:23:20: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:23:27: 1000000 INFO @ Fri, 10 Nov 2017 19:23:27: 1000000 INFO @ Fri, 10 Nov 2017 19:23:27: 1000000 INFO @ Fri, 10 Nov 2017 19:23:33: 2000000 INFO @ Fri, 10 Nov 2017 19:23:34: 2000000 INFO @ Fri, 10 Nov 2017 19:23:34: 2000000 INFO @ Fri, 10 Nov 2017 19:23:40: 3000000 INFO @ Fri, 10 Nov 2017 19:23:41: 3000000 INFO @ Fri, 10 Nov 2017 19:23:41: 3000000 INFO @ Fri, 10 Nov 2017 19:23:46: 4000000 INFO @ Fri, 10 Nov 2017 19:23:48: 4000000 INFO @ Fri, 10 Nov 2017 19:23:48: 4000000 INFO @ Fri, 10 Nov 2017 19:23:53: 5000000 INFO @ Fri, 10 Nov 2017 19:23:55: 5000000 INFO @ Fri, 10 Nov 2017 19:23:55: 5000000 INFO @ Fri, 10 Nov 2017 19:23:59: 6000000 INFO @ Fri, 10 Nov 2017 19:24:02: 6000000 INFO @ Fri, 10 Nov 2017 19:24:02: 6000000 INFO @ Fri, 10 Nov 2017 19:24:06: 7000000 INFO @ Fri, 10 Nov 2017 19:24:09: 7000000 INFO @ Fri, 10 Nov 2017 19:24:09: 7000000 INFO @ Fri, 10 Nov 2017 19:24:12: 8000000 INFO @ Fri, 10 Nov 2017 19:24:16: 8000000 INFO @ Fri, 10 Nov 2017 19:24:16: 8000000 INFO @ Fri, 10 Nov 2017 19:24:19: 9000000 INFO @ Fri, 10 Nov 2017 19:24:23: 9000000 INFO @ Fri, 10 Nov 2017 19:24:23: 9000000 INFO @ Fri, 10 Nov 2017 19:24:25: 10000000 INFO @ Fri, 10 Nov 2017 19:24:30: 10000000 INFO @ Fri, 10 Nov 2017 19:24:30: 10000000 INFO @ Fri, 10 Nov 2017 19:24:32: 11000000 INFO @ Fri, 10 Nov 2017 19:24:37: 11000000 INFO @ Fri, 10 Nov 2017 19:24:37: 11000000 INFO @ Fri, 10 Nov 2017 19:24:38: 12000000 INFO @ Fri, 10 Nov 2017 19:24:44: 12000000 INFO @ Fri, 10 Nov 2017 19:24:44: 12000000 INFO @ Fri, 10 Nov 2017 19:24:45: 13000000 INFO @ Fri, 10 Nov 2017 19:24:51: 13000000 INFO @ Fri, 10 Nov 2017 19:24:51: 14000000 INFO @ Fri, 10 Nov 2017 19:24:52: 13000000 INFO @ Fri, 10 Nov 2017 19:24:58: 14000000 INFO @ Fri, 10 Nov 2017 19:24:58: 15000000 INFO @ Fri, 10 Nov 2017 19:24:59: 14000000 INFO @ Fri, 10 Nov 2017 19:25:04: 15000000 INFO @ Fri, 10 Nov 2017 19:25:05: 16000000 INFO @ Fri, 10 Nov 2017 19:25:07: 15000000 INFO @ Fri, 10 Nov 2017 19:25:12: 16000000 INFO @ Fri, 10 Nov 2017 19:25:12: 17000000 INFO @ Fri, 10 Nov 2017 19:25:14: 16000000 INFO @ Fri, 10 Nov 2017 19:25:19: 18000000 INFO @ Fri, 10 Nov 2017 19:25:19: 17000000 INFO @ Fri, 10 Nov 2017 19:25:21: 17000000 INFO @ Fri, 10 Nov 2017 19:25:25: 19000000 INFO @ Fri, 10 Nov 2017 19:25:26: 18000000 INFO @ Fri, 10 Nov 2017 19:25:28: 18000000 INFO @ Fri, 10 Nov 2017 19:25:32: 20000000 INFO @ Fri, 10 Nov 2017 19:25:33: 19000000 INFO @ Fri, 10 Nov 2017 19:25:35: 19000000 INFO @ Fri, 10 Nov 2017 19:25:39: 21000000 INFO @ Fri, 10 Nov 2017 19:25:41: 20000000 INFO @ Fri, 10 Nov 2017 19:25:43: 20000000 INFO @ Fri, 10 Nov 2017 19:25:45: 22000000 INFO @ Fri, 10 Nov 2017 19:25:48: 21000000 INFO @ Fri, 10 Nov 2017 19:25:50: 21000000 INFO @ Fri, 10 Nov 2017 19:25:52: 23000000 INFO @ Fri, 10 Nov 2017 19:25:55: 22000000 INFO @ Fri, 10 Nov 2017 19:25:57: 22000000 INFO @ Fri, 10 Nov 2017 19:25:58: 24000000 INFO @ Fri, 10 Nov 2017 19:26:03: 23000000 INFO @ Fri, 10 Nov 2017 19:26:05: 25000000 INFO @ Fri, 10 Nov 2017 19:26:05: 23000000 INFO @ Fri, 10 Nov 2017 19:26:10: 24000000 INFO @ Fri, 10 Nov 2017 19:26:11: 26000000 INFO @ Fri, 10 Nov 2017 19:26:12: 24000000 INFO @ Fri, 10 Nov 2017 19:26:17: 25000000 INFO @ Fri, 10 Nov 2017 19:26:18: 27000000 INFO @ Fri, 10 Nov 2017 19:26:19: 25000000 INFO @ Fri, 10 Nov 2017 19:26:24: 28000000 INFO @ Fri, 10 Nov 2017 19:26:25: 26000000 INFO @ Fri, 10 Nov 2017 19:26:27: 26000000 INFO @ Fri, 10 Nov 2017 19:26:31: 29000000 INFO @ Fri, 10 Nov 2017 19:26:32: 27000000 INFO @ Fri, 10 Nov 2017 19:26:34: 27000000 INFO @ Fri, 10 Nov 2017 19:26:38: 30000000 INFO @ Fri, 10 Nov 2017 19:26:39: 28000000 INFO @ Fri, 10 Nov 2017 19:26:42: 28000000 INFO @ Fri, 10 Nov 2017 19:26:45: 31000000 INFO @ Fri, 10 Nov 2017 19:26:45: 29000000 INFO @ Fri, 10 Nov 2017 19:26:50: 29000000 INFO @ Fri, 10 Nov 2017 19:26:52: 30000000 INFO @ Fri, 10 Nov 2017 19:26:53: 32000000 INFO @ Fri, 10 Nov 2017 19:26:53: #1 tag size is determined as 36 bps INFO @ Fri, 10 Nov 2017 19:26:53: #1 tag size = 36 INFO @ Fri, 10 Nov 2017 19:26:53: #1 total tags in treatment: 32044098 INFO @ Fri, 10 Nov 2017 19:26:53: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:26:53: #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 19:26:54: #1 tags after filtering in treatment: 32044012 INFO @ Fri, 10 Nov 2017 19:26:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:26:54: #1 finished! INFO @ Fri, 10 Nov 2017 19:26:54: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:26:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:26:57: 30000000 INFO @ Fri, 10 Nov 2017 19:26:57: #2 number of paired peaks: 4448 INFO @ Fri, 10 Nov 2017 19:26:57: start model_add_line... INFO @ Fri, 10 Nov 2017 19:26:57: start X-correlation... INFO @ Fri, 10 Nov 2017 19:26:57: end of X-cor INFO @ Fri, 10 Nov 2017 19:26:57: #2 finished! INFO @ Fri, 10 Nov 2017 19:26:57: #2 predicted fragment length is 35 bps INFO @ Fri, 10 Nov 2017 19:26:57: #2 alternative fragment length(s) may be 35,210,395,583 bps INFO @ Fri, 10 Nov 2017 19:26:57: #2.2 Generate R script for model : SRX831354.05_model.r WARNING @ Fri, 10 Nov 2017 19:26:57: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 19:26:57: #2 You may need to consider one of the other alternative d(s): 35,210,395,583 WARNING @ Fri, 10 Nov 2017 19:26:57: #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 19:26:57: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:26:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:26:59: 31000000 INFO @ Fri, 10 Nov 2017 19:27:04: 31000000 INFO @ Fri, 10 Nov 2017 19:27:05: 32000000 INFO @ Fri, 10 Nov 2017 19:27:06: #1 tag size is determined as 36 bps INFO @ Fri, 10 Nov 2017 19:27:06: #1 tag size = 36 INFO @ Fri, 10 Nov 2017 19:27:06: #1 total tags in treatment: 32044098 INFO @ Fri, 10 Nov 2017 19:27:06: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:27:06: #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 19:27:07: #1 tags after filtering in treatment: 32044012 INFO @ Fri, 10 Nov 2017 19:27:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:27:07: #1 finished! INFO @ Fri, 10 Nov 2017 19:27:07: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:27:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:27:10: #2 number of paired peaks: 4448 INFO @ Fri, 10 Nov 2017 19:27:10: start model_add_line... INFO @ Fri, 10 Nov 2017 19:27:10: start X-correlation... INFO @ Fri, 10 Nov 2017 19:27:10: end of X-cor INFO @ Fri, 10 Nov 2017 19:27:10: #2 finished! INFO @ Fri, 10 Nov 2017 19:27:10: #2 predicted fragment length is 35 bps INFO @ Fri, 10 Nov 2017 19:27:10: #2 alternative fragment length(s) may be 35,210,395,583 bps INFO @ Fri, 10 Nov 2017 19:27:10: #2.2 Generate R script for model : SRX831354.10_model.r WARNING @ Fri, 10 Nov 2017 19:27:10: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 19:27:10: #2 You may need to consider one of the other alternative d(s): 35,210,395,583 WARNING @ Fri, 10 Nov 2017 19:27:10: #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 19:27:10: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:27:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:27:10: 32000000 INFO @ Fri, 10 Nov 2017 19:27:11: #1 tag size is determined as 36 bps INFO @ Fri, 10 Nov 2017 19:27:11: #1 tag size = 36 INFO @ Fri, 10 Nov 2017 19:27:11: #1 total tags in treatment: 32044098 INFO @ Fri, 10 Nov 2017 19:27:11: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:27:11: #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 19:27:12: #1 tags after filtering in treatment: 32044012 INFO @ Fri, 10 Nov 2017 19:27:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:27:12: #1 finished! INFO @ Fri, 10 Nov 2017 19:27:12: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:27:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:27:15: #2 number of paired peaks: 4448 INFO @ Fri, 10 Nov 2017 19:27:15: start model_add_line... INFO @ Fri, 10 Nov 2017 19:27:16: start X-correlation... INFO @ Fri, 10 Nov 2017 19:27:16: end of X-cor INFO @ Fri, 10 Nov 2017 19:27:16: #2 finished! INFO @ Fri, 10 Nov 2017 19:27:16: #2 predicted fragment length is 35 bps INFO @ Fri, 10 Nov 2017 19:27:16: #2 alternative fragment length(s) may be 35,210,395,583 bps INFO @ Fri, 10 Nov 2017 19:27:16: #2.2 Generate R script for model : SRX831354.20_model.r WARNING @ Fri, 10 Nov 2017 19:27:16: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 19:27:16: #2 You may need to consider one of the other alternative d(s): 35,210,395,583 WARNING @ Fri, 10 Nov 2017 19:27:16: #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 19:27:16: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:27:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:28:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:28:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:28:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:28:55: #4 Write output xls file... SRX831354.05_peaks.xls INFO @ Fri, 10 Nov 2017 19:28:55: #4 Write peak in narrowPeak format file... SRX831354.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:28:55: #4 Write summits bed file... SRX831354.05_summits.bed INFO @ Fri, 10 Nov 2017 19:28:55: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (1757 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:29:08: #4 Write output xls file... SRX831354.20_peaks.xls INFO @ Fri, 10 Nov 2017 19:29:08: #4 Write peak in narrowPeak format file... SRX831354.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:29:08: #4 Write summits bed file... SRX831354.20_summits.bed INFO @ Fri, 10 Nov 2017 19:29:08: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (440 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:29:10: #4 Write output xls file... SRX831354.10_peaks.xls INFO @ Fri, 10 Nov 2017 19:29:11: #4 Write peak in narrowPeak format file... SRX831354.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:29:11: #4 Write summits bed file... SRX831354.10_summits.bed INFO @ Fri, 10 Nov 2017 19:29:11: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (1021 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。