Job ID = 10194941 sra ファイルのダウンロード中... Completed: 802358K bytes transferred in 20 seconds (318432K 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 23776887 spots for /home/okishinya/chipatlas/results/rn6/SRX2568194/SRR5264106.sra Written 23776887 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:14:52 23776887 reads; of these: 23776887 (100.00%) were unpaired; of these: 893795 (3.76%) aligned 0 times 17241678 (72.51%) aligned exactly 1 time 5641414 (23.73%) aligned >1 times 96.24% overall alignment rate Time searching: 01:14:57 Overall time: 01:14:57 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] 3295849 / 22883092 = 0.1440 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 01:24:28: # Command line: callpeak -t SRX2568194.bam -f BAM -g 2.15e9 -n SRX2568194.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2568194.20 # format = BAM # ChIP-seq file = ['SRX2568194.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 01:24:28: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:24:28: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:24:28: # Command line: callpeak -t SRX2568194.bam -f BAM -g 2.15e9 -n SRX2568194.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2568194.05 # format = BAM # ChIP-seq file = ['SRX2568194.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 01:24:28: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:24:28: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:24:28: # Command line: callpeak -t SRX2568194.bam -f BAM -g 2.15e9 -n SRX2568194.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2568194.10 # format = BAM # ChIP-seq file = ['SRX2568194.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 01:24:28: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:24:28: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:24:44: 1000000 INFO @ Sat, 11 Nov 2017 01:24:52: 1000000 INFO @ Sat, 11 Nov 2017 01:24:52: 1000000 INFO @ Sat, 11 Nov 2017 01:24:59: 2000000 INFO @ Sat, 11 Nov 2017 01:25:14: 3000000 INFO @ Sat, 11 Nov 2017 01:25:16: 2000000 INFO @ Sat, 11 Nov 2017 01:25:16: 2000000 INFO @ Sat, 11 Nov 2017 01:25:30: 4000000 INFO @ Sat, 11 Nov 2017 01:25:39: 3000000 INFO @ Sat, 11 Nov 2017 01:25:39: 3000000 INFO @ Sat, 11 Nov 2017 01:25:45: 5000000 INFO @ Sat, 11 Nov 2017 01:26:00: 6000000 INFO @ Sat, 11 Nov 2017 01:26:01: 4000000 INFO @ Sat, 11 Nov 2017 01:26:01: 4000000 INFO @ Sat, 11 Nov 2017 01:26:16: 7000000 INFO @ Sat, 11 Nov 2017 01:26:24: 5000000 INFO @ Sat, 11 Nov 2017 01:26:25: 5000000 INFO @ Sat, 11 Nov 2017 01:26:31: 8000000 INFO @ Sat, 11 Nov 2017 01:26:37: 6000000 INFO @ Sat, 11 Nov 2017 01:26:47: 9000000 INFO @ Sat, 11 Nov 2017 01:26:50: 6000000 INFO @ Sat, 11 Nov 2017 01:26:52: 7000000 INFO @ Sat, 11 Nov 2017 01:27:02: 10000000 INFO @ Sat, 11 Nov 2017 01:27:05: 8000000 INFO @ Sat, 11 Nov 2017 01:27:13: 7000000 INFO @ Sat, 11 Nov 2017 01:27:17: 11000000 INFO @ Sat, 11 Nov 2017 01:27:22: 9000000 INFO @ Sat, 11 Nov 2017 01:27:33: 12000000 INFO @ Sat, 11 Nov 2017 01:27:36: 8000000 INFO @ Sat, 11 Nov 2017 01:27:47: 10000000 INFO @ Sat, 11 Nov 2017 01:27:48: 13000000 INFO @ Sat, 11 Nov 2017 01:27:58: 9000000 INFO @ Sat, 11 Nov 2017 01:28:01: 14000000 INFO @ Sat, 11 Nov 2017 01:28:08: 11000000 INFO @ Sat, 11 Nov 2017 01:28:15: 15000000 INFO @ Sat, 11 Nov 2017 01:28:19: 10000000 INFO @ Sat, 11 Nov 2017 01:28:28: 16000000 INFO @ Sat, 11 Nov 2017 01:28:31: 12000000 INFO @ Sat, 11 Nov 2017 01:28:41: 11000000 INFO @ Sat, 11 Nov 2017 01:28:42: 17000000 INFO @ Sat, 11 Nov 2017 01:28:53: 13000000 INFO @ Sat, 11 Nov 2017 01:28:55: 18000000 INFO @ Sat, 11 Nov 2017 01:29:02: 12000000 INFO @ Sat, 11 Nov 2017 01:29:07: 19000000 INFO @ Sat, 11 Nov 2017 01:29:12: 14000000 INFO @ Sat, 11 Nov 2017 01:29:14: #1 tag size is determined as 75 bps INFO @ Sat, 11 Nov 2017 01:29:14: #1 tag size = 75 INFO @ Sat, 11 Nov 2017 01:29:14: #1 total tags in treatment: 19587243 INFO @ Sat, 11 Nov 2017 01:29:14: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:29:14: #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 01:29:15: #1 tags after filtering in treatment: 19587098 INFO @ Sat, 11 Nov 2017 01:29:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:29:15: #1 finished! INFO @ Sat, 11 Nov 2017 01:29:15: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:29:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:29:17: #2 number of paired peaks: 4623 INFO @ Sat, 11 Nov 2017 01:29:17: start model_add_line... INFO @ Sat, 11 Nov 2017 01:29:18: start X-correlation... INFO @ Sat, 11 Nov 2017 01:29:18: end of X-cor INFO @ Sat, 11 Nov 2017 01:29:18: #2 finished! INFO @ Sat, 11 Nov 2017 01:29:18: #2 predicted fragment length is 75 bps INFO @ Sat, 11 Nov 2017 01:29:18: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 11 Nov 2017 01:29:18: #2.2 Generate R script for model : SRX2568194.20_model.r WARNING @ Sat, 11 Nov 2017 01:29:18: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:29:18: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 11 Nov 2017 01:29:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 01:29:18: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:29:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:29:19: 13000000 INFO @ Sat, 11 Nov 2017 01:29:29: 15000000 INFO @ Sat, 11 Nov 2017 01:29:34: 14000000 INFO @ Sat, 11 Nov 2017 01:29:45: 16000000 INFO @ Sat, 11 Nov 2017 01:29:50: 15000000 INFO @ Sat, 11 Nov 2017 01:30:01: 17000000 INFO @ Sat, 11 Nov 2017 01:30:07: 16000000 INFO @ Sat, 11 Nov 2017 01:30:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:30:17: 18000000 INFO @ Sat, 11 Nov 2017 01:30:26: 17000000 INFO @ Sat, 11 Nov 2017 01:30:32: 19000000 INFO @ Sat, 11 Nov 2017 01:30:41: #1 tag size is determined as 75 bps INFO @ Sat, 11 Nov 2017 01:30:41: #1 tag size = 75 INFO @ Sat, 11 Nov 2017 01:30:41: #1 total tags in treatment: 19587243 INFO @ Sat, 11 Nov 2017 01:30:41: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:30:41: #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 01:30:42: #1 tags after filtering in treatment: 19587098 INFO @ Sat, 11 Nov 2017 01:30:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:30:42: #1 finished! INFO @ Sat, 11 Nov 2017 01:30:42: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:30:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:30:42: 18000000 INFO @ Sat, 11 Nov 2017 01:30:44: #2 number of paired peaks: 4623 INFO @ Sat, 11 Nov 2017 01:30:44: start model_add_line... INFO @ Sat, 11 Nov 2017 01:30:44: start X-correlation... INFO @ Sat, 11 Nov 2017 01:30:44: end of X-cor INFO @ Sat, 11 Nov 2017 01:30:44: #2 finished! INFO @ Sat, 11 Nov 2017 01:30:44: #2 predicted fragment length is 75 bps INFO @ Sat, 11 Nov 2017 01:30:44: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 11 Nov 2017 01:30:44: #2.2 Generate R script for model : SRX2568194.05_model.r WARNING @ Sat, 11 Nov 2017 01:30:44: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:30:44: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 11 Nov 2017 01:30:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 01:30:44: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:30:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:30:49: #4 Write output xls file... SRX2568194.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:30:49: #4 Write peak in narrowPeak format file... SRX2568194.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:30:49: #4 Write summits bed file... SRX2568194.20_summits.bed INFO @ Sat, 11 Nov 2017 01:30:49: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (390 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:30:56: 19000000 INFO @ Sat, 11 Nov 2017 01:31:04: #1 tag size is determined as 75 bps INFO @ Sat, 11 Nov 2017 01:31:04: #1 tag size = 75 INFO @ Sat, 11 Nov 2017 01:31:04: #1 total tags in treatment: 19587243 INFO @ Sat, 11 Nov 2017 01:31:04: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:31:04: #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 01:31:05: #1 tags after filtering in treatment: 19587098 INFO @ Sat, 11 Nov 2017 01:31:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:31:05: #1 finished! INFO @ Sat, 11 Nov 2017 01:31:05: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:31:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:31:07: #2 number of paired peaks: 4623 INFO @ Sat, 11 Nov 2017 01:31:07: start model_add_line... INFO @ Sat, 11 Nov 2017 01:31:07: start X-correlation... INFO @ Sat, 11 Nov 2017 01:31:07: end of X-cor INFO @ Sat, 11 Nov 2017 01:31:07: #2 finished! INFO @ Sat, 11 Nov 2017 01:31:07: #2 predicted fragment length is 75 bps INFO @ Sat, 11 Nov 2017 01:31:07: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 11 Nov 2017 01:31:07: #2.2 Generate R script for model : SRX2568194.10_model.r WARNING @ Sat, 11 Nov 2017 01:31:07: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:31:07: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 11 Nov 2017 01:31:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 01:31:07: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:31:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:31:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:32:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:32:17: #4 Write output xls file... SRX2568194.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:32:17: #4 Write peak in narrowPeak format file... SRX2568194.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:32:17: #4 Write summits bed file... SRX2568194.05_summits.bed INFO @ Sat, 11 Nov 2017 01:32:17: Done! pass1 - making usageList (48 chroms): 2 millis pass2 - checking and writing primary data (1169 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:32:43: #4 Write output xls file... SRX2568194.10_peaks.xls INFO @ Sat, 11 Nov 2017 01:32:43: #4 Write peak in narrowPeak format file... SRX2568194.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:32:43: #4 Write summits bed file... SRX2568194.10_summits.bed INFO @ Sat, 11 Nov 2017 01:32:43: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (705 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。