Job ID = 11388795 sra ファイルのダウンロード中... Completed: 264119K bytes transferred in 8 seconds (263776K bits/sec), in 1 file. Completed: 276185K bytes transferred in 9 seconds (249161K 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 12092255 spots for /home/okishinya/chipatlas/results/rn6/SRX3657367/SRR6681051.sra Written 12092255 spots for /home/okishinya/chipatlas/results/rn6/SRX3657367/SRR6681051.sra Read 12514899 spots for /home/okishinya/chipatlas/results/rn6/SRX3657367/SRR6681052.sra Written 12514899 spots for /home/okishinya/chipatlas/results/rn6/SRX3657367/SRR6681052.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 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: 00:47:04 24607154 reads; of these: 24607154 (100.00%) were unpaired; of these: 692280 (2.81%) aligned 0 times 17186839 (69.84%) aligned exactly 1 time 6728035 (27.34%) aligned >1 times 97.19% overall alignment rate Time searching: 00:47:08 Overall time: 00:47:08 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] 872590 / 23914874 = 0.0365 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 23:43:25: # Command line: callpeak -t SRX3657367.bam -f BAM -g 2.15e9 -n SRX3657367.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3657367.05 # format = BAM # ChIP-seq file = ['SRX3657367.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 23:43:25: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:43:25: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:43:25: # Command line: callpeak -t SRX3657367.bam -f BAM -g 2.15e9 -n SRX3657367.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3657367.20 # format = BAM # ChIP-seq file = ['SRX3657367.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 23:43:25: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:43:25: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:43:25: # Command line: callpeak -t SRX3657367.bam -f BAM -g 2.15e9 -n SRX3657367.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3657367.10 # format = BAM # ChIP-seq file = ['SRX3657367.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 23:43:25: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:43:25: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:43:35: 1000000 INFO @ Wed, 12 Dec 2018 23:43:36: 1000000 INFO @ Wed, 12 Dec 2018 23:43:36: 1000000 INFO @ Wed, 12 Dec 2018 23:43:45: 2000000 INFO @ Wed, 12 Dec 2018 23:43:45: 2000000 INFO @ Wed, 12 Dec 2018 23:43:46: 2000000 INFO @ Wed, 12 Dec 2018 23:43:55: 3000000 INFO @ Wed, 12 Dec 2018 23:43:56: 3000000 INFO @ Wed, 12 Dec 2018 23:43:57: 3000000 INFO @ Wed, 12 Dec 2018 23:44:04: 4000000 INFO @ Wed, 12 Dec 2018 23:44:07: 4000000 INFO @ Wed, 12 Dec 2018 23:44:11: 4000000 INFO @ Wed, 12 Dec 2018 23:44:16: 5000000 INFO @ Wed, 12 Dec 2018 23:44:18: 5000000 INFO @ Wed, 12 Dec 2018 23:44:25: 5000000 INFO @ Wed, 12 Dec 2018 23:44:29: 6000000 INFO @ Wed, 12 Dec 2018 23:44:30: 6000000 INFO @ Wed, 12 Dec 2018 23:44:40: 7000000 INFO @ Wed, 12 Dec 2018 23:44:40: 6000000 INFO @ Wed, 12 Dec 2018 23:44:42: 7000000 INFO @ Wed, 12 Dec 2018 23:44:53: 8000000 INFO @ Wed, 12 Dec 2018 23:44:54: 8000000 INFO @ Wed, 12 Dec 2018 23:44:54: 7000000 INFO @ Wed, 12 Dec 2018 23:45:03: 9000000 INFO @ Wed, 12 Dec 2018 23:45:10: 9000000 INFO @ Wed, 12 Dec 2018 23:45:12: 8000000 INFO @ Wed, 12 Dec 2018 23:45:14: 10000000 INFO @ Wed, 12 Dec 2018 23:45:22: 10000000 INFO @ Wed, 12 Dec 2018 23:45:23: 11000000 INFO @ Wed, 12 Dec 2018 23:45:25: 9000000 INFO @ Wed, 12 Dec 2018 23:45:33: 12000000 INFO @ Wed, 12 Dec 2018 23:45:36: 11000000 INFO @ Wed, 12 Dec 2018 23:45:37: 10000000 INFO @ Wed, 12 Dec 2018 23:45:42: 13000000 INFO @ Wed, 12 Dec 2018 23:45:50: 12000000 INFO @ Wed, 12 Dec 2018 23:45:51: 11000000 INFO @ Wed, 12 Dec 2018 23:45:58: 14000000 INFO @ Wed, 12 Dec 2018 23:46:06: 13000000 INFO @ Wed, 12 Dec 2018 23:46:07: 12000000 INFO @ Wed, 12 Dec 2018 23:46:13: 15000000 INFO @ Wed, 12 Dec 2018 23:46:19: 13000000 INFO @ Wed, 12 Dec 2018 23:46:20: 14000000 INFO @ Wed, 12 Dec 2018 23:46:28: 16000000 INFO @ Wed, 12 Dec 2018 23:46:35: 15000000 INFO @ Wed, 12 Dec 2018 23:46:36: 14000000 INFO @ Wed, 12 Dec 2018 23:46:38: 17000000 INFO @ Wed, 12 Dec 2018 23:46:48: 18000000 INFO @ Wed, 12 Dec 2018 23:46:49: 16000000 INFO @ Wed, 12 Dec 2018 23:46:50: 15000000 INFO @ Wed, 12 Dec 2018 23:46:57: 19000000 INFO @ Wed, 12 Dec 2018 23:47:02: 17000000 INFO @ Wed, 12 Dec 2018 23:47:02: 16000000 INFO @ Wed, 12 Dec 2018 23:47:06: 20000000 INFO @ Wed, 12 Dec 2018 23:47:15: 18000000 INFO @ Wed, 12 Dec 2018 23:47:16: 17000000 INFO @ Wed, 12 Dec 2018 23:47:17: 21000000 INFO @ Wed, 12 Dec 2018 23:47:28: 22000000 INFO @ Wed, 12 Dec 2018 23:47:31: 19000000 INFO @ Wed, 12 Dec 2018 23:47:35: 18000000 INFO @ Wed, 12 Dec 2018 23:47:40: 23000000 INFO @ Wed, 12 Dec 2018 23:47:41: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:47:41: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:47:41: #1 total tags in treatment: 23042284 INFO @ Wed, 12 Dec 2018 23:47:41: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:47:41: #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 23:47:41: #1 tags after filtering in treatment: 23042153 INFO @ Wed, 12 Dec 2018 23:47:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:47:41: #1 finished! INFO @ Wed, 12 Dec 2018 23:47:41: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:47:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:47:44: #2 number of paired peaks: 5312 INFO @ Wed, 12 Dec 2018 23:47:44: start model_add_line... INFO @ Wed, 12 Dec 2018 23:47:45: start X-correlation... INFO @ Wed, 12 Dec 2018 23:47:45: end of X-cor INFO @ Wed, 12 Dec 2018 23:47:45: #2 finished! INFO @ Wed, 12 Dec 2018 23:47:45: #2 predicted fragment length is 50 bps INFO @ Wed, 12 Dec 2018 23:47:45: #2 alternative fragment length(s) may be 50,219,566 bps INFO @ Wed, 12 Dec 2018 23:47:45: #2.2 Generate R script for model : SRX3657367.10_model.r WARNING @ Wed, 12 Dec 2018 23:47:45: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:47:45: #2 You may need to consider one of the other alternative d(s): 50,219,566 WARNING @ Wed, 12 Dec 2018 23:47:45: #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 23:47:45: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:47:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:47:48: 20000000 INFO @ Wed, 12 Dec 2018 23:47:49: 19000000 INFO @ Wed, 12 Dec 2018 23:48:02: 20000000 INFO @ Wed, 12 Dec 2018 23:48:07: 21000000 INFO @ Wed, 12 Dec 2018 23:48:19: 21000000 INFO @ Wed, 12 Dec 2018 23:48:23: 22000000 INFO @ Wed, 12 Dec 2018 23:48:34: 22000000 INFO @ Wed, 12 Dec 2018 23:48:38: 23000000 INFO @ Wed, 12 Dec 2018 23:48:39: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:48:39: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:48:39: #1 total tags in treatment: 23042284 INFO @ Wed, 12 Dec 2018 23:48:39: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:48:39: #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 23:48:40: #1 tags after filtering in treatment: 23042153 INFO @ Wed, 12 Dec 2018 23:48:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:48:40: #1 finished! INFO @ Wed, 12 Dec 2018 23:48:40: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:48:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:48:43: #2 number of paired peaks: 5312 INFO @ Wed, 12 Dec 2018 23:48:43: start model_add_line... INFO @ Wed, 12 Dec 2018 23:48:43: start X-correlation... INFO @ Wed, 12 Dec 2018 23:48:43: end of X-cor INFO @ Wed, 12 Dec 2018 23:48:43: #2 finished! INFO @ Wed, 12 Dec 2018 23:48:43: #2 predicted fragment length is 50 bps INFO @ Wed, 12 Dec 2018 23:48:43: #2 alternative fragment length(s) may be 50,219,566 bps INFO @ Wed, 12 Dec 2018 23:48:43: #2.2 Generate R script for model : SRX3657367.20_model.r WARNING @ Wed, 12 Dec 2018 23:48:43: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:48:43: #2 You may need to consider one of the other alternative d(s): 50,219,566 WARNING @ Wed, 12 Dec 2018 23:48:43: #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 23:48:43: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:48:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:48:51: 23000000 INFO @ Wed, 12 Dec 2018 23:48:51: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:48:52: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:48:52: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:48:52: #1 total tags in treatment: 23042284 INFO @ Wed, 12 Dec 2018 23:48:52: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:48:52: #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 23:48:52: #1 tags after filtering in treatment: 23042153 INFO @ Wed, 12 Dec 2018 23:48:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:48:52: #1 finished! INFO @ Wed, 12 Dec 2018 23:48:52: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:48:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:48:55: #2 number of paired peaks: 5312 INFO @ Wed, 12 Dec 2018 23:48:55: start model_add_line... INFO @ Wed, 12 Dec 2018 23:48:56: start X-correlation... INFO @ Wed, 12 Dec 2018 23:48:56: end of X-cor INFO @ Wed, 12 Dec 2018 23:48:56: #2 finished! INFO @ Wed, 12 Dec 2018 23:48:56: #2 predicted fragment length is 50 bps INFO @ Wed, 12 Dec 2018 23:48:56: #2 alternative fragment length(s) may be 50,219,566 bps INFO @ Wed, 12 Dec 2018 23:48:56: #2.2 Generate R script for model : SRX3657367.05_model.r WARNING @ Wed, 12 Dec 2018 23:48:56: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:48:56: #2 You may need to consider one of the other alternative d(s): 50,219,566 WARNING @ Wed, 12 Dec 2018 23:48:56: #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 23:48:56: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:48:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:49:30: #4 Write output xls file... SRX3657367.10_peaks.xls INFO @ Wed, 12 Dec 2018 23:49:30: #4 Write peak in narrowPeak format file... SRX3657367.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:49:30: #4 Write summits bed file... SRX3657367.10_summits.bed INFO @ Wed, 12 Dec 2018 23:49:30: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (934 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:49:50: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:50:03: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:50:29: #4 Write output xls file... SRX3657367.20_peaks.xls INFO @ Wed, 12 Dec 2018 23:50:29: #4 Write peak in narrowPeak format file... SRX3657367.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:50:29: #4 Write summits bed file... SRX3657367.20_summits.bed INFO @ Wed, 12 Dec 2018 23:50:29: Done! pass1 - making usageList (34 chroms): 3 millis pass2 - checking and writing primary data (458 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:50:46: #4 Write output xls file... SRX3657367.05_peaks.xls INFO @ Wed, 12 Dec 2018 23:50:46: #4 Write peak in narrowPeak format file... SRX3657367.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:50:46: #4 Write summits bed file... SRX3657367.05_summits.bed INFO @ Wed, 12 Dec 2018 23:50:46: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (1567 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。