Job ID = 2640596 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,700,372 reads read : 43,400,744 reads written : 21,700,372 reads 0-length : 21,700,372 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:01 Multiseed full-index search: 00:18:25 21700372 reads; of these: 21700372 (100.00%) were unpaired; of these: 514140 (2.37%) aligned 0 times 15527937 (71.56%) aligned exactly 1 time 5658295 (26.07%) aligned >1 times 97.63% overall alignment rate Time searching: 00:18:28 Overall time: 00:18:28 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] 9700178 / 21186232 = 0.4579 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:26:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.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, 24 Aug 2019 18:26:21: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:26:21: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:26:27: 1000000 INFO @ Sat, 24 Aug 2019 18:26:35: 2000000 INFO @ Sat, 24 Aug 2019 18:26:43: 3000000 INFO @ Sat, 24 Aug 2019 18:26:51: 4000000 INFO @ Sat, 24 Aug 2019 18:26:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.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, 24 Aug 2019 18:26:51: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:26:51: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:26:58: 5000000 INFO @ Sat, 24 Aug 2019 18:26:59: 1000000 INFO @ Sat, 24 Aug 2019 18:27:07: 6000000 INFO @ Sat, 24 Aug 2019 18:27:07: 2000000 INFO @ Sat, 24 Aug 2019 18:27:14: 7000000 INFO @ Sat, 24 Aug 2019 18:27:15: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:27:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.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, 24 Aug 2019 18:27:21: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:27:21: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:27:22: 8000000 INFO @ Sat, 24 Aug 2019 18:27:22: 4000000 INFO @ Sat, 24 Aug 2019 18:27:28: 1000000 INFO @ Sat, 24 Aug 2019 18:27:29: 9000000 INFO @ Sat, 24 Aug 2019 18:27:30: 5000000 INFO @ Sat, 24 Aug 2019 18:27:35: 2000000 INFO @ Sat, 24 Aug 2019 18:27:37: 10000000 INFO @ Sat, 24 Aug 2019 18:27:38: 6000000 INFO @ Sat, 24 Aug 2019 18:27:44: 3000000 INFO @ Sat, 24 Aug 2019 18:27:45: 11000000 INFO @ Sat, 24 Aug 2019 18:27:45: 7000000 INFO @ Sat, 24 Aug 2019 18:27:49: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:27:49: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:27:49: #1 total tags in treatment: 11486054 INFO @ Sat, 24 Aug 2019 18:27:49: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:27:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:27:49: #1 tags after filtering in treatment: 11485870 INFO @ Sat, 24 Aug 2019 18:27:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:27:49: #1 finished! INFO @ Sat, 24 Aug 2019 18:27:49: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:27:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:27:51: #2 number of paired peaks: 12240 INFO @ Sat, 24 Aug 2019 18:27:51: start model_add_line... INFO @ Sat, 24 Aug 2019 18:27:51: start X-correlation... INFO @ Sat, 24 Aug 2019 18:27:51: end of X-cor INFO @ Sat, 24 Aug 2019 18:27:51: #2 finished! INFO @ Sat, 24 Aug 2019 18:27:51: #2 predicted fragment length is 53 bps INFO @ Sat, 24 Aug 2019 18:27:51: #2 alternative fragment length(s) may be 53,104,577 bps INFO @ Sat, 24 Aug 2019 18:27:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.05_model.r WARNING @ Sat, 24 Aug 2019 18:27:51: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:27:51: #2 You may need to consider one of the other alternative d(s): 53,104,577 WARNING @ Sat, 24 Aug 2019 18:27:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 18:27:51: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:27:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:27:52: 4000000 INFO @ Sat, 24 Aug 2019 18:27:52: 8000000 INFO @ Sat, 24 Aug 2019 18:27:59: 9000000 INFO @ Sat, 24 Aug 2019 18:28:00: 5000000 INFO @ Sat, 24 Aug 2019 18:28:06: 10000000 INFO @ Sat, 24 Aug 2019 18:28:09: 6000000 INFO @ Sat, 24 Aug 2019 18:28:13: 11000000 INFO @ Sat, 24 Aug 2019 18:28:16: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:28:16: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:28:16: #1 total tags in treatment: 11486054 INFO @ Sat, 24 Aug 2019 18:28:16: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:28:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:28:16: 7000000 INFO @ Sat, 24 Aug 2019 18:28:17: #1 tags after filtering in treatment: 11485870 INFO @ Sat, 24 Aug 2019 18:28:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:28:17: #1 finished! INFO @ Sat, 24 Aug 2019 18:28:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:28:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:28:18: #2 number of paired peaks: 12240 INFO @ Sat, 24 Aug 2019 18:28:18: start model_add_line... INFO @ Sat, 24 Aug 2019 18:28:19: start X-correlation... INFO @ Sat, 24 Aug 2019 18:28:19: end of X-cor INFO @ Sat, 24 Aug 2019 18:28:19: #2 finished! INFO @ Sat, 24 Aug 2019 18:28:19: #2 predicted fragment length is 53 bps INFO @ Sat, 24 Aug 2019 18:28:19: #2 alternative fragment length(s) may be 53,104,577 bps INFO @ Sat, 24 Aug 2019 18:28:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.10_model.r WARNING @ Sat, 24 Aug 2019 18:28:19: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:28:19: #2 You may need to consider one of the other alternative d(s): 53,104,577 WARNING @ Sat, 24 Aug 2019 18:28:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 18:28:19: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:28:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:28:25: 8000000 INFO @ Sat, 24 Aug 2019 18:28:28: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:28:33: 9000000 INFO @ Sat, 24 Aug 2019 18:28:41: 10000000 INFO @ Sat, 24 Aug 2019 18:28:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:28:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:28:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.05_summits.bed INFO @ Sat, 24 Aug 2019 18:28:47: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (1006 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:28:49: 11000000 INFO @ Sat, 24 Aug 2019 18:28:53: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:28:53: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:28:53: #1 total tags in treatment: 11486054 INFO @ Sat, 24 Aug 2019 18:28:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:28:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:28:54: #1 tags after filtering in treatment: 11485870 INFO @ Sat, 24 Aug 2019 18:28:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:28:54: #1 finished! INFO @ Sat, 24 Aug 2019 18:28:54: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:28:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:28:55: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:28:56: #2 number of paired peaks: 12240 INFO @ Sat, 24 Aug 2019 18:28:56: start model_add_line... INFO @ Sat, 24 Aug 2019 18:28:56: start X-correlation... INFO @ Sat, 24 Aug 2019 18:28:56: end of X-cor INFO @ Sat, 24 Aug 2019 18:28:56: #2 finished! INFO @ Sat, 24 Aug 2019 18:28:56: #2 predicted fragment length is 53 bps INFO @ Sat, 24 Aug 2019 18:28:56: #2 alternative fragment length(s) may be 53,104,577 bps INFO @ Sat, 24 Aug 2019 18:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.20_model.r WARNING @ Sat, 24 Aug 2019 18:28:56: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:28:56: #2 You may need to consider one of the other alternative d(s): 53,104,577 WARNING @ Sat, 24 Aug 2019 18:28:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 18:28:56: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:29:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:29:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:29:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.10_summits.bed INFO @ Sat, 24 Aug 2019 18:29:14: Done! pass1 - making usageList (29 chroms): 2 millis pass2 - checking and writing primary data (585 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:29:32: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:29:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:29:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:29:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375030/SRX5375030.20_summits.bed INFO @ Sat, 24 Aug 2019 18:29:52: Done! pass1 - making usageList (23 chroms): 1 millis pass2 - checking and writing primary data (270 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。