Job ID = 2640728 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,068,609 reads read : 26,068,609 reads written : 26,068,609 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1302422.sra.cache’: 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: 00:11:12 26068609 reads; of these: 26068609 (100.00%) were unpaired; of these: 5153434 (19.77%) aligned 0 times 15211979 (58.35%) aligned exactly 1 time 5703196 (21.88%) aligned >1 times 80.23% overall alignment rate Time searching: 00:11:15 Overall time: 00:11:15 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 8 files... [bam_rmdupse_core] 3673500 / 20915175 = 0.1756 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:53:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.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 18:53:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:53:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:53:47: 1000000 INFO @ Sat, 24 Aug 2019 18:53:56: 2000000 INFO @ Sat, 24 Aug 2019 18:54:06: 3000000 INFO @ Sat, 24 Aug 2019 18:54:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.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 18:54:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:54:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:54:16: 4000000 INFO @ Sat, 24 Aug 2019 18:54:19: 1000000 INFO @ Sat, 24 Aug 2019 18:54:26: 5000000 INFO @ Sat, 24 Aug 2019 18:54:29: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:54:36: 6000000 INFO @ Sat, 24 Aug 2019 18:54:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.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 18:54:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:54:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:54:40: 3000000 INFO @ Sat, 24 Aug 2019 18:54:46: 1000000 INFO @ Sat, 24 Aug 2019 18:54:46: 7000000 INFO @ Sat, 24 Aug 2019 18:54:50: 4000000 INFO @ Sat, 24 Aug 2019 18:54:53: 2000000 INFO @ Sat, 24 Aug 2019 18:54:56: 8000000 INFO @ Sat, 24 Aug 2019 18:55:01: 3000000 INFO @ Sat, 24 Aug 2019 18:55:01: 5000000 INFO @ Sat, 24 Aug 2019 18:55:06: 9000000 INFO @ Sat, 24 Aug 2019 18:55:08: 4000000 INFO @ Sat, 24 Aug 2019 18:55:11: 6000000 INFO @ Sat, 24 Aug 2019 18:55:15: 10000000 INFO @ Sat, 24 Aug 2019 18:55:16: 5000000 INFO @ Sat, 24 Aug 2019 18:55:21: 7000000 INFO @ Sat, 24 Aug 2019 18:55:23: 6000000 INFO @ Sat, 24 Aug 2019 18:55:23: 11000000 INFO @ Sat, 24 Aug 2019 18:55:30: 7000000 INFO @ Sat, 24 Aug 2019 18:55:31: 8000000 INFO @ Sat, 24 Aug 2019 18:55:32: 12000000 INFO @ Sat, 24 Aug 2019 18:55:38: 8000000 INFO @ Sat, 24 Aug 2019 18:55:41: 9000000 INFO @ Sat, 24 Aug 2019 18:55:41: 13000000 INFO @ Sat, 24 Aug 2019 18:55:45: 9000000 INFO @ Sat, 24 Aug 2019 18:55:51: 10000000 INFO @ Sat, 24 Aug 2019 18:55:51: 14000000 INFO @ Sat, 24 Aug 2019 18:55:53: 10000000 INFO @ Sat, 24 Aug 2019 18:56:00: 11000000 INFO @ Sat, 24 Aug 2019 18:56:01: 15000000 INFO @ Sat, 24 Aug 2019 18:56:02: 11000000 INFO @ Sat, 24 Aug 2019 18:56:08: 12000000 INFO @ Sat, 24 Aug 2019 18:56:10: 16000000 INFO @ Sat, 24 Aug 2019 18:56:12: 12000000 INFO @ Sat, 24 Aug 2019 18:56:15: 13000000 INFO @ Sat, 24 Aug 2019 18:56:19: 17000000 INFO @ Sat, 24 Aug 2019 18:56:21: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 18:56:21: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 18:56:21: #1 total tags in treatment: 17241675 INFO @ Sat, 24 Aug 2019 18:56:21: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:56:21: #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 18:56:22: #1 tags after filtering in treatment: 17241525 INFO @ Sat, 24 Aug 2019 18:56:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:56:22: #1 finished! INFO @ Sat, 24 Aug 2019 18:56:22: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:56:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:56:22: 13000000 INFO @ Sat, 24 Aug 2019 18:56:22: 14000000 INFO @ Sat, 24 Aug 2019 18:56:24: #2 number of paired peaks: 12234 INFO @ Sat, 24 Aug 2019 18:56:24: start model_add_line... INFO @ Sat, 24 Aug 2019 18:56:24: start X-correlation... INFO @ Sat, 24 Aug 2019 18:56:24: end of X-cor INFO @ Sat, 24 Aug 2019 18:56:24: #2 finished! INFO @ Sat, 24 Aug 2019 18:56:24: #2 predicted fragment length is 43 bps INFO @ Sat, 24 Aug 2019 18:56:24: #2 alternative fragment length(s) may be 43 bps INFO @ Sat, 24 Aug 2019 18:56:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.05_model.r WARNING @ Sat, 24 Aug 2019 18:56:24: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:56:24: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Sat, 24 Aug 2019 18:56:24: #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 18:56:24: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:56:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:56:30: 15000000 INFO @ Sat, 24 Aug 2019 18:56:32: 14000000 INFO @ Sat, 24 Aug 2019 18:56:37: 16000000 INFO @ Sat, 24 Aug 2019 18:56:41: 15000000 INFO @ Sat, 24 Aug 2019 18:56:45: 17000000 INFO @ Sat, 24 Aug 2019 18:56:47: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 18:56:47: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 18:56:47: #1 total tags in treatment: 17241675 INFO @ Sat, 24 Aug 2019 18:56:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:56:47: #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 18:56:47: #1 tags after filtering in treatment: 17241525 INFO @ Sat, 24 Aug 2019 18:56:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:56:47: #1 finished! INFO @ Sat, 24 Aug 2019 18:56:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:56:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:56:50: #2 number of paired peaks: 12234 INFO @ Sat, 24 Aug 2019 18:56:50: start model_add_line... INFO @ Sat, 24 Aug 2019 18:56:50: start X-correlation... INFO @ Sat, 24 Aug 2019 18:56:50: end of X-cor INFO @ Sat, 24 Aug 2019 18:56:50: #2 finished! INFO @ Sat, 24 Aug 2019 18:56:50: #2 predicted fragment length is 43 bps INFO @ Sat, 24 Aug 2019 18:56:50: #2 alternative fragment length(s) may be 43 bps INFO @ Sat, 24 Aug 2019 18:56:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.20_model.r WARNING @ Sat, 24 Aug 2019 18:56:50: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:56:50: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Sat, 24 Aug 2019 18:56:50: #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 18:56:50: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:56:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:56:51: 16000000 INFO @ Sat, 24 Aug 2019 18:57:00: 17000000 INFO @ Sat, 24 Aug 2019 18:57:02: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 18:57:02: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 18:57:02: #1 total tags in treatment: 17241675 INFO @ Sat, 24 Aug 2019 18:57:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:57:02: #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 18:57:03: #1 tags after filtering in treatment: 17241525 INFO @ Sat, 24 Aug 2019 18:57:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:57:03: #1 finished! INFO @ Sat, 24 Aug 2019 18:57:03: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:57:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:57:05: #2 number of paired peaks: 12234 INFO @ Sat, 24 Aug 2019 18:57:05: start model_add_line... INFO @ Sat, 24 Aug 2019 18:57:05: start X-correlation... INFO @ Sat, 24 Aug 2019 18:57:05: end of X-cor INFO @ Sat, 24 Aug 2019 18:57:05: #2 finished! INFO @ Sat, 24 Aug 2019 18:57:05: #2 predicted fragment length is 43 bps INFO @ Sat, 24 Aug 2019 18:57:05: #2 alternative fragment length(s) may be 43 bps INFO @ Sat, 24 Aug 2019 18:57:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.10_model.r WARNING @ Sat, 24 Aug 2019 18:57:05: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:57:05: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Sat, 24 Aug 2019 18:57:05: #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 18:57:05: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:57:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:57:18: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:57:44: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:57:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:57:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:57:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.05_summits.bed INFO @ Sat, 24 Aug 2019 18:57:44: Done! pass1 - making usageList (67 chroms): 2 millis pass2 - checking and writing primary data (1749 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:58:00: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:58:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:58:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:58:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.20_summits.bed INFO @ Sat, 24 Aug 2019 18:58:10: Done! pass1 - making usageList (49 chroms): 2 millis pass2 - checking and writing primary data (484 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:58:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:58:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:58:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555172/SRX555172.10_summits.bed INFO @ Sat, 24 Aug 2019 18:58:26: Done! pass1 - making usageList (60 chroms): 2 millis pass2 - checking and writing primary data (1041 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。