Job ID = 1293149 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,869,622 reads read : 24,869,622 reads written : 24,869,622 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:31 24869622 reads; of these: 24869622 (100.00%) were unpaired; of these: 3248456 (13.06%) aligned 0 times 18835798 (75.74%) aligned exactly 1 time 2785368 (11.20%) aligned >1 times 86.94% overall alignment rate Time searching: 00:05:31 Overall time: 00:05:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3688797 / 21621166 = 0.1706 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 @ Sun, 02 Jun 2019 22:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 22:23:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:23:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 22:23:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:23:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 22:23:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:23:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:23:27: 1000000 INFO @ Sun, 02 Jun 2019 22:23:28: 1000000 INFO @ Sun, 02 Jun 2019 22:23:28: 1000000 INFO @ Sun, 02 Jun 2019 22:23:36: 2000000 INFO @ Sun, 02 Jun 2019 22:23:37: 2000000 INFO @ Sun, 02 Jun 2019 22:23:37: 2000000 INFO @ Sun, 02 Jun 2019 22:23:44: 3000000 INFO @ Sun, 02 Jun 2019 22:23:46: 3000000 INFO @ Sun, 02 Jun 2019 22:23:47: 3000000 INFO @ Sun, 02 Jun 2019 22:23:53: 4000000 INFO @ Sun, 02 Jun 2019 22:23:56: 4000000 INFO @ Sun, 02 Jun 2019 22:23:56: 4000000 INFO @ Sun, 02 Jun 2019 22:24:02: 5000000 INFO @ Sun, 02 Jun 2019 22:24:05: 5000000 INFO @ Sun, 02 Jun 2019 22:24:06: 5000000 INFO @ Sun, 02 Jun 2019 22:24:11: 6000000 INFO @ Sun, 02 Jun 2019 22:24:13: 6000000 INFO @ Sun, 02 Jun 2019 22:24:15: 6000000 INFO @ Sun, 02 Jun 2019 22:24:19: 7000000 INFO @ Sun, 02 Jun 2019 22:24:23: 7000000 INFO @ Sun, 02 Jun 2019 22:24:24: 7000000 INFO @ Sun, 02 Jun 2019 22:24:28: 8000000 INFO @ Sun, 02 Jun 2019 22:24:31: 8000000 INFO @ Sun, 02 Jun 2019 22:24:34: 8000000 INFO @ Sun, 02 Jun 2019 22:24:37: 9000000 INFO @ Sun, 02 Jun 2019 22:24:40: 9000000 INFO @ Sun, 02 Jun 2019 22:24:43: 9000000 INFO @ Sun, 02 Jun 2019 22:24:45: 10000000 INFO @ Sun, 02 Jun 2019 22:24:49: 10000000 INFO @ Sun, 02 Jun 2019 22:24:52: 10000000 INFO @ Sun, 02 Jun 2019 22:24:54: 11000000 INFO @ Sun, 02 Jun 2019 22:24:58: 11000000 INFO @ Sun, 02 Jun 2019 22:25:02: 11000000 INFO @ Sun, 02 Jun 2019 22:25:03: 12000000 INFO @ Sun, 02 Jun 2019 22:25:09: 12000000 INFO @ Sun, 02 Jun 2019 22:25:11: 12000000 INFO @ Sun, 02 Jun 2019 22:25:12: 13000000 INFO @ Sun, 02 Jun 2019 22:25:18: 13000000 INFO @ Sun, 02 Jun 2019 22:25:20: 14000000 INFO @ Sun, 02 Jun 2019 22:25:20: 13000000 INFO @ Sun, 02 Jun 2019 22:25:27: 14000000 INFO @ Sun, 02 Jun 2019 22:25:29: 15000000 INFO @ Sun, 02 Jun 2019 22:25:30: 14000000 INFO @ Sun, 02 Jun 2019 22:25:37: 15000000 INFO @ Sun, 02 Jun 2019 22:25:38: 16000000 INFO @ Sun, 02 Jun 2019 22:25:40: 15000000 INFO @ Sun, 02 Jun 2019 22:25:47: 16000000 INFO @ Sun, 02 Jun 2019 22:25:48: 17000000 INFO @ Sun, 02 Jun 2019 22:25:49: 16000000 INFO @ Sun, 02 Jun 2019 22:25:56: 17000000 INFO @ Sun, 02 Jun 2019 22:25:57: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:25:57: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:25:57: #1 total tags in treatment: 17932369 INFO @ Sun, 02 Jun 2019 22:25:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:25:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:25:57: #1 tags after filtering in treatment: 17932369 INFO @ Sun, 02 Jun 2019 22:25:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:25:57: #1 finished! INFO @ Sun, 02 Jun 2019 22:25:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:25:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:25:58: 17000000 INFO @ Sun, 02 Jun 2019 22:25:59: #2 number of paired peaks: 713 WARNING @ Sun, 02 Jun 2019 22:25:59: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Sun, 02 Jun 2019 22:25:59: start model_add_line... INFO @ Sun, 02 Jun 2019 22:25:59: start X-correlation... INFO @ Sun, 02 Jun 2019 22:25:59: end of X-cor INFO @ Sun, 02 Jun 2019 22:25:59: #2 finished! INFO @ Sun, 02 Jun 2019 22:25:59: #2 predicted fragment length is 80 bps INFO @ Sun, 02 Jun 2019 22:25:59: #2 alternative fragment length(s) may be 3,61,80 bps INFO @ Sun, 02 Jun 2019 22:25:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.10_model.r WARNING @ Sun, 02 Jun 2019 22:25:59: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:25:59: #2 You may need to consider one of the other alternative d(s): 3,61,80 WARNING @ Sun, 02 Jun 2019 22:25:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:25:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:25:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:26:03: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:26:03: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:26:03: #1 total tags in treatment: 17932369 INFO @ Sun, 02 Jun 2019 22:26:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:26:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:26:04: #1 tags after filtering in treatment: 17932369 INFO @ Sun, 02 Jun 2019 22:26:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:26:04: #1 finished! INFO @ Sun, 02 Jun 2019 22:26:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:26:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:26:05: #2 number of paired peaks: 713 WARNING @ Sun, 02 Jun 2019 22:26:05: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Sun, 02 Jun 2019 22:26:05: start model_add_line... INFO @ Sun, 02 Jun 2019 22:26:06: start X-correlation... INFO @ Sun, 02 Jun 2019 22:26:06: end of X-cor INFO @ Sun, 02 Jun 2019 22:26:06: #2 finished! INFO @ Sun, 02 Jun 2019 22:26:06: #2 predicted fragment length is 80 bps INFO @ Sun, 02 Jun 2019 22:26:06: #2 alternative fragment length(s) may be 3,61,80 bps INFO @ Sun, 02 Jun 2019 22:26:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.05_model.r WARNING @ Sun, 02 Jun 2019 22:26:06: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:26:06: #2 You may need to consider one of the other alternative d(s): 3,61,80 WARNING @ Sun, 02 Jun 2019 22:26:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:26:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:26:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:26:06: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:26:06: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:26:06: #1 total tags in treatment: 17932369 INFO @ Sun, 02 Jun 2019 22:26:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:26:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:26:06: #1 tags after filtering in treatment: 17932369 INFO @ Sun, 02 Jun 2019 22:26:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:26:06: #1 finished! INFO @ Sun, 02 Jun 2019 22:26:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:26:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:26:08: #2 number of paired peaks: 713 WARNING @ Sun, 02 Jun 2019 22:26:08: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Sun, 02 Jun 2019 22:26:08: start model_add_line... INFO @ Sun, 02 Jun 2019 22:26:08: start X-correlation... INFO @ Sun, 02 Jun 2019 22:26:08: end of X-cor INFO @ Sun, 02 Jun 2019 22:26:08: #2 finished! INFO @ Sun, 02 Jun 2019 22:26:08: #2 predicted fragment length is 80 bps INFO @ Sun, 02 Jun 2019 22:26:08: #2 alternative fragment length(s) may be 3,61,80 bps INFO @ Sun, 02 Jun 2019 22:26:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.20_model.r WARNING @ Sun, 02 Jun 2019 22:26:08: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:26:08: #2 You may need to consider one of the other alternative d(s): 3,61,80 WARNING @ Sun, 02 Jun 2019 22:26:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:26:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:26:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:26:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:26:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:26:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:27:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:27:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:27:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.10_summits.bed INFO @ Sun, 02 Jun 2019 22:27:05: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (7063 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:27:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:27:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:27:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.05_summits.bed INFO @ Sun, 02 Jun 2019 22:27:13: Done! pass1 - making usageList (7 chroms): 6 millis pass2 - checking and writing primary data (14183 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:27:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:27:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:27:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402717/SRX5402717.20_summits.bed INFO @ Sun, 02 Jun 2019 22:27:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1714 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。