Job ID = 1293121 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,711,065 reads read : 30,711,065 reads written : 30,711,065 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: 00:07:29 30711065 reads; of these: 30711065 (100.00%) were unpaired; of these: 4698482 (15.30%) aligned 0 times 19260480 (62.72%) aligned exactly 1 time 6752103 (21.99%) aligned >1 times 84.70% overall alignment rate Time searching: 00:07:29 Overall time: 00:07:29 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] 6554125 / 26012583 = 0.2520 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 22:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.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 22:17:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:17:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.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 22:17:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:17:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.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 22:17:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:17:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:18:06: 1000000 INFO @ Sun, 02 Jun 2019 22:18:07: 1000000 INFO @ Sun, 02 Jun 2019 22:18:08: 1000000 INFO @ Sun, 02 Jun 2019 22:18:15: 2000000 INFO @ Sun, 02 Jun 2019 22:18:17: 2000000 INFO @ Sun, 02 Jun 2019 22:18:17: 2000000 INFO @ Sun, 02 Jun 2019 22:18:23: 3000000 INFO @ Sun, 02 Jun 2019 22:18:27: 3000000 INFO @ Sun, 02 Jun 2019 22:18:27: 3000000 INFO @ Sun, 02 Jun 2019 22:18:31: 4000000 INFO @ Sun, 02 Jun 2019 22:18:36: 4000000 INFO @ Sun, 02 Jun 2019 22:18:37: 4000000 INFO @ Sun, 02 Jun 2019 22:18:38: 5000000 INFO @ Sun, 02 Jun 2019 22:18:46: 5000000 INFO @ Sun, 02 Jun 2019 22:18:46: 6000000 INFO @ Sun, 02 Jun 2019 22:18:47: 5000000 INFO @ Sun, 02 Jun 2019 22:18:54: 7000000 INFO @ Sun, 02 Jun 2019 22:18:56: 6000000 INFO @ Sun, 02 Jun 2019 22:18:57: 6000000 INFO @ Sun, 02 Jun 2019 22:19:01: 8000000 INFO @ Sun, 02 Jun 2019 22:19:05: 7000000 INFO @ Sun, 02 Jun 2019 22:19:07: 7000000 INFO @ Sun, 02 Jun 2019 22:19:10: 9000000 INFO @ Sun, 02 Jun 2019 22:19:15: 8000000 INFO @ Sun, 02 Jun 2019 22:19:17: 8000000 INFO @ Sun, 02 Jun 2019 22:19:17: 10000000 INFO @ Sun, 02 Jun 2019 22:19:25: 9000000 INFO @ Sun, 02 Jun 2019 22:19:26: 11000000 INFO @ Sun, 02 Jun 2019 22:19:27: 9000000 INFO @ Sun, 02 Jun 2019 22:19:34: 12000000 INFO @ Sun, 02 Jun 2019 22:19:34: 10000000 INFO @ Sun, 02 Jun 2019 22:19:36: 10000000 INFO @ Sun, 02 Jun 2019 22:19:42: 13000000 INFO @ Sun, 02 Jun 2019 22:19:43: 11000000 INFO @ Sun, 02 Jun 2019 22:19:46: 11000000 INFO @ Sun, 02 Jun 2019 22:19:50: 14000000 INFO @ Sun, 02 Jun 2019 22:19:53: 12000000 INFO @ Sun, 02 Jun 2019 22:19:56: 12000000 INFO @ Sun, 02 Jun 2019 22:19:58: 15000000 INFO @ Sun, 02 Jun 2019 22:20:02: 13000000 INFO @ Sun, 02 Jun 2019 22:20:06: 16000000 INFO @ Sun, 02 Jun 2019 22:20:06: 13000000 INFO @ Sun, 02 Jun 2019 22:20:12: 14000000 INFO @ Sun, 02 Jun 2019 22:20:14: 17000000 INFO @ Sun, 02 Jun 2019 22:20:17: 14000000 INFO @ Sun, 02 Jun 2019 22:20:22: 15000000 INFO @ Sun, 02 Jun 2019 22:20:22: 18000000 INFO @ Sun, 02 Jun 2019 22:20:27: 15000000 INFO @ Sun, 02 Jun 2019 22:20:30: 19000000 INFO @ Sun, 02 Jun 2019 22:20:31: 16000000 INFO @ Sun, 02 Jun 2019 22:20:34: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:20:34: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:20:34: #1 total tags in treatment: 19458458 INFO @ Sun, 02 Jun 2019 22:20:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:20:34: #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 22:20:35: #1 tags after filtering in treatment: 19458458 INFO @ Sun, 02 Jun 2019 22:20:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:20:35: #1 finished! INFO @ Sun, 02 Jun 2019 22:20:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:20:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:20:36: #2 number of paired peaks: 377 WARNING @ Sun, 02 Jun 2019 22:20:36: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Sun, 02 Jun 2019 22:20:36: start model_add_line... INFO @ Sun, 02 Jun 2019 22:20:37: start X-correlation... INFO @ Sun, 02 Jun 2019 22:20:37: end of X-cor INFO @ Sun, 02 Jun 2019 22:20:37: #2 finished! INFO @ Sun, 02 Jun 2019 22:20:37: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:20:37: #2 alternative fragment length(s) may be 1,30,38,45,577 bps INFO @ Sun, 02 Jun 2019 22:20:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.20_model.r WARNING @ Sun, 02 Jun 2019 22:20:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:20:37: #2 You may need to consider one of the other alternative d(s): 1,30,38,45,577 WARNING @ Sun, 02 Jun 2019 22:20:37: #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 22:20:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:20:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:20:37: 16000000 INFO @ Sun, 02 Jun 2019 22:20:41: 17000000 INFO @ Sun, 02 Jun 2019 22:20:47: 17000000 INFO @ Sun, 02 Jun 2019 22:20:50: 18000000 INFO @ Sun, 02 Jun 2019 22:20:57: 18000000 INFO @ Sun, 02 Jun 2019 22:21:00: 19000000 INFO @ Sun, 02 Jun 2019 22:21:04: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:21:04: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:21:04: #1 total tags in treatment: 19458458 INFO @ Sun, 02 Jun 2019 22:21:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:21:04: #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 22:21:05: #1 tags after filtering in treatment: 19458458 INFO @ Sun, 02 Jun 2019 22:21:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:21:05: #1 finished! INFO @ Sun, 02 Jun 2019 22:21:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:21:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:21:06: #2 number of paired peaks: 377 WARNING @ Sun, 02 Jun 2019 22:21:06: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Sun, 02 Jun 2019 22:21:06: start model_add_line... INFO @ Sun, 02 Jun 2019 22:21:07: start X-correlation... INFO @ Sun, 02 Jun 2019 22:21:07: end of X-cor INFO @ Sun, 02 Jun 2019 22:21:07: #2 finished! INFO @ Sun, 02 Jun 2019 22:21:07: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:21:07: #2 alternative fragment length(s) may be 1,30,38,45,577 bps INFO @ Sun, 02 Jun 2019 22:21:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.05_model.r WARNING @ Sun, 02 Jun 2019 22:21:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:21:07: #2 You may need to consider one of the other alternative d(s): 1,30,38,45,577 WARNING @ Sun, 02 Jun 2019 22:21:07: #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 22:21:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:21:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:21:07: 19000000 INFO @ Sun, 02 Jun 2019 22:21:12: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:21:12: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:21:12: #1 total tags in treatment: 19458458 INFO @ Sun, 02 Jun 2019 22:21:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:21:12: #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 22:21:12: #1 tags after filtering in treatment: 19458458 INFO @ Sun, 02 Jun 2019 22:21:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:21:12: #1 finished! INFO @ Sun, 02 Jun 2019 22:21:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:21:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:21:14: #2 number of paired peaks: 377 WARNING @ Sun, 02 Jun 2019 22:21:14: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Sun, 02 Jun 2019 22:21:14: start model_add_line... INFO @ Sun, 02 Jun 2019 22:21:14: start X-correlation... INFO @ Sun, 02 Jun 2019 22:21:14: end of X-cor INFO @ Sun, 02 Jun 2019 22:21:14: #2 finished! INFO @ Sun, 02 Jun 2019 22:21:14: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:21:14: #2 alternative fragment length(s) may be 1,30,38,45,577 bps INFO @ Sun, 02 Jun 2019 22:21:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.10_model.r WARNING @ Sun, 02 Jun 2019 22:21:14: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:21:14: #2 You may need to consider one of the other alternative d(s): 1,30,38,45,577 WARNING @ Sun, 02 Jun 2019 22:21:14: #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 22:21:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:21:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:21:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:21:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:21:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:21:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.20_summits.bed INFO @ Sun, 02 Jun 2019 22:21:43: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:21:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:22:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:22:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:22:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:22:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.05_summits.bed INFO @ Sun, 02 Jun 2019 22:22:15: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:22:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:22:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:22:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402697/SRX5402697.10_summits.bed INFO @ Sun, 02 Jun 2019 22:22:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。