Job ID = 1291517 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,990,405 reads read : 27,990,405 reads written : 27,990,405 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: 00:04:45 27990405 reads; of these: 27990405 (100.00%) were unpaired; of these: 5469967 (19.54%) aligned 0 times 18596413 (66.44%) aligned exactly 1 time 3924025 (14.02%) aligned >1 times 80.46% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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 8 files... [bam_rmdupse_core] 2739087 / 22520438 = 0.1216 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 16:13:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.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 16:13:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:13:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:13:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.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 16:13:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:13:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:13:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.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 16:13:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:13:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:13:56: 1000000 INFO @ Sun, 02 Jun 2019 16:13:57: 1000000 INFO @ Sun, 02 Jun 2019 16:13:58: 1000000 INFO @ Sun, 02 Jun 2019 16:14:03: 2000000 INFO @ Sun, 02 Jun 2019 16:14:06: 2000000 INFO @ Sun, 02 Jun 2019 16:14:06: 2000000 INFO @ Sun, 02 Jun 2019 16:14:11: 3000000 INFO @ Sun, 02 Jun 2019 16:14:14: 3000000 INFO @ Sun, 02 Jun 2019 16:14:15: 3000000 INFO @ Sun, 02 Jun 2019 16:14:18: 4000000 INFO @ Sun, 02 Jun 2019 16:14:22: 4000000 INFO @ Sun, 02 Jun 2019 16:14:23: 4000000 INFO @ Sun, 02 Jun 2019 16:14:25: 5000000 INFO @ Sun, 02 Jun 2019 16:14:30: 5000000 INFO @ Sun, 02 Jun 2019 16:14:32: 5000000 INFO @ Sun, 02 Jun 2019 16:14:32: 6000000 INFO @ Sun, 02 Jun 2019 16:14:38: 6000000 INFO @ Sun, 02 Jun 2019 16:14:39: 7000000 INFO @ Sun, 02 Jun 2019 16:14:40: 6000000 INFO @ Sun, 02 Jun 2019 16:14:46: 7000000 INFO @ Sun, 02 Jun 2019 16:14:47: 8000000 INFO @ Sun, 02 Jun 2019 16:14:48: 7000000 INFO @ Sun, 02 Jun 2019 16:14:54: 8000000 INFO @ Sun, 02 Jun 2019 16:14:54: 9000000 INFO @ Sun, 02 Jun 2019 16:14:57: 8000000 INFO @ Sun, 02 Jun 2019 16:15:01: 10000000 INFO @ Sun, 02 Jun 2019 16:15:02: 9000000 INFO @ Sun, 02 Jun 2019 16:15:05: 9000000 INFO @ Sun, 02 Jun 2019 16:15:08: 11000000 INFO @ Sun, 02 Jun 2019 16:15:10: 10000000 INFO @ Sun, 02 Jun 2019 16:15:13: 10000000 INFO @ Sun, 02 Jun 2019 16:15:16: 12000000 INFO @ Sun, 02 Jun 2019 16:15:18: 11000000 INFO @ Sun, 02 Jun 2019 16:15:21: 11000000 INFO @ Sun, 02 Jun 2019 16:15:23: 13000000 INFO @ Sun, 02 Jun 2019 16:15:25: 12000000 INFO @ Sun, 02 Jun 2019 16:15:30: 12000000 INFO @ Sun, 02 Jun 2019 16:15:30: 14000000 INFO @ Sun, 02 Jun 2019 16:15:33: 13000000 INFO @ Sun, 02 Jun 2019 16:15:37: 15000000 INFO @ Sun, 02 Jun 2019 16:15:38: 13000000 INFO @ Sun, 02 Jun 2019 16:15:41: 14000000 INFO @ Sun, 02 Jun 2019 16:15:45: 16000000 INFO @ Sun, 02 Jun 2019 16:15:46: 14000000 INFO @ Sun, 02 Jun 2019 16:15:49: 15000000 INFO @ Sun, 02 Jun 2019 16:15:52: 17000000 INFO @ Sun, 02 Jun 2019 16:15:54: 15000000 INFO @ Sun, 02 Jun 2019 16:15:57: 16000000 INFO @ Sun, 02 Jun 2019 16:15:59: 18000000 INFO @ Sun, 02 Jun 2019 16:16:03: 16000000 INFO @ Sun, 02 Jun 2019 16:16:05: 17000000 INFO @ Sun, 02 Jun 2019 16:16:07: 19000000 INFO @ Sun, 02 Jun 2019 16:16:11: 17000000 INFO @ Sun, 02 Jun 2019 16:16:12: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:16:12: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:16:12: #1 total tags in treatment: 19781351 INFO @ Sun, 02 Jun 2019 16:16:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:16:12: #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 16:16:13: 18000000 INFO @ Sun, 02 Jun 2019 16:16:13: #1 tags after filtering in treatment: 19781351 INFO @ Sun, 02 Jun 2019 16:16:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:16:13: #1 finished! INFO @ Sun, 02 Jun 2019 16:16:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:16:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:16:15: #2 number of paired peaks: 184 WARNING @ Sun, 02 Jun 2019 16:16:15: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Sun, 02 Jun 2019 16:16:15: start model_add_line... INFO @ Sun, 02 Jun 2019 16:16:15: start X-correlation... INFO @ Sun, 02 Jun 2019 16:16:15: end of X-cor INFO @ Sun, 02 Jun 2019 16:16:15: #2 finished! INFO @ Sun, 02 Jun 2019 16:16:15: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:16:15: #2 alternative fragment length(s) may be 1,31,533,566,597 bps INFO @ Sun, 02 Jun 2019 16:16:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.10_model.r WARNING @ Sun, 02 Jun 2019 16:16:15: #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 16:16:15: #2 You may need to consider one of the other alternative d(s): 1,31,533,566,597 WARNING @ Sun, 02 Jun 2019 16:16:15: #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 16:16:15: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:16:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:16:19: 18000000 INFO @ Sun, 02 Jun 2019 16:16:21: 19000000 INFO @ Sun, 02 Jun 2019 16:16:27: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:16:27: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:16:27: #1 total tags in treatment: 19781351 INFO @ Sun, 02 Jun 2019 16:16:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:16:27: #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 16:16:27: 19000000 INFO @ Sun, 02 Jun 2019 16:16:28: #1 tags after filtering in treatment: 19781351 INFO @ Sun, 02 Jun 2019 16:16:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:16:28: #1 finished! INFO @ Sun, 02 Jun 2019 16:16:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:16:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:16:29: #2 number of paired peaks: 184 WARNING @ Sun, 02 Jun 2019 16:16:29: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Sun, 02 Jun 2019 16:16:29: start model_add_line... INFO @ Sun, 02 Jun 2019 16:16:29: start X-correlation... INFO @ Sun, 02 Jun 2019 16:16:29: end of X-cor INFO @ Sun, 02 Jun 2019 16:16:29: #2 finished! INFO @ Sun, 02 Jun 2019 16:16:29: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:16:29: #2 alternative fragment length(s) may be 1,31,533,566,597 bps INFO @ Sun, 02 Jun 2019 16:16:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.20_model.r WARNING @ Sun, 02 Jun 2019 16:16:29: #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 16:16:29: #2 You may need to consider one of the other alternative d(s): 1,31,533,566,597 WARNING @ Sun, 02 Jun 2019 16:16:29: #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 16:16:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:16:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:16:34: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:16:34: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:16:34: #1 total tags in treatment: 19781351 INFO @ Sun, 02 Jun 2019 16:16:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:16:34: #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 16:16:34: #1 tags after filtering in treatment: 19781351 INFO @ Sun, 02 Jun 2019 16:16:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:16:34: #1 finished! INFO @ Sun, 02 Jun 2019 16:16:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:16:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:16:36: #2 number of paired peaks: 184 WARNING @ Sun, 02 Jun 2019 16:16:36: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Sun, 02 Jun 2019 16:16:36: start model_add_line... INFO @ Sun, 02 Jun 2019 16:16:36: start X-correlation... INFO @ Sun, 02 Jun 2019 16:16:36: end of X-cor INFO @ Sun, 02 Jun 2019 16:16:36: #2 finished! INFO @ Sun, 02 Jun 2019 16:16:36: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:16:36: #2 alternative fragment length(s) may be 1,31,533,566,597 bps INFO @ Sun, 02 Jun 2019 16:16:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.05_model.r WARNING @ Sun, 02 Jun 2019 16:16:36: #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 16:16:36: #2 You may need to consider one of the other alternative d(s): 1,31,533,566,597 WARNING @ Sun, 02 Jun 2019 16:16:36: #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 16:16:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:16:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:16:57: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:17:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:17:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:17:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:17:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.10_summits.bed INFO @ Sun, 02 Jun 2019 16:17:17: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:17:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:17:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:17:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:17:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.20_summits.bed INFO @ Sun, 02 Jun 2019 16:17:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:17:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:17:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:17:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX105310/SRX105310.05_summits.bed INFO @ Sun, 02 Jun 2019 16:17:38: 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。