Job ID = 1291519 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,041,160 reads read : 29,041,160 reads written : 29,041,160 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: 00:05:29 29041160 reads; of these: 29041160 (100.00%) were unpaired; of these: 10751658 (37.02%) aligned 0 times 15212294 (52.38%) aligned exactly 1 time 3077208 (10.60%) aligned >1 times 62.98% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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 8 files... [bam_rmdupse_core] 1906370 / 18289502 = 0.1042 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/SRX105312/SRX105312.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.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/SRX105312/SRX105312.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.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 16:13:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.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 16:13:58: 1000000 INFO @ Sun, 02 Jun 2019 16:13:59: 1000000 INFO @ Sun, 02 Jun 2019 16:13:59: 1000000 INFO @ Sun, 02 Jun 2019 16:14:07: 2000000 INFO @ Sun, 02 Jun 2019 16:14:08: 2000000 INFO @ Sun, 02 Jun 2019 16:14:09: 2000000 INFO @ Sun, 02 Jun 2019 16:14:17: 3000000 INFO @ Sun, 02 Jun 2019 16:14:18: 3000000 INFO @ Sun, 02 Jun 2019 16:14:19: 3000000 INFO @ Sun, 02 Jun 2019 16:14:27: 4000000 INFO @ Sun, 02 Jun 2019 16:14:27: 4000000 INFO @ Sun, 02 Jun 2019 16:14:28: 4000000 INFO @ Sun, 02 Jun 2019 16:14:36: 5000000 INFO @ Sun, 02 Jun 2019 16:14:37: 5000000 INFO @ Sun, 02 Jun 2019 16:14:38: 5000000 INFO @ Sun, 02 Jun 2019 16:14:46: 6000000 INFO @ Sun, 02 Jun 2019 16:14:46: 6000000 INFO @ Sun, 02 Jun 2019 16:14:48: 6000000 INFO @ Sun, 02 Jun 2019 16:14:55: 7000000 INFO @ Sun, 02 Jun 2019 16:14:56: 7000000 INFO @ Sun, 02 Jun 2019 16:14:58: 7000000 INFO @ Sun, 02 Jun 2019 16:15:04: 8000000 INFO @ Sun, 02 Jun 2019 16:15:05: 8000000 INFO @ Sun, 02 Jun 2019 16:15:08: 8000000 INFO @ Sun, 02 Jun 2019 16:15:13: 9000000 INFO @ Sun, 02 Jun 2019 16:15:14: 9000000 INFO @ Sun, 02 Jun 2019 16:15:18: 9000000 INFO @ Sun, 02 Jun 2019 16:15:23: 10000000 INFO @ Sun, 02 Jun 2019 16:15:24: 10000000 INFO @ Sun, 02 Jun 2019 16:15:28: 10000000 INFO @ Sun, 02 Jun 2019 16:15:33: 11000000 INFO @ Sun, 02 Jun 2019 16:15:33: 11000000 INFO @ Sun, 02 Jun 2019 16:15:38: 11000000 INFO @ Sun, 02 Jun 2019 16:15:42: 12000000 INFO @ Sun, 02 Jun 2019 16:15:42: 12000000 INFO @ Sun, 02 Jun 2019 16:15:48: 12000000 INFO @ Sun, 02 Jun 2019 16:15:52: 13000000 INFO @ Sun, 02 Jun 2019 16:15:52: 13000000 INFO @ Sun, 02 Jun 2019 16:15:58: 13000000 INFO @ Sun, 02 Jun 2019 16:16:01: 14000000 INFO @ Sun, 02 Jun 2019 16:16:01: 14000000 INFO @ Sun, 02 Jun 2019 16:16:08: 14000000 INFO @ Sun, 02 Jun 2019 16:16:10: 15000000 INFO @ Sun, 02 Jun 2019 16:16:11: 15000000 INFO @ Sun, 02 Jun 2019 16:16:18: 15000000 INFO @ Sun, 02 Jun 2019 16:16:19: 16000000 INFO @ Sun, 02 Jun 2019 16:16:21: 16000000 INFO @ Sun, 02 Jun 2019 16:16:22: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:16:22: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:16:22: #1 total tags in treatment: 16383132 INFO @ Sun, 02 Jun 2019 16:16:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:16:22: #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 16:16:22: #1 tags after filtering in treatment: 16383132 INFO @ Sun, 02 Jun 2019 16:16:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:16:22: #1 finished! INFO @ Sun, 02 Jun 2019 16:16:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:16:24: #2 number of paired peaks: 214 WARNING @ Sun, 02 Jun 2019 16:16:24: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Sun, 02 Jun 2019 16:16:24: start model_add_line... INFO @ Sun, 02 Jun 2019 16:16:24: start X-correlation... INFO @ Sun, 02 Jun 2019 16:16:24: end of X-cor INFO @ Sun, 02 Jun 2019 16:16:24: #2 finished! INFO @ Sun, 02 Jun 2019 16:16:24: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:16:24: #2 alternative fragment length(s) may be 1,28,550,596 bps INFO @ Sun, 02 Jun 2019 16:16:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.10_model.r WARNING @ Sun, 02 Jun 2019 16:16:24: #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 16:16:24: #2 You may need to consider one of the other alternative d(s): 1,28,550,596 WARNING @ Sun, 02 Jun 2019 16:16:24: #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 16:16:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:16:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:16:25: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:16:25: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:16:25: #1 total tags in treatment: 16383132 INFO @ Sun, 02 Jun 2019 16:16:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:16:25: #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 16:16:25: #1 tags after filtering in treatment: 16383132 INFO @ Sun, 02 Jun 2019 16:16:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:16:25: #1 finished! INFO @ Sun, 02 Jun 2019 16:16:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:16:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:16:27: #2 number of paired peaks: 214 WARNING @ Sun, 02 Jun 2019 16:16:27: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Sun, 02 Jun 2019 16:16:27: start model_add_line... INFO @ Sun, 02 Jun 2019 16:16:27: start X-correlation... INFO @ Sun, 02 Jun 2019 16:16:27: end of X-cor INFO @ Sun, 02 Jun 2019 16:16:27: #2 finished! INFO @ Sun, 02 Jun 2019 16:16:27: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:16:27: #2 alternative fragment length(s) may be 1,28,550,596 bps INFO @ Sun, 02 Jun 2019 16:16:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.05_model.r WARNING @ Sun, 02 Jun 2019 16:16:27: #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 16:16:27: #2 You may need to consider one of the other alternative d(s): 1,28,550,596 WARNING @ Sun, 02 Jun 2019 16:16:27: #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 16:16:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:16:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:16:27: 16000000 INFO @ Sun, 02 Jun 2019 16:16:31: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:16:31: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:16:31: #1 total tags in treatment: 16383132 INFO @ Sun, 02 Jun 2019 16:16:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:16:31: #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 16:16:31: #1 tags after filtering in treatment: 16383132 INFO @ Sun, 02 Jun 2019 16:16:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:16:31: #1 finished! INFO @ Sun, 02 Jun 2019 16:16:31: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:16:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:16:33: #2 number of paired peaks: 214 WARNING @ Sun, 02 Jun 2019 16:16:33: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Sun, 02 Jun 2019 16:16:33: start model_add_line... INFO @ Sun, 02 Jun 2019 16:16:33: start X-correlation... INFO @ Sun, 02 Jun 2019 16:16:33: end of X-cor INFO @ Sun, 02 Jun 2019 16:16:33: #2 finished! INFO @ Sun, 02 Jun 2019 16:16:33: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:16:33: #2 alternative fragment length(s) may be 1,28,550,596 bps INFO @ Sun, 02 Jun 2019 16:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.20_model.r WARNING @ Sun, 02 Jun 2019 16:16:33: #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 16:16:33: #2 You may need to consider one of the other alternative d(s): 1,28,550,596 WARNING @ Sun, 02 Jun 2019 16:16:33: #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 16:16:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:17:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:17:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:17:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:17:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:17:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:17:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.10_summits.bed INFO @ Sun, 02 Jun 2019 16:17:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:17:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:17:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:17:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.05_summits.bed INFO @ Sun, 02 Jun 2019 16:17:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:17:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:17:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:17:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX105312/SRX105312.20_summits.bed INFO @ Sun, 02 Jun 2019 16:17:31: Done! pass1 - making usageList (0 chroms): 2 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。