Job ID = 2589684 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,881,109 reads read : 11,881,109 reads written : 11,881,109 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947285.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:10 11881109 reads; of these: 11881109 (100.00%) were unpaired; of these: 316031 (2.66%) aligned 0 times 9548371 (80.37%) aligned exactly 1 time 2016707 (16.97%) aligned >1 times 97.34% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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_rmdupse_core] 1246852 / 11565078 = 0.1078 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 @ Mon, 12 Aug 2019 18:19:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.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 @ Mon, 12 Aug 2019 18:19:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:19:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:19:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.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 @ Mon, 12 Aug 2019 18:19:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:19:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:19:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.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 @ Mon, 12 Aug 2019 18:19:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:19:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:19:10: 1000000 INFO @ Mon, 12 Aug 2019 18:19:12: 1000000 INFO @ Mon, 12 Aug 2019 18:19:13: 1000000 INFO @ Mon, 12 Aug 2019 18:19:18: 2000000 INFO @ Mon, 12 Aug 2019 18:19:19: 2000000 INFO @ Mon, 12 Aug 2019 18:19:20: 2000000 INFO @ Mon, 12 Aug 2019 18:19:25: 3000000 INFO @ Mon, 12 Aug 2019 18:19:27: 3000000 INFO @ Mon, 12 Aug 2019 18:19:29: 3000000 INFO @ Mon, 12 Aug 2019 18:19:32: 4000000 INFO @ Mon, 12 Aug 2019 18:19:34: 4000000 INFO @ Mon, 12 Aug 2019 18:19:38: 4000000 INFO @ Mon, 12 Aug 2019 18:19:38: 5000000 INFO @ Mon, 12 Aug 2019 18:19:42: 5000000 INFO @ Mon, 12 Aug 2019 18:19:45: 6000000 INFO @ Mon, 12 Aug 2019 18:19:47: 5000000 INFO @ Mon, 12 Aug 2019 18:19:49: 6000000 INFO @ Mon, 12 Aug 2019 18:19:54: 7000000 INFO @ Mon, 12 Aug 2019 18:19:55: 6000000 INFO @ Mon, 12 Aug 2019 18:19:57: 7000000 INFO @ Mon, 12 Aug 2019 18:20:02: 8000000 INFO @ Mon, 12 Aug 2019 18:20:04: 7000000 INFO @ Mon, 12 Aug 2019 18:20:04: 8000000 INFO @ Mon, 12 Aug 2019 18:20:10: 9000000 INFO @ Mon, 12 Aug 2019 18:20:11: 9000000 INFO @ Mon, 12 Aug 2019 18:20:13: 8000000 INFO @ Mon, 12 Aug 2019 18:20:19: 10000000 INFO @ Mon, 12 Aug 2019 18:20:19: 10000000 INFO @ Mon, 12 Aug 2019 18:20:21: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:20:21: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:20:21: #1 total tags in treatment: 10318226 INFO @ Mon, 12 Aug 2019 18:20:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:20:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:20:21: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:20:21: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:20:21: #1 total tags in treatment: 10318226 INFO @ Mon, 12 Aug 2019 18:20:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:20:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:20:21: 9000000 INFO @ Mon, 12 Aug 2019 18:20:21: #1 tags after filtering in treatment: 10318226 INFO @ Mon, 12 Aug 2019 18:20:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:20:21: #1 finished! INFO @ Mon, 12 Aug 2019 18:20:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:20:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:20:21: #1 tags after filtering in treatment: 10318226 INFO @ Mon, 12 Aug 2019 18:20:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:20:21: #1 finished! INFO @ Mon, 12 Aug 2019 18:20:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:20:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:20:22: #2 number of paired peaks: 388 WARNING @ Mon, 12 Aug 2019 18:20:22: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Mon, 12 Aug 2019 18:20:22: start model_add_line... INFO @ Mon, 12 Aug 2019 18:20:22: #2 number of paired peaks: 388 WARNING @ Mon, 12 Aug 2019 18:20:22: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Mon, 12 Aug 2019 18:20:22: start model_add_line... INFO @ Mon, 12 Aug 2019 18:20:23: start X-correlation... INFO @ Mon, 12 Aug 2019 18:20:23: end of X-cor INFO @ Mon, 12 Aug 2019 18:20:23: #2 finished! INFO @ Mon, 12 Aug 2019 18:20:23: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:20:23: #2 alternative fragment length(s) may be 1,24,538,558,573 bps INFO @ Mon, 12 Aug 2019 18:20:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.10_model.r WARNING @ Mon, 12 Aug 2019 18:20:23: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:20:23: #2 You may need to consider one of the other alternative d(s): 1,24,538,558,573 WARNING @ Mon, 12 Aug 2019 18:20:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:20:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:20:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:20:23: start X-correlation... INFO @ Mon, 12 Aug 2019 18:20:23: end of X-cor INFO @ Mon, 12 Aug 2019 18:20:23: #2 finished! INFO @ Mon, 12 Aug 2019 18:20:23: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:20:23: #2 alternative fragment length(s) may be 1,24,538,558,573 bps INFO @ Mon, 12 Aug 2019 18:20:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.05_model.r WARNING @ Mon, 12 Aug 2019 18:20:23: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:20:23: #2 You may need to consider one of the other alternative d(s): 1,24,538,558,573 WARNING @ Mon, 12 Aug 2019 18:20:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:20:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:20:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:20:29: 10000000 INFO @ Mon, 12 Aug 2019 18:20:32: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:20:32: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:20:32: #1 total tags in treatment: 10318226 INFO @ Mon, 12 Aug 2019 18:20:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:20:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:20:32: #1 tags after filtering in treatment: 10318226 INFO @ Mon, 12 Aug 2019 18:20:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:20:32: #1 finished! INFO @ Mon, 12 Aug 2019 18:20:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:20:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:20:33: #2 number of paired peaks: 388 WARNING @ Mon, 12 Aug 2019 18:20:33: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Mon, 12 Aug 2019 18:20:33: start model_add_line... INFO @ Mon, 12 Aug 2019 18:20:33: start X-correlation... INFO @ Mon, 12 Aug 2019 18:20:33: end of X-cor INFO @ Mon, 12 Aug 2019 18:20:33: #2 finished! INFO @ Mon, 12 Aug 2019 18:20:33: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:20:33: #2 alternative fragment length(s) may be 1,24,538,558,573 bps INFO @ Mon, 12 Aug 2019 18:20:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.20_model.r WARNING @ Mon, 12 Aug 2019 18:20:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:20:33: #2 You may need to consider one of the other alternative d(s): 1,24,538,558,573 WARNING @ Mon, 12 Aug 2019 18:20:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:20:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:20:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:20:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:20:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:20:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:21:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:21:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:21:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.05_summits.bed INFO @ Mon, 12 Aug 2019 18:21:00: Done! INFO @ Mon, 12 Aug 2019 18:21:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:21:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:21:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.10_summits.bed INFO @ Mon, 12 Aug 2019 18:21:00: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:21:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:21:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:21:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331061/SRX331061.20_summits.bed INFO @ Mon, 12 Aug 2019 18:21:11: 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。