Job ID = 1291765 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,734,004 reads read : 21,734,004 reads written : 21,734,004 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: 00:03:59 21734004 reads; of these: 21734004 (100.00%) were unpaired; of these: 1833516 (8.44%) aligned 0 times 16568315 (76.23%) aligned exactly 1 time 3332173 (15.33%) aligned >1 times 91.56% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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] 1647021 / 19900488 = 0.0828 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 16:42:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.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 16:42:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:42:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:42:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.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 16:42:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:42:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:42:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.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 16:42:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:42:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:42:13: 1000000 INFO @ Sun, 02 Jun 2019 16:42:15: 1000000 INFO @ Sun, 02 Jun 2019 16:42:15: 1000000 INFO @ Sun, 02 Jun 2019 16:42:21: 2000000 INFO @ Sun, 02 Jun 2019 16:42:24: 2000000 INFO @ Sun, 02 Jun 2019 16:42:24: 2000000 INFO @ Sun, 02 Jun 2019 16:42:29: 3000000 INFO @ Sun, 02 Jun 2019 16:42:32: 3000000 INFO @ Sun, 02 Jun 2019 16:42:34: 3000000 INFO @ Sun, 02 Jun 2019 16:42:37: 4000000 INFO @ Sun, 02 Jun 2019 16:42:39: 4000000 INFO @ Sun, 02 Jun 2019 16:42:43: 4000000 INFO @ Sun, 02 Jun 2019 16:42:44: 5000000 INFO @ Sun, 02 Jun 2019 16:42:46: 5000000 INFO @ Sun, 02 Jun 2019 16:42:52: 6000000 INFO @ Sun, 02 Jun 2019 16:42:52: 5000000 INFO @ Sun, 02 Jun 2019 16:42:53: 6000000 INFO @ Sun, 02 Jun 2019 16:43:00: 7000000 INFO @ Sun, 02 Jun 2019 16:43:00: 7000000 INFO @ Sun, 02 Jun 2019 16:43:01: 6000000 INFO @ Sun, 02 Jun 2019 16:43:07: 8000000 INFO @ Sun, 02 Jun 2019 16:43:08: 8000000 INFO @ Sun, 02 Jun 2019 16:43:10: 7000000 INFO @ Sun, 02 Jun 2019 16:43:14: 9000000 INFO @ Sun, 02 Jun 2019 16:43:15: 9000000 INFO @ Sun, 02 Jun 2019 16:43:20: 8000000 INFO @ Sun, 02 Jun 2019 16:43:21: 10000000 INFO @ Sun, 02 Jun 2019 16:43:23: 10000000 INFO @ Sun, 02 Jun 2019 16:43:28: 11000000 INFO @ Sun, 02 Jun 2019 16:43:29: 9000000 INFO @ Sun, 02 Jun 2019 16:43:31: 11000000 INFO @ Sun, 02 Jun 2019 16:43:35: 12000000 INFO @ Sun, 02 Jun 2019 16:43:38: 12000000 INFO @ Sun, 02 Jun 2019 16:43:38: 10000000 INFO @ Sun, 02 Jun 2019 16:43:42: 13000000 INFO @ Sun, 02 Jun 2019 16:43:46: 13000000 INFO @ Sun, 02 Jun 2019 16:43:47: 11000000 INFO @ Sun, 02 Jun 2019 16:43:49: 14000000 INFO @ Sun, 02 Jun 2019 16:43:53: 14000000 INFO @ Sun, 02 Jun 2019 16:43:56: 15000000 INFO @ Sun, 02 Jun 2019 16:43:56: 12000000 INFO @ Sun, 02 Jun 2019 16:44:01: 15000000 INFO @ Sun, 02 Jun 2019 16:44:03: 16000000 INFO @ Sun, 02 Jun 2019 16:44:05: 13000000 INFO @ Sun, 02 Jun 2019 16:44:08: 16000000 INFO @ Sun, 02 Jun 2019 16:44:10: 17000000 INFO @ Sun, 02 Jun 2019 16:44:14: 14000000 INFO @ Sun, 02 Jun 2019 16:44:16: 17000000 INFO @ Sun, 02 Jun 2019 16:44:16: 18000000 INFO @ Sun, 02 Jun 2019 16:44:18: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:44:18: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:44:18: #1 total tags in treatment: 18253467 INFO @ Sun, 02 Jun 2019 16:44:18: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:44:18: #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 16:44:19: #1 tags after filtering in treatment: 18253467 INFO @ Sun, 02 Jun 2019 16:44:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:44:19: #1 finished! INFO @ Sun, 02 Jun 2019 16:44:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:44:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:44:20: #2 number of paired peaks: 222 WARNING @ Sun, 02 Jun 2019 16:44:20: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Sun, 02 Jun 2019 16:44:20: start model_add_line... INFO @ Sun, 02 Jun 2019 16:44:20: start X-correlation... INFO @ Sun, 02 Jun 2019 16:44:20: end of X-cor INFO @ Sun, 02 Jun 2019 16:44:20: #2 finished! INFO @ Sun, 02 Jun 2019 16:44:20: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:44:20: #2 alternative fragment length(s) may be 1,33,490,511,529 bps INFO @ Sun, 02 Jun 2019 16:44:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.10_model.r WARNING @ Sun, 02 Jun 2019 16:44:20: #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 16:44:20: #2 You may need to consider one of the other alternative d(s): 1,33,490,511,529 WARNING @ Sun, 02 Jun 2019 16:44:20: #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 16:44:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:44:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:44:23: 18000000 INFO @ Sun, 02 Jun 2019 16:44:23: 15000000 INFO @ Sun, 02 Jun 2019 16:44:25: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:44:25: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:44:25: #1 total tags in treatment: 18253467 INFO @ Sun, 02 Jun 2019 16:44:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:44:25: #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 16:44:26: #1 tags after filtering in treatment: 18253467 INFO @ Sun, 02 Jun 2019 16:44:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:44:26: #1 finished! INFO @ Sun, 02 Jun 2019 16:44:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:44:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:44:27: #2 number of paired peaks: 222 WARNING @ Sun, 02 Jun 2019 16:44:27: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Sun, 02 Jun 2019 16:44:27: start model_add_line... INFO @ Sun, 02 Jun 2019 16:44:27: start X-correlation... INFO @ Sun, 02 Jun 2019 16:44:27: end of X-cor INFO @ Sun, 02 Jun 2019 16:44:27: #2 finished! INFO @ Sun, 02 Jun 2019 16:44:27: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:44:27: #2 alternative fragment length(s) may be 1,33,490,511,529 bps INFO @ Sun, 02 Jun 2019 16:44:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.05_model.r WARNING @ Sun, 02 Jun 2019 16:44:27: #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 16:44:27: #2 You may need to consider one of the other alternative d(s): 1,33,490,511,529 WARNING @ Sun, 02 Jun 2019 16:44:27: #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 16:44:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:44:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:44:32: 16000000 INFO @ Sun, 02 Jun 2019 16:44:41: 17000000 INFO @ Sun, 02 Jun 2019 16:44:50: 18000000 INFO @ Sun, 02 Jun 2019 16:44:52: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:44:52: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:44:52: #1 total tags in treatment: 18253467 INFO @ Sun, 02 Jun 2019 16:44:52: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:44:52: #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 16:44:52: #1 tags after filtering in treatment: 18253467 INFO @ Sun, 02 Jun 2019 16:44:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:44:52: #1 finished! INFO @ Sun, 02 Jun 2019 16:44:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:44:54: #2 number of paired peaks: 222 WARNING @ Sun, 02 Jun 2019 16:44:54: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Sun, 02 Jun 2019 16:44:54: start model_add_line... INFO @ Sun, 02 Jun 2019 16:44:54: start X-correlation... INFO @ Sun, 02 Jun 2019 16:44:54: end of X-cor INFO @ Sun, 02 Jun 2019 16:44:54: #2 finished! INFO @ Sun, 02 Jun 2019 16:44:54: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:44:54: #2 alternative fragment length(s) may be 1,33,490,511,529 bps INFO @ Sun, 02 Jun 2019 16:44:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.20_model.r WARNING @ Sun, 02 Jun 2019 16:44:54: #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 16:44:54: #2 You may need to consider one of the other alternative d(s): 1,33,490,511,529 WARNING @ Sun, 02 Jun 2019 16:44:54: #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 16:44:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:44:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:45:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:45:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:45:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:45:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:45:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.10_summits.bed INFO @ Sun, 02 Jun 2019 16:45:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:45:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:45:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:45:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.05_summits.bed INFO @ Sun, 02 Jun 2019 16:45:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:45:34: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:45:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:45:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:45:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX245914/SRX245914.20_summits.bed INFO @ Sun, 02 Jun 2019 16:45:52: 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。