Job ID = 1292309 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,509,609 reads read : 21,509,609 reads written : 21,509,609 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: 00:04:13 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 256465 (1.19%) aligned 0 times 17820696 (82.85%) aligned exactly 1 time 3432448 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 3667181 / 21253144 = 0.1725 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 18:16:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.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 18:16:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:16:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:16:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.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 18:16:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:16:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:16:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.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 18:16:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:16:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:17:00: 1000000 INFO @ Sun, 02 Jun 2019 18:17:00: 1000000 INFO @ Sun, 02 Jun 2019 18:17:00: 1000000 INFO @ Sun, 02 Jun 2019 18:17:07: 2000000 INFO @ Sun, 02 Jun 2019 18:17:07: 2000000 INFO @ Sun, 02 Jun 2019 18:17:07: 2000000 INFO @ Sun, 02 Jun 2019 18:17:13: 3000000 INFO @ Sun, 02 Jun 2019 18:17:13: 3000000 INFO @ Sun, 02 Jun 2019 18:17:14: 3000000 INFO @ Sun, 02 Jun 2019 18:17:19: 4000000 INFO @ Sun, 02 Jun 2019 18:17:19: 4000000 INFO @ Sun, 02 Jun 2019 18:17:21: 4000000 INFO @ Sun, 02 Jun 2019 18:17:26: 5000000 INFO @ Sun, 02 Jun 2019 18:17:26: 5000000 INFO @ Sun, 02 Jun 2019 18:17:27: 5000000 INFO @ Sun, 02 Jun 2019 18:17:32: 6000000 INFO @ Sun, 02 Jun 2019 18:17:32: 6000000 INFO @ Sun, 02 Jun 2019 18:17:34: 6000000 INFO @ Sun, 02 Jun 2019 18:17:38: 7000000 INFO @ Sun, 02 Jun 2019 18:17:38: 7000000 INFO @ Sun, 02 Jun 2019 18:17:40: 7000000 INFO @ Sun, 02 Jun 2019 18:17:44: 8000000 INFO @ Sun, 02 Jun 2019 18:17:45: 8000000 INFO @ Sun, 02 Jun 2019 18:17:47: 8000000 INFO @ Sun, 02 Jun 2019 18:17:51: 9000000 INFO @ Sun, 02 Jun 2019 18:17:51: 9000000 INFO @ Sun, 02 Jun 2019 18:17:54: 9000000 INFO @ Sun, 02 Jun 2019 18:17:57: 10000000 INFO @ Sun, 02 Jun 2019 18:17:58: 10000000 INFO @ Sun, 02 Jun 2019 18:18:01: 10000000 INFO @ Sun, 02 Jun 2019 18:18:04: 11000000 INFO @ Sun, 02 Jun 2019 18:18:04: 11000000 INFO @ Sun, 02 Jun 2019 18:18:07: 11000000 INFO @ Sun, 02 Jun 2019 18:18:10: 12000000 INFO @ Sun, 02 Jun 2019 18:18:10: 12000000 INFO @ Sun, 02 Jun 2019 18:18:14: 12000000 INFO @ Sun, 02 Jun 2019 18:18:16: 13000000 INFO @ Sun, 02 Jun 2019 18:18:17: 13000000 INFO @ Sun, 02 Jun 2019 18:18:21: 13000000 INFO @ Sun, 02 Jun 2019 18:18:23: 14000000 INFO @ Sun, 02 Jun 2019 18:18:23: 14000000 INFO @ Sun, 02 Jun 2019 18:18:27: 14000000 INFO @ Sun, 02 Jun 2019 18:18:29: 15000000 INFO @ Sun, 02 Jun 2019 18:18:29: 15000000 INFO @ Sun, 02 Jun 2019 18:18:34: 15000000 INFO @ Sun, 02 Jun 2019 18:18:35: 16000000 INFO @ Sun, 02 Jun 2019 18:18:35: 16000000 INFO @ Sun, 02 Jun 2019 18:18:41: 16000000 INFO @ Sun, 02 Jun 2019 18:18:41: 17000000 INFO @ Sun, 02 Jun 2019 18:18:42: 17000000 INFO @ Sun, 02 Jun 2019 18:18:45: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:18:45: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:18:45: #1 total tags in treatment: 17585963 INFO @ Sun, 02 Jun 2019 18:18:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:18:45: #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 18:18:46: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:18:46: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:18:46: #1 total tags in treatment: 17585963 INFO @ Sun, 02 Jun 2019 18:18:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:18:46: #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 18:18:46: #1 tags after filtering in treatment: 17585963 INFO @ Sun, 02 Jun 2019 18:18:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:18:46: #1 finished! INFO @ Sun, 02 Jun 2019 18:18:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:18:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:18:46: #1 tags after filtering in treatment: 17585963 INFO @ Sun, 02 Jun 2019 18:18:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:18:46: #1 finished! INFO @ Sun, 02 Jun 2019 18:18:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:18:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:18:47: #2 number of paired peaks: 213 WARNING @ Sun, 02 Jun 2019 18:18:47: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Sun, 02 Jun 2019 18:18:47: start model_add_line... INFO @ Sun, 02 Jun 2019 18:18:47: 17000000 INFO @ Sun, 02 Jun 2019 18:18:47: start X-correlation... INFO @ Sun, 02 Jun 2019 18:18:47: end of X-cor INFO @ Sun, 02 Jun 2019 18:18:47: #2 finished! INFO @ Sun, 02 Jun 2019 18:18:47: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:18:47: #2 alternative fragment length(s) may be 1,36,562 bps INFO @ Sun, 02 Jun 2019 18:18:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.05_model.r WARNING @ Sun, 02 Jun 2019 18:18:47: #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 18:18:47: #2 You may need to consider one of the other alternative d(s): 1,36,562 WARNING @ Sun, 02 Jun 2019 18:18:47: #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 18:18:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:18:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:18:47: #2 number of paired peaks: 213 WARNING @ Sun, 02 Jun 2019 18:18:47: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Sun, 02 Jun 2019 18:18:47: start model_add_line... INFO @ Sun, 02 Jun 2019 18:18:48: start X-correlation... INFO @ Sun, 02 Jun 2019 18:18:48: end of X-cor INFO @ Sun, 02 Jun 2019 18:18:48: #2 finished! INFO @ Sun, 02 Jun 2019 18:18:48: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:18:48: #2 alternative fragment length(s) may be 1,36,562 bps INFO @ Sun, 02 Jun 2019 18:18:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.20_model.r WARNING @ Sun, 02 Jun 2019 18:18:48: #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 18:18:48: #2 You may need to consider one of the other alternative d(s): 1,36,562 WARNING @ Sun, 02 Jun 2019 18:18:48: #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 18:18:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:18:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:18:52: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:18:52: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:18:52: #1 total tags in treatment: 17585963 INFO @ Sun, 02 Jun 2019 18:18:52: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:18:52: #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 18:18:52: #1 tags after filtering in treatment: 17585963 INFO @ Sun, 02 Jun 2019 18:18:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:18:52: #1 finished! INFO @ Sun, 02 Jun 2019 18:18:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:18:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:18:53: #2 number of paired peaks: 213 WARNING @ Sun, 02 Jun 2019 18:18:53: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Sun, 02 Jun 2019 18:18:53: start model_add_line... INFO @ Sun, 02 Jun 2019 18:18:54: start X-correlation... INFO @ Sun, 02 Jun 2019 18:18:54: end of X-cor INFO @ Sun, 02 Jun 2019 18:18:54: #2 finished! INFO @ Sun, 02 Jun 2019 18:18:54: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:18:54: #2 alternative fragment length(s) may be 1,36,562 bps INFO @ Sun, 02 Jun 2019 18:18:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.10_model.r WARNING @ Sun, 02 Jun 2019 18:18:54: #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 18:18:54: #2 You may need to consider one of the other alternative d(s): 1,36,562 WARNING @ Sun, 02 Jun 2019 18:18:54: #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 18:18:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:18:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:19:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:19:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:19:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:19:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:19:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:19:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.05_summits.bed INFO @ Sun, 02 Jun 2019 18:19:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:19:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:19:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:19:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.20_summits.bed INFO @ Sun, 02 Jun 2019 18:19:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:19:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:19:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:19:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331334/SRX331334.10_summits.bed INFO @ Sun, 02 Jun 2019 18:19:51: 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。