Job ID = 1292467 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 46,755,661 reads read : 46,755,661 reads written : 46,755,661 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: 00:07:22 46755661 reads; of these: 46755661 (100.00%) were unpaired; of these: 14945846 (31.97%) aligned 0 times 26131019 (55.89%) aligned exactly 1 time 5678796 (12.15%) aligned >1 times 68.03% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 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] 4505771 / 31809815 = 0.1416 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 19:19:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.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 19:19:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:19:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:19:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.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 19:19:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:19:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:19:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.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 19:19:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:19:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:19:29: 1000000 INFO @ Sun, 02 Jun 2019 19:19:29: 1000000 INFO @ Sun, 02 Jun 2019 19:19:29: 1000000 INFO @ Sun, 02 Jun 2019 19:19:37: 2000000 INFO @ Sun, 02 Jun 2019 19:19:37: 2000000 INFO @ Sun, 02 Jun 2019 19:19:37: 2000000 INFO @ Sun, 02 Jun 2019 19:19:44: 3000000 INFO @ Sun, 02 Jun 2019 19:19:44: 3000000 INFO @ Sun, 02 Jun 2019 19:19:46: 3000000 INFO @ Sun, 02 Jun 2019 19:19:52: 4000000 INFO @ Sun, 02 Jun 2019 19:19:52: 4000000 INFO @ Sun, 02 Jun 2019 19:19:54: 4000000 INFO @ Sun, 02 Jun 2019 19:19:59: 5000000 INFO @ Sun, 02 Jun 2019 19:19:59: 5000000 INFO @ Sun, 02 Jun 2019 19:20:02: 5000000 INFO @ Sun, 02 Jun 2019 19:20:06: 6000000 INFO @ Sun, 02 Jun 2019 19:20:06: 6000000 INFO @ Sun, 02 Jun 2019 19:20:11: 6000000 INFO @ Sun, 02 Jun 2019 19:20:13: 7000000 INFO @ Sun, 02 Jun 2019 19:20:14: 7000000 INFO @ Sun, 02 Jun 2019 19:20:19: 7000000 INFO @ Sun, 02 Jun 2019 19:20:20: 8000000 INFO @ Sun, 02 Jun 2019 19:20:21: 8000000 INFO @ Sun, 02 Jun 2019 19:20:27: 8000000 INFO @ Sun, 02 Jun 2019 19:20:27: 9000000 INFO @ Sun, 02 Jun 2019 19:20:28: 9000000 INFO @ Sun, 02 Jun 2019 19:20:34: 10000000 INFO @ Sun, 02 Jun 2019 19:20:35: 10000000 INFO @ Sun, 02 Jun 2019 19:20:35: 9000000 INFO @ Sun, 02 Jun 2019 19:20:41: 11000000 INFO @ Sun, 02 Jun 2019 19:20:42: 11000000 INFO @ Sun, 02 Jun 2019 19:20:43: 10000000 INFO @ Sun, 02 Jun 2019 19:20:48: 12000000 INFO @ Sun, 02 Jun 2019 19:20:49: 12000000 INFO @ Sun, 02 Jun 2019 19:20:51: 11000000 INFO @ Sun, 02 Jun 2019 19:20:55: 13000000 INFO @ Sun, 02 Jun 2019 19:20:56: 13000000 INFO @ Sun, 02 Jun 2019 19:20:59: 12000000 INFO @ Sun, 02 Jun 2019 19:21:02: 14000000 INFO @ Sun, 02 Jun 2019 19:21:03: 14000000 INFO @ Sun, 02 Jun 2019 19:21:07: 13000000 INFO @ Sun, 02 Jun 2019 19:21:09: 15000000 INFO @ Sun, 02 Jun 2019 19:21:10: 15000000 INFO @ Sun, 02 Jun 2019 19:21:15: 14000000 INFO @ Sun, 02 Jun 2019 19:21:16: 16000000 INFO @ Sun, 02 Jun 2019 19:21:17: 16000000 INFO @ Sun, 02 Jun 2019 19:21:23: 17000000 INFO @ Sun, 02 Jun 2019 19:21:23: 15000000 INFO @ Sun, 02 Jun 2019 19:21:24: 17000000 INFO @ Sun, 02 Jun 2019 19:21:30: 18000000 INFO @ Sun, 02 Jun 2019 19:21:31: 18000000 INFO @ Sun, 02 Jun 2019 19:21:31: 16000000 INFO @ Sun, 02 Jun 2019 19:21:37: 19000000 INFO @ Sun, 02 Jun 2019 19:21:38: 19000000 INFO @ Sun, 02 Jun 2019 19:21:39: 17000000 INFO @ Sun, 02 Jun 2019 19:21:43: 20000000 INFO @ Sun, 02 Jun 2019 19:21:45: 20000000 INFO @ Sun, 02 Jun 2019 19:21:47: 18000000 INFO @ Sun, 02 Jun 2019 19:21:50: 21000000 INFO @ Sun, 02 Jun 2019 19:21:52: 21000000 INFO @ Sun, 02 Jun 2019 19:21:55: 19000000 INFO @ Sun, 02 Jun 2019 19:21:57: 22000000 INFO @ Sun, 02 Jun 2019 19:21:59: 22000000 INFO @ Sun, 02 Jun 2019 19:22:03: 20000000 INFO @ Sun, 02 Jun 2019 19:22:04: 23000000 INFO @ Sun, 02 Jun 2019 19:22:06: 23000000 INFO @ Sun, 02 Jun 2019 19:22:11: 21000000 INFO @ Sun, 02 Jun 2019 19:22:11: 24000000 INFO @ Sun, 02 Jun 2019 19:22:13: 24000000 INFO @ Sun, 02 Jun 2019 19:22:18: 25000000 INFO @ Sun, 02 Jun 2019 19:22:19: 22000000 INFO @ Sun, 02 Jun 2019 19:22:20: 25000000 INFO @ Sun, 02 Jun 2019 19:22:24: 26000000 INFO @ Sun, 02 Jun 2019 19:22:27: 26000000 INFO @ Sun, 02 Jun 2019 19:22:27: 23000000 INFO @ Sun, 02 Jun 2019 19:22:31: 27000000 INFO @ Sun, 02 Jun 2019 19:22:33: 27000000 INFO @ Sun, 02 Jun 2019 19:22:33: #1 tag size is determined as 37 bps INFO @ Sun, 02 Jun 2019 19:22:33: #1 tag size = 37 INFO @ Sun, 02 Jun 2019 19:22:33: #1 total tags in treatment: 27304044 INFO @ Sun, 02 Jun 2019 19:22:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:22:33: #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 19:22:34: #1 tags after filtering in treatment: 27304044 INFO @ Sun, 02 Jun 2019 19:22:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:22:34: #1 finished! INFO @ Sun, 02 Jun 2019 19:22:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:22:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:22:35: 24000000 INFO @ Sun, 02 Jun 2019 19:22:36: #1 tag size is determined as 37 bps INFO @ Sun, 02 Jun 2019 19:22:36: #1 tag size = 37 INFO @ Sun, 02 Jun 2019 19:22:36: #1 total tags in treatment: 27304044 INFO @ Sun, 02 Jun 2019 19:22:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:22:36: #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 19:22:36: #2 number of paired peaks: 130 WARNING @ Sun, 02 Jun 2019 19:22:36: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sun, 02 Jun 2019 19:22:36: start model_add_line... INFO @ Sun, 02 Jun 2019 19:22:36: #1 tags after filtering in treatment: 27304044 INFO @ Sun, 02 Jun 2019 19:22:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:22:36: #1 finished! INFO @ Sun, 02 Jun 2019 19:22:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:22:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:22:36: start X-correlation... INFO @ Sun, 02 Jun 2019 19:22:37: end of X-cor INFO @ Sun, 02 Jun 2019 19:22:37: #2 finished! INFO @ Sun, 02 Jun 2019 19:22:37: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 19:22:37: #2 alternative fragment length(s) may be 0,19,28,221,403,443,465,516,529,537,545,564 bps INFO @ Sun, 02 Jun 2019 19:22:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.05_model.r WARNING @ Sun, 02 Jun 2019 19:22:37: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:22:37: #2 You may need to consider one of the other alternative d(s): 0,19,28,221,403,443,465,516,529,537,545,564 WARNING @ Sun, 02 Jun 2019 19:22:37: #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 19:22:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:22:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:22:38: #2 number of paired peaks: 130 WARNING @ Sun, 02 Jun 2019 19:22:38: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sun, 02 Jun 2019 19:22:38: start model_add_line... INFO @ Sun, 02 Jun 2019 19:22:39: start X-correlation... INFO @ Sun, 02 Jun 2019 19:22:39: end of X-cor INFO @ Sun, 02 Jun 2019 19:22:39: #2 finished! INFO @ Sun, 02 Jun 2019 19:22:39: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 19:22:39: #2 alternative fragment length(s) may be 0,19,28,221,403,443,465,516,529,537,545,564 bps INFO @ Sun, 02 Jun 2019 19:22:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.10_model.r WARNING @ Sun, 02 Jun 2019 19:22:39: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:22:39: #2 You may need to consider one of the other alternative d(s): 0,19,28,221,403,443,465,516,529,537,545,564 WARNING @ Sun, 02 Jun 2019 19:22:39: #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 19:22:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:22:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:22:42: 25000000 INFO @ Sun, 02 Jun 2019 19:22:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:22:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:22:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:22:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.05_summits.bed INFO @ Sun, 02 Jun 2019 19:22:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:22:48: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:22:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:22:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:22:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.10_summits.bed INFO @ Sun, 02 Jun 2019 19:22:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:22:50: 26000000 INFO @ Sun, 02 Jun 2019 19:22:58: 27000000 INFO @ Sun, 02 Jun 2019 19:23:00: #1 tag size is determined as 37 bps INFO @ Sun, 02 Jun 2019 19:23:00: #1 tag size = 37 INFO @ Sun, 02 Jun 2019 19:23:00: #1 total tags in treatment: 27304044 INFO @ Sun, 02 Jun 2019 19:23:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:23:00: #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 19:23:01: #1 tags after filtering in treatment: 27304044 INFO @ Sun, 02 Jun 2019 19:23:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:23:01: #1 finished! INFO @ Sun, 02 Jun 2019 19:23:01: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:23:03: #2 number of paired peaks: 130 WARNING @ Sun, 02 Jun 2019 19:23:03: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sun, 02 Jun 2019 19:23:03: start model_add_line... INFO @ Sun, 02 Jun 2019 19:23:03: start X-correlation... INFO @ Sun, 02 Jun 2019 19:23:03: end of X-cor INFO @ Sun, 02 Jun 2019 19:23:03: #2 finished! INFO @ Sun, 02 Jun 2019 19:23:03: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 19:23:03: #2 alternative fragment length(s) may be 0,19,28,221,403,443,465,516,529,537,545,564 bps INFO @ Sun, 02 Jun 2019 19:23:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.20_model.r WARNING @ Sun, 02 Jun 2019 19:23:03: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:23:03: #2 You may need to consider one of the other alternative d(s): 0,19,28,221,403,443,465,516,529,537,545,564 WARNING @ Sun, 02 Jun 2019 19:23:03: #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 19:23:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:23:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:23:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:23:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:23:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:23:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX463080/SRX463080.20_summits.bed INFO @ Sun, 02 Jun 2019 19:23:12: 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。