Job ID = 1292855 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,854,814 reads read : 18,854,814 reads written : 18,854,814 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 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 289113 (1.53%) aligned 0 times 14953734 (79.31%) aligned exactly 1 time 3611967 (19.16%) aligned >1 times 98.47% 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] 3522450 / 18565701 = 0.1897 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 21:06:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.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 21:06:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:06:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.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 21:06:20: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:06:20: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.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 21:06:20: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:06:20: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:06:28: 1000000 INFO @ Sun, 02 Jun 2019 21:06:28: 1000000 INFO @ Sun, 02 Jun 2019 21:06:29: 1000000 INFO @ Sun, 02 Jun 2019 21:06:35: 2000000 INFO @ Sun, 02 Jun 2019 21:06:37: 2000000 INFO @ Sun, 02 Jun 2019 21:06:37: 2000000 INFO @ Sun, 02 Jun 2019 21:06:42: 3000000 INFO @ Sun, 02 Jun 2019 21:06:46: 3000000 INFO @ Sun, 02 Jun 2019 21:06:46: 3000000 INFO @ Sun, 02 Jun 2019 21:06:50: 4000000 INFO @ Sun, 02 Jun 2019 21:06:54: 4000000 INFO @ Sun, 02 Jun 2019 21:06:55: 4000000 INFO @ Sun, 02 Jun 2019 21:06:57: 5000000 INFO @ Sun, 02 Jun 2019 21:07:02: 5000000 INFO @ Sun, 02 Jun 2019 21:07:03: 5000000 INFO @ Sun, 02 Jun 2019 21:07:04: 6000000 INFO @ Sun, 02 Jun 2019 21:07:10: 6000000 INFO @ Sun, 02 Jun 2019 21:07:11: 6000000 INFO @ Sun, 02 Jun 2019 21:07:12: 7000000 INFO @ Sun, 02 Jun 2019 21:07:19: 7000000 INFO @ Sun, 02 Jun 2019 21:07:20: 7000000 INFO @ Sun, 02 Jun 2019 21:07:20: 8000000 INFO @ Sun, 02 Jun 2019 21:07:27: 8000000 INFO @ Sun, 02 Jun 2019 21:07:28: 9000000 INFO @ Sun, 02 Jun 2019 21:07:29: 8000000 INFO @ Sun, 02 Jun 2019 21:07:35: 10000000 INFO @ Sun, 02 Jun 2019 21:07:36: 9000000 INFO @ Sun, 02 Jun 2019 21:07:37: 9000000 INFO @ Sun, 02 Jun 2019 21:07:42: 11000000 INFO @ Sun, 02 Jun 2019 21:07:44: 10000000 INFO @ Sun, 02 Jun 2019 21:07:44: 10000000 INFO @ Sun, 02 Jun 2019 21:07:49: 12000000 INFO @ Sun, 02 Jun 2019 21:07:52: 11000000 INFO @ Sun, 02 Jun 2019 21:07:52: 11000000 INFO @ Sun, 02 Jun 2019 21:07:56: 13000000 INFO @ Sun, 02 Jun 2019 21:08:00: 12000000 INFO @ Sun, 02 Jun 2019 21:08:01: 12000000 INFO @ Sun, 02 Jun 2019 21:08:03: 14000000 INFO @ Sun, 02 Jun 2019 21:08:07: 13000000 INFO @ Sun, 02 Jun 2019 21:08:09: 13000000 INFO @ Sun, 02 Jun 2019 21:08:10: 15000000 INFO @ Sun, 02 Jun 2019 21:08:11: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:08:11: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:08:11: #1 total tags in treatment: 15043251 INFO @ Sun, 02 Jun 2019 21:08:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:08:11: #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 21:08:11: #1 tags after filtering in treatment: 15043251 INFO @ Sun, 02 Jun 2019 21:08:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:08:11: #1 finished! INFO @ Sun, 02 Jun 2019 21:08:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:08:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:08:13: #2 number of paired peaks: 426 WARNING @ Sun, 02 Jun 2019 21:08:13: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Sun, 02 Jun 2019 21:08:13: start model_add_line... INFO @ Sun, 02 Jun 2019 21:08:13: start X-correlation... INFO @ Sun, 02 Jun 2019 21:08:13: end of X-cor INFO @ Sun, 02 Jun 2019 21:08:13: #2 finished! INFO @ Sun, 02 Jun 2019 21:08:13: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 21:08:13: #2 alternative fragment length(s) may be 2,44,580 bps INFO @ Sun, 02 Jun 2019 21:08:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.05_model.r WARNING @ Sun, 02 Jun 2019 21:08:13: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:08:13: #2 You may need to consider one of the other alternative d(s): 2,44,580 WARNING @ Sun, 02 Jun 2019 21:08:13: #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 21:08:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:08:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:08:15: 14000000 INFO @ Sun, 02 Jun 2019 21:08:17: 14000000 INFO @ Sun, 02 Jun 2019 21:08:22: 15000000 INFO @ Sun, 02 Jun 2019 21:08:22: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:08:22: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:08:22: #1 total tags in treatment: 15043251 INFO @ Sun, 02 Jun 2019 21:08:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:08:22: #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 21:08:23: #1 tags after filtering in treatment: 15043251 INFO @ Sun, 02 Jun 2019 21:08:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:08:23: #1 finished! INFO @ Sun, 02 Jun 2019 21:08:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:08:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:08:24: #2 number of paired peaks: 426 WARNING @ Sun, 02 Jun 2019 21:08:24: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Sun, 02 Jun 2019 21:08:24: start model_add_line... INFO @ Sun, 02 Jun 2019 21:08:24: start X-correlation... INFO @ Sun, 02 Jun 2019 21:08:24: end of X-cor INFO @ Sun, 02 Jun 2019 21:08:24: #2 finished! INFO @ Sun, 02 Jun 2019 21:08:24: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 21:08:24: #2 alternative fragment length(s) may be 2,44,580 bps INFO @ Sun, 02 Jun 2019 21:08:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.10_model.r WARNING @ Sun, 02 Jun 2019 21:08:24: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:08:24: #2 You may need to consider one of the other alternative d(s): 2,44,580 WARNING @ Sun, 02 Jun 2019 21:08:24: #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 21:08:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:08:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:08:25: 15000000 INFO @ Sun, 02 Jun 2019 21:08:25: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:08:25: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:08:25: #1 total tags in treatment: 15043251 INFO @ Sun, 02 Jun 2019 21:08:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:08:25: #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 21:08:26: #1 tags after filtering in treatment: 15043251 INFO @ Sun, 02 Jun 2019 21:08:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:08:26: #1 finished! INFO @ Sun, 02 Jun 2019 21:08:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:08:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:08:27: #2 number of paired peaks: 426 WARNING @ Sun, 02 Jun 2019 21:08:27: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Sun, 02 Jun 2019 21:08:27: start model_add_line... INFO @ Sun, 02 Jun 2019 21:08:27: start X-correlation... INFO @ Sun, 02 Jun 2019 21:08:27: end of X-cor INFO @ Sun, 02 Jun 2019 21:08:27: #2 finished! INFO @ Sun, 02 Jun 2019 21:08:27: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 21:08:27: #2 alternative fragment length(s) may be 2,44,580 bps INFO @ Sun, 02 Jun 2019 21:08:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.20_model.r WARNING @ Sun, 02 Jun 2019 21:08:27: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:08:27: #2 You may need to consider one of the other alternative d(s): 2,44,580 WARNING @ Sun, 02 Jun 2019 21:08:27: #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 21:08:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:08:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:08:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:09:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:09:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:09:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:09:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:09:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.05_summits.bed INFO @ Sun, 02 Jun 2019 21:09:10: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3604 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:09:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:09:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:09:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.10_summits.bed INFO @ Sun, 02 Jun 2019 21:09:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (924 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:09:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:09:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:09:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495082/SRX495082.20_summits.bed INFO @ Sun, 02 Jun 2019 21:09:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (256 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。