Job ID = 2590166 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,628,764 reads read : 23,628,764 reads written : 23,628,764 rm: cannot remove ‘[DSE]RR*’: 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: 00:05:31 23628764 reads; of these: 23628764 (100.00%) were unpaired; of these: 7049574 (29.83%) aligned 0 times 12298310 (52.05%) aligned exactly 1 time 4280880 (18.12%) aligned >1 times 70.17% overall alignment rate Time searching: 00:05:31 Overall time: 00:05:31 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] 7153444 / 16579190 = 0.4315 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 20:11:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.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 20:11:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:11:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:11:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.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 20:11:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:11:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:11:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.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 20:11:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:11:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:11:22: 1000000 INFO @ Mon, 12 Aug 2019 20:11:23: 1000000 INFO @ Mon, 12 Aug 2019 20:11:24: 1000000 INFO @ Mon, 12 Aug 2019 20:11:29: 2000000 INFO @ Mon, 12 Aug 2019 20:11:30: 2000000 INFO @ Mon, 12 Aug 2019 20:11:33: 2000000 INFO @ Mon, 12 Aug 2019 20:11:37: 3000000 INFO @ Mon, 12 Aug 2019 20:11:38: 3000000 INFO @ Mon, 12 Aug 2019 20:11:41: 3000000 INFO @ Mon, 12 Aug 2019 20:11:44: 4000000 INFO @ Mon, 12 Aug 2019 20:11:45: 4000000 INFO @ Mon, 12 Aug 2019 20:11:50: 4000000 INFO @ Mon, 12 Aug 2019 20:11:52: 5000000 INFO @ Mon, 12 Aug 2019 20:11:53: 5000000 INFO @ Mon, 12 Aug 2019 20:11:58: 5000000 INFO @ Mon, 12 Aug 2019 20:11:59: 6000000 INFO @ Mon, 12 Aug 2019 20:12:00: 6000000 INFO @ Mon, 12 Aug 2019 20:12:07: 7000000 INFO @ Mon, 12 Aug 2019 20:12:07: 6000000 INFO @ Mon, 12 Aug 2019 20:12:08: 7000000 INFO @ Mon, 12 Aug 2019 20:12:14: 8000000 INFO @ Mon, 12 Aug 2019 20:12:15: 8000000 INFO @ Mon, 12 Aug 2019 20:12:15: 7000000 INFO @ Mon, 12 Aug 2019 20:12:22: 9000000 INFO @ Mon, 12 Aug 2019 20:12:23: 9000000 INFO @ Mon, 12 Aug 2019 20:12:24: 8000000 INFO @ Mon, 12 Aug 2019 20:12:25: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:12:25: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:12:25: #1 total tags in treatment: 9425746 INFO @ Mon, 12 Aug 2019 20:12:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:12:25: #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 20:12:25: #1 tags after filtering in treatment: 9425746 INFO @ Mon, 12 Aug 2019 20:12:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:12:25: #1 finished! INFO @ Mon, 12 Aug 2019 20:12:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:12:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:12:26: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:12:26: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:12:26: #1 total tags in treatment: 9425746 INFO @ Mon, 12 Aug 2019 20:12:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:12:26: #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 20:12:26: #1 tags after filtering in treatment: 9425746 INFO @ Mon, 12 Aug 2019 20:12:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:12:26: #1 finished! INFO @ Mon, 12 Aug 2019 20:12:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:12:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:12:26: #2 number of paired peaks: 794 WARNING @ Mon, 12 Aug 2019 20:12:26: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Mon, 12 Aug 2019 20:12:26: start model_add_line... INFO @ Mon, 12 Aug 2019 20:12:26: start X-correlation... INFO @ Mon, 12 Aug 2019 20:12:26: end of X-cor INFO @ Mon, 12 Aug 2019 20:12:26: #2 finished! INFO @ Mon, 12 Aug 2019 20:12:26: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 20:12:26: #2 alternative fragment length(s) may be 2,47 bps INFO @ Mon, 12 Aug 2019 20:12:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.05_model.r WARNING @ Mon, 12 Aug 2019 20:12:26: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:12:26: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Mon, 12 Aug 2019 20:12:26: #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 20:12:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:12:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:12:27: #2 number of paired peaks: 794 WARNING @ Mon, 12 Aug 2019 20:12:27: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Mon, 12 Aug 2019 20:12:27: start model_add_line... INFO @ Mon, 12 Aug 2019 20:12:27: start X-correlation... INFO @ Mon, 12 Aug 2019 20:12:27: end of X-cor INFO @ Mon, 12 Aug 2019 20:12:27: #2 finished! INFO @ Mon, 12 Aug 2019 20:12:27: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 20:12:27: #2 alternative fragment length(s) may be 2,47 bps INFO @ Mon, 12 Aug 2019 20:12:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.10_model.r WARNING @ Mon, 12 Aug 2019 20:12:27: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:12:27: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Mon, 12 Aug 2019 20:12:27: #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 20:12:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:12:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:12:32: 9000000 INFO @ Mon, 12 Aug 2019 20:12:35: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:12:35: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:12:35: #1 total tags in treatment: 9425746 INFO @ Mon, 12 Aug 2019 20:12:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:12:35: #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 20:12:36: #1 tags after filtering in treatment: 9425746 INFO @ Mon, 12 Aug 2019 20:12:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:12:36: #1 finished! INFO @ Mon, 12 Aug 2019 20:12:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:12:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:12:36: #2 number of paired peaks: 794 WARNING @ Mon, 12 Aug 2019 20:12:36: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Mon, 12 Aug 2019 20:12:36: start model_add_line... INFO @ Mon, 12 Aug 2019 20:12:37: start X-correlation... INFO @ Mon, 12 Aug 2019 20:12:37: end of X-cor INFO @ Mon, 12 Aug 2019 20:12:37: #2 finished! INFO @ Mon, 12 Aug 2019 20:12:37: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 20:12:37: #2 alternative fragment length(s) may be 2,47 bps INFO @ Mon, 12 Aug 2019 20:12:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.20_model.r WARNING @ Mon, 12 Aug 2019 20:12:37: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:12:37: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Mon, 12 Aug 2019 20:12:37: #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 20:12:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:12:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:12:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:12:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:13:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:13:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:13:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:13:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.05_summits.bed INFO @ Mon, 12 Aug 2019 20:13:04: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2017 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:13:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:13:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:13:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.10_summits.bed INFO @ Mon, 12 Aug 2019 20:13:05: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (845 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:13:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:13:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:13:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495040/SRX495040.20_summits.bed INFO @ Mon, 12 Aug 2019 20:13:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (274 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。