Job ID = 2589756 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,588,024 reads read : 7,588,024 reads written : 7,588,024 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947362.sra.cache’: 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: 00:01:22 7588024 reads; of these: 7588024 (100.00%) were unpaired; of these: 82116 (1.08%) aligned 0 times 6335237 (83.49%) aligned exactly 1 time 1170671 (15.43%) aligned >1 times 98.92% overall alignment rate Time searching: 00:01:22 Overall time: 00:01:22 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_rmdupse_core] 628682 / 7505908 = 0.0838 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 18:26:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.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 18:26:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:26:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:26:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.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 18:26:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:26:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:26:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.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 18:26:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:26:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:26:48: 1000000 INFO @ Mon, 12 Aug 2019 18:26:49: 1000000 INFO @ Mon, 12 Aug 2019 18:26:50: 1000000 INFO @ Mon, 12 Aug 2019 18:26:56: 2000000 INFO @ Mon, 12 Aug 2019 18:26:57: 2000000 INFO @ Mon, 12 Aug 2019 18:26:58: 2000000 INFO @ Mon, 12 Aug 2019 18:27:04: 3000000 INFO @ Mon, 12 Aug 2019 18:27:04: 3000000 INFO @ Mon, 12 Aug 2019 18:27:05: 3000000 INFO @ Mon, 12 Aug 2019 18:27:11: 4000000 INFO @ Mon, 12 Aug 2019 18:27:11: 4000000 INFO @ Mon, 12 Aug 2019 18:27:13: 4000000 INFO @ Mon, 12 Aug 2019 18:27:19: 5000000 INFO @ Mon, 12 Aug 2019 18:27:19: 5000000 INFO @ Mon, 12 Aug 2019 18:27:20: 5000000 INFO @ Mon, 12 Aug 2019 18:27:26: 6000000 INFO @ Mon, 12 Aug 2019 18:27:26: 6000000 INFO @ Mon, 12 Aug 2019 18:27:28: 6000000 INFO @ Mon, 12 Aug 2019 18:27:33: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:27:33: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:27:33: #1 total tags in treatment: 6877226 INFO @ Mon, 12 Aug 2019 18:27:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:27:33: #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 18:27:33: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:27:33: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:27:33: #1 total tags in treatment: 6877226 INFO @ Mon, 12 Aug 2019 18:27:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:27:33: #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 18:27:33: #1 tags after filtering in treatment: 6877226 INFO @ Mon, 12 Aug 2019 18:27:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:27:33: #1 finished! INFO @ Mon, 12 Aug 2019 18:27:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:27:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:27:33: #1 tags after filtering in treatment: 6877226 INFO @ Mon, 12 Aug 2019 18:27:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:27:33: #1 finished! INFO @ Mon, 12 Aug 2019 18:27:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:27:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:27:34: #2 number of paired peaks: 429 WARNING @ Mon, 12 Aug 2019 18:27:34: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Mon, 12 Aug 2019 18:27:34: start model_add_line... INFO @ Mon, 12 Aug 2019 18:27:34: start X-correlation... INFO @ Mon, 12 Aug 2019 18:27:34: end of X-cor INFO @ Mon, 12 Aug 2019 18:27:34: #2 finished! INFO @ Mon, 12 Aug 2019 18:27:34: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 18:27:34: #2 alternative fragment length(s) may be 3,30,544,590 bps INFO @ Mon, 12 Aug 2019 18:27:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.05_model.r WARNING @ Mon, 12 Aug 2019 18:27:34: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:27:34: #2 You may need to consider one of the other alternative d(s): 3,30,544,590 WARNING @ Mon, 12 Aug 2019 18:27:34: #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 18:27:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:27:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:27:34: #2 number of paired peaks: 429 WARNING @ Mon, 12 Aug 2019 18:27:34: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Mon, 12 Aug 2019 18:27:34: start model_add_line... INFO @ Mon, 12 Aug 2019 18:27:34: start X-correlation... INFO @ Mon, 12 Aug 2019 18:27:34: end of X-cor INFO @ Mon, 12 Aug 2019 18:27:34: #2 finished! INFO @ Mon, 12 Aug 2019 18:27:34: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 18:27:34: #2 alternative fragment length(s) may be 3,30,544,590 bps INFO @ Mon, 12 Aug 2019 18:27:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.10_model.r WARNING @ Mon, 12 Aug 2019 18:27:34: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:27:34: #2 You may need to consider one of the other alternative d(s): 3,30,544,590 WARNING @ Mon, 12 Aug 2019 18:27:34: #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 18:27:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:27:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:27:34: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:27:34: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:27:34: #1 total tags in treatment: 6877226 INFO @ Mon, 12 Aug 2019 18:27:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:27:34: #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 18:27:34: #1 tags after filtering in treatment: 6877226 INFO @ Mon, 12 Aug 2019 18:27:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:27:34: #1 finished! INFO @ Mon, 12 Aug 2019 18:27:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:27:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:27:35: #2 number of paired peaks: 429 WARNING @ Mon, 12 Aug 2019 18:27:35: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Mon, 12 Aug 2019 18:27:35: start model_add_line... INFO @ Mon, 12 Aug 2019 18:27:35: start X-correlation... INFO @ Mon, 12 Aug 2019 18:27:35: end of X-cor INFO @ Mon, 12 Aug 2019 18:27:35: #2 finished! INFO @ Mon, 12 Aug 2019 18:27:35: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 18:27:35: #2 alternative fragment length(s) may be 3,30,544,590 bps INFO @ Mon, 12 Aug 2019 18:27:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.20_model.r WARNING @ Mon, 12 Aug 2019 18:27:35: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:27:35: #2 You may need to consider one of the other alternative d(s): 3,30,544,590 WARNING @ Mon, 12 Aug 2019 18:27:35: #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 18:27:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:27:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:27:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:27:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:27:54: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:28:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.10_summits.bed INFO @ Mon, 12 Aug 2019 18:28:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (259 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:28:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.05_summits.bed INFO @ Mon, 12 Aug 2019 18:28:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (505 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:28:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:28:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:28:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331131/SRX331131.20_summits.bed INFO @ Mon, 12 Aug 2019 18:28:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (65 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。