Job ID = 1293065 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,808,518 reads read : 12,808,518 reads written : 12,808,518 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: 00:03:13 12808518 reads; of these: 12808518 (100.00%) were unpaired; of these: 107105 (0.84%) aligned 0 times 10514447 (82.09%) aligned exactly 1 time 2186966 (17.07%) aligned >1 times 99.16% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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] 941765 / 12701413 = 0.0741 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 21:44:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.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 21:44:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:44:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:44:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.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 21:44:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:44:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:44:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.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 21:44:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:44:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:44:10: 1000000 INFO @ Sun, 02 Jun 2019 21:44:13: 1000000 INFO @ Sun, 02 Jun 2019 21:44:13: 1000000 INFO @ Sun, 02 Jun 2019 21:44:18: 2000000 INFO @ Sun, 02 Jun 2019 21:44:22: 2000000 INFO @ Sun, 02 Jun 2019 21:44:23: 2000000 INFO @ Sun, 02 Jun 2019 21:44:25: 3000000 INFO @ Sun, 02 Jun 2019 21:44:32: 3000000 INFO @ Sun, 02 Jun 2019 21:44:32: 3000000 INFO @ Sun, 02 Jun 2019 21:44:32: 4000000 INFO @ Sun, 02 Jun 2019 21:44:40: 5000000 INFO @ Sun, 02 Jun 2019 21:44:42: 4000000 INFO @ Sun, 02 Jun 2019 21:44:42: 4000000 INFO @ Sun, 02 Jun 2019 21:44:47: 6000000 INFO @ Sun, 02 Jun 2019 21:44:51: 5000000 INFO @ Sun, 02 Jun 2019 21:44:51: 5000000 INFO @ Sun, 02 Jun 2019 21:44:55: 7000000 INFO @ Sun, 02 Jun 2019 21:45:00: 6000000 INFO @ Sun, 02 Jun 2019 21:45:01: 6000000 INFO @ Sun, 02 Jun 2019 21:45:02: 8000000 INFO @ Sun, 02 Jun 2019 21:45:09: 9000000 INFO @ Sun, 02 Jun 2019 21:45:09: 7000000 INFO @ Sun, 02 Jun 2019 21:45:10: 7000000 INFO @ Sun, 02 Jun 2019 21:45:16: 10000000 INFO @ Sun, 02 Jun 2019 21:45:19: 8000000 INFO @ Sun, 02 Jun 2019 21:45:19: 8000000 INFO @ Sun, 02 Jun 2019 21:45:24: 11000000 INFO @ Sun, 02 Jun 2019 21:45:28: 9000000 INFO @ Sun, 02 Jun 2019 21:45:28: 9000000 INFO @ Sun, 02 Jun 2019 21:45:29: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:45:29: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:45:29: #1 total tags in treatment: 11759648 INFO @ Sun, 02 Jun 2019 21:45:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:45:29: #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 21:45:29: #1 tags after filtering in treatment: 11759648 INFO @ Sun, 02 Jun 2019 21:45:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:45:29: #1 finished! INFO @ Sun, 02 Jun 2019 21:45:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:45:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:45:30: #2 number of paired peaks: 305 WARNING @ Sun, 02 Jun 2019 21:45:30: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Sun, 02 Jun 2019 21:45:30: start model_add_line... INFO @ Sun, 02 Jun 2019 21:45:30: start X-correlation... INFO @ Sun, 02 Jun 2019 21:45:31: end of X-cor INFO @ Sun, 02 Jun 2019 21:45:31: #2 finished! INFO @ Sun, 02 Jun 2019 21:45:31: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 21:45:31: #2 alternative fragment length(s) may be 2,49,510 bps INFO @ Sun, 02 Jun 2019 21:45:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.10_model.r WARNING @ Sun, 02 Jun 2019 21:45:31: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:45:31: #2 You may need to consider one of the other alternative d(s): 2,49,510 WARNING @ Sun, 02 Jun 2019 21:45:31: #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 21:45:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:45:37: 10000000 INFO @ Sun, 02 Jun 2019 21:45:38: 10000000 INFO @ Sun, 02 Jun 2019 21:45:47: 11000000 INFO @ Sun, 02 Jun 2019 21:45:47: 11000000 INFO @ Sun, 02 Jun 2019 21:45:54: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:45:54: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:45:54: #1 total tags in treatment: 11759648 INFO @ Sun, 02 Jun 2019 21:45:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:45:54: #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 21:45:54: #1 tags after filtering in treatment: 11759648 INFO @ Sun, 02 Jun 2019 21:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:45:54: #1 finished! INFO @ Sun, 02 Jun 2019 21:45:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:45:54: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:45:54: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:45:54: #1 total tags in treatment: 11759648 INFO @ Sun, 02 Jun 2019 21:45:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:45:54: #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 21:45:54: #1 tags after filtering in treatment: 11759648 INFO @ Sun, 02 Jun 2019 21:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:45:54: #1 finished! INFO @ Sun, 02 Jun 2019 21:45:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:45:55: #2 number of paired peaks: 305 WARNING @ Sun, 02 Jun 2019 21:45:55: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Sun, 02 Jun 2019 21:45:55: start model_add_line... INFO @ Sun, 02 Jun 2019 21:45:55: start X-correlation... INFO @ Sun, 02 Jun 2019 21:45:55: end of X-cor INFO @ Sun, 02 Jun 2019 21:45:55: #2 finished! INFO @ Sun, 02 Jun 2019 21:45:55: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 21:45:55: #2 alternative fragment length(s) may be 2,49,510 bps INFO @ Sun, 02 Jun 2019 21:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.05_model.r WARNING @ Sun, 02 Jun 2019 21:45:55: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:45:55: #2 You may need to consider one of the other alternative d(s): 2,49,510 WARNING @ Sun, 02 Jun 2019 21:45:55: #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 21:45:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:45:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:45:55: #2 number of paired peaks: 305 WARNING @ Sun, 02 Jun 2019 21:45:55: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Sun, 02 Jun 2019 21:45:55: start model_add_line... INFO @ Sun, 02 Jun 2019 21:45:55: start X-correlation... INFO @ Sun, 02 Jun 2019 21:45:55: end of X-cor INFO @ Sun, 02 Jun 2019 21:45:55: #2 finished! INFO @ Sun, 02 Jun 2019 21:45:55: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 21:45:55: #2 alternative fragment length(s) may be 2,49,510 bps INFO @ Sun, 02 Jun 2019 21:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.20_model.r WARNING @ Sun, 02 Jun 2019 21:45:55: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:45:55: #2 You may need to consider one of the other alternative d(s): 2,49,510 WARNING @ Sun, 02 Jun 2019 21:45:55: #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 21:45:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:45:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:46:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:46:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:46:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:46:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.10_summits.bed INFO @ Sun, 02 Jun 2019 21:46:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (412 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:46:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:46:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:46:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:46:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:46:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.20_summits.bed INFO @ Sun, 02 Jun 2019 21:46:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (178 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:46:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:46:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:46:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020827/SRX5020827.05_summits.bed INFO @ Sun, 02 Jun 2019 21:46:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (629 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。