Job ID = 1293055 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,391,404 reads read : 8,391,404 reads written : 8,391,404 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: 00:02:04 8391404 reads; of these: 8391404 (100.00%) were unpaired; of these: 98456 (1.17%) aligned 0 times 6920733 (82.47%) aligned exactly 1 time 1372215 (16.35%) aligned >1 times 98.83% overall alignment rate Time searching: 00:02:04 Overall time: 00:02:04 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] 424614 / 8292948 = 0.0512 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 21:37:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.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 21:37:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:37:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:37:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.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 21:37:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:37:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:37:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.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 21:37:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:37:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:37:53: 1000000 INFO @ Sun, 02 Jun 2019 21:37:55: 1000000 INFO @ Sun, 02 Jun 2019 21:37:56: 1000000 INFO @ Sun, 02 Jun 2019 21:38:01: 2000000 INFO @ Sun, 02 Jun 2019 21:38:05: 2000000 INFO @ Sun, 02 Jun 2019 21:38:05: 2000000 INFO @ Sun, 02 Jun 2019 21:38:09: 3000000 INFO @ Sun, 02 Jun 2019 21:38:14: 3000000 INFO @ Sun, 02 Jun 2019 21:38:15: 3000000 INFO @ Sun, 02 Jun 2019 21:38:16: 4000000 INFO @ Sun, 02 Jun 2019 21:38:23: 5000000 INFO @ Sun, 02 Jun 2019 21:38:23: 4000000 INFO @ Sun, 02 Jun 2019 21:38:24: 4000000 INFO @ Sun, 02 Jun 2019 21:38:32: 6000000 INFO @ Sun, 02 Jun 2019 21:38:33: 5000000 INFO @ Sun, 02 Jun 2019 21:38:34: 5000000 INFO @ Sun, 02 Jun 2019 21:38:41: 7000000 INFO @ Sun, 02 Jun 2019 21:38:43: 6000000 INFO @ Sun, 02 Jun 2019 21:38:44: 6000000 INFO @ Sun, 02 Jun 2019 21:38:48: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:38:48: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:38:48: #1 total tags in treatment: 7868334 INFO @ Sun, 02 Jun 2019 21:38:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:38:48: #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 21:38:49: #1 tags after filtering in treatment: 7868334 INFO @ Sun, 02 Jun 2019 21:38:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:38:49: #1 finished! INFO @ Sun, 02 Jun 2019 21:38:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:38:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:38:49: #2 number of paired peaks: 351 WARNING @ Sun, 02 Jun 2019 21:38:49: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Sun, 02 Jun 2019 21:38:49: start model_add_line... INFO @ Sun, 02 Jun 2019 21:38:49: start X-correlation... INFO @ Sun, 02 Jun 2019 21:38:49: end of X-cor INFO @ Sun, 02 Jun 2019 21:38:49: #2 finished! INFO @ Sun, 02 Jun 2019 21:38:49: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 21:38:49: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 02 Jun 2019 21:38:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.20_model.r WARNING @ Sun, 02 Jun 2019 21:38:49: #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 21:38:49: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 02 Jun 2019 21:38:49: #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 21:38:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:38:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:38:53: 7000000 INFO @ Sun, 02 Jun 2019 21:38:54: 7000000 INFO @ Sun, 02 Jun 2019 21:39:01: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:39:01: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:39:01: #1 total tags in treatment: 7868334 INFO @ Sun, 02 Jun 2019 21:39:01: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:39:01: #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 21:39:01: #1 tags after filtering in treatment: 7868334 INFO @ Sun, 02 Jun 2019 21:39:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:39:01: #1 finished! INFO @ Sun, 02 Jun 2019 21:39:01: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:39:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:39:02: #2 number of paired peaks: 351 WARNING @ Sun, 02 Jun 2019 21:39:02: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Sun, 02 Jun 2019 21:39:02: start model_add_line... INFO @ Sun, 02 Jun 2019 21:39:02: start X-correlation... INFO @ Sun, 02 Jun 2019 21:39:02: end of X-cor INFO @ Sun, 02 Jun 2019 21:39:02: #2 finished! INFO @ Sun, 02 Jun 2019 21:39:02: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 21:39:02: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 02 Jun 2019 21:39:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.10_model.r WARNING @ Sun, 02 Jun 2019 21:39:02: #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 21:39:02: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 02 Jun 2019 21:39:02: #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 21:39:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:39:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:39:03: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:39:03: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:39:03: #1 total tags in treatment: 7868334 INFO @ Sun, 02 Jun 2019 21:39:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:39:03: #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 21:39:03: #1 tags after filtering in treatment: 7868334 INFO @ Sun, 02 Jun 2019 21:39:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:39:03: #1 finished! INFO @ Sun, 02 Jun 2019 21:39:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:39:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:39:03: #2 number of paired peaks: 351 WARNING @ Sun, 02 Jun 2019 21:39:03: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Sun, 02 Jun 2019 21:39:03: start model_add_line... INFO @ Sun, 02 Jun 2019 21:39:04: start X-correlation... INFO @ Sun, 02 Jun 2019 21:39:04: end of X-cor INFO @ Sun, 02 Jun 2019 21:39:04: #2 finished! INFO @ Sun, 02 Jun 2019 21:39:04: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 21:39:04: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 02 Jun 2019 21:39:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.05_model.r WARNING @ Sun, 02 Jun 2019 21:39:04: #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 21:39:04: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 02 Jun 2019 21:39:04: #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 21:39:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:39:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:39:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:39:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:39:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:39:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.20_summits.bed INFO @ Sun, 02 Jun 2019 21:39:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (146 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:39:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:39:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:39:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:39:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:39:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.10_summits.bed INFO @ Sun, 02 Jun 2019 21:39:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (359 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:39:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:39:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:39:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020819/SRX5020819.05_summits.bed INFO @ Sun, 02 Jun 2019 21:39:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (561 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。