Job ID = 1293058 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,038,573 reads read : 12,038,573 reads written : 12,038,573 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: 00:02:52 12038573 reads; of these: 12038573 (100.00%) were unpaired; of these: 161346 (1.34%) aligned 0 times 9942849 (82.59%) aligned exactly 1 time 1934378 (16.07%) aligned >1 times 98.66% overall alignment rate Time searching: 00:02:52 Overall time: 00:02:52 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] 887347 / 11877227 = 0.0747 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 21:42:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.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 21:42:11: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:42:11: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.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 21:42:11: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:42:11: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.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 21:42:11: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:42:11: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:18: 1000000 INFO @ Sun, 02 Jun 2019 21:42:19: 1000000 INFO @ Sun, 02 Jun 2019 21:42:21: 1000000 INFO @ Sun, 02 Jun 2019 21:42:25: 2000000 INFO @ Sun, 02 Jun 2019 21:42:28: 2000000 INFO @ Sun, 02 Jun 2019 21:42:30: 2000000 INFO @ Sun, 02 Jun 2019 21:42:33: 3000000 INFO @ Sun, 02 Jun 2019 21:42:36: 3000000 INFO @ Sun, 02 Jun 2019 21:42:40: 3000000 INFO @ Sun, 02 Jun 2019 21:42:40: 4000000 INFO @ Sun, 02 Jun 2019 21:42:44: 4000000 INFO @ Sun, 02 Jun 2019 21:42:48: 5000000 INFO @ Sun, 02 Jun 2019 21:42:49: 4000000 INFO @ Sun, 02 Jun 2019 21:42:53: 5000000 INFO @ Sun, 02 Jun 2019 21:42:55: 6000000 INFO @ Sun, 02 Jun 2019 21:42:59: 5000000 INFO @ Sun, 02 Jun 2019 21:43:01: 6000000 INFO @ Sun, 02 Jun 2019 21:43:02: 7000000 INFO @ Sun, 02 Jun 2019 21:43:08: 6000000 INFO @ Sun, 02 Jun 2019 21:43:09: 7000000 INFO @ Sun, 02 Jun 2019 21:43:10: 8000000 INFO @ Sun, 02 Jun 2019 21:43:17: 9000000 INFO @ Sun, 02 Jun 2019 21:43:17: 7000000 INFO @ Sun, 02 Jun 2019 21:43:17: 8000000 INFO @ Sun, 02 Jun 2019 21:43:24: 10000000 INFO @ Sun, 02 Jun 2019 21:43:25: 9000000 INFO @ Sun, 02 Jun 2019 21:43:26: 8000000 INFO @ Sun, 02 Jun 2019 21:43:31: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:43:31: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:43:31: #1 total tags in treatment: 10989880 INFO @ Sun, 02 Jun 2019 21:43:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:43:31: #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 21:43:31: #1 tags after filtering in treatment: 10989880 INFO @ Sun, 02 Jun 2019 21:43:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:43:31: #1 finished! INFO @ Sun, 02 Jun 2019 21:43:31: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:43:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:43:32: #2 number of paired peaks: 287 WARNING @ Sun, 02 Jun 2019 21:43:32: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Sun, 02 Jun 2019 21:43:32: start model_add_line... INFO @ Sun, 02 Jun 2019 21:43:32: start X-correlation... INFO @ Sun, 02 Jun 2019 21:43:32: end of X-cor INFO @ Sun, 02 Jun 2019 21:43:32: #2 finished! INFO @ Sun, 02 Jun 2019 21:43:32: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 21:43:32: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 02 Jun 2019 21:43:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.10_model.r WARNING @ Sun, 02 Jun 2019 21:43:32: #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 21:43:32: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 02 Jun 2019 21:43:32: #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 21:43:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:43:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:43:33: 10000000 INFO @ Sun, 02 Jun 2019 21:43:36: 9000000 INFO @ Sun, 02 Jun 2019 21:43:41: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:43:41: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:43:41: #1 total tags in treatment: 10989880 INFO @ Sun, 02 Jun 2019 21:43:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:43:41: #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 21:43:42: #1 tags after filtering in treatment: 10989880 INFO @ Sun, 02 Jun 2019 21:43:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:43:42: #1 finished! INFO @ Sun, 02 Jun 2019 21:43:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:43:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:43:43: #2 number of paired peaks: 287 WARNING @ Sun, 02 Jun 2019 21:43:43: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Sun, 02 Jun 2019 21:43:43: start model_add_line... INFO @ Sun, 02 Jun 2019 21:43:43: start X-correlation... INFO @ Sun, 02 Jun 2019 21:43:43: end of X-cor INFO @ Sun, 02 Jun 2019 21:43:43: #2 finished! INFO @ Sun, 02 Jun 2019 21:43:43: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 21:43:43: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 02 Jun 2019 21:43:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.20_model.r WARNING @ Sun, 02 Jun 2019 21:43:43: #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 21:43:43: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 02 Jun 2019 21:43:43: #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 21:43:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:43:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:43:45: 10000000 INFO @ Sun, 02 Jun 2019 21:43:54: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:43:54: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:43:54: #1 total tags in treatment: 10989880 INFO @ Sun, 02 Jun 2019 21:43:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:43:54: #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 21:43:54: #1 tags after filtering in treatment: 10989880 INFO @ Sun, 02 Jun 2019 21:43:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:43:54: #1 finished! INFO @ Sun, 02 Jun 2019 21:43:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:43:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:43:55: #2 number of paired peaks: 287 WARNING @ Sun, 02 Jun 2019 21:43:55: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Sun, 02 Jun 2019 21:43:55: start model_add_line... INFO @ Sun, 02 Jun 2019 21:43:55: start X-correlation... INFO @ Sun, 02 Jun 2019 21:43:55: end of X-cor INFO @ Sun, 02 Jun 2019 21:43:55: #2 finished! INFO @ Sun, 02 Jun 2019 21:43:55: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 21:43:55: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 02 Jun 2019 21:43:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.05_model.r WARNING @ Sun, 02 Jun 2019 21:43:55: #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 21:43:55: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 02 Jun 2019 21:43:55: #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 21:43:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:43:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:44:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:44:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:44:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:44:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:44:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.10_summits.bed INFO @ Sun, 02 Jun 2019 21:44:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (390 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:44:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:44:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:44:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:44:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.20_summits.bed INFO @ Sun, 02 Jun 2019 21:44:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (160 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:44:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:44:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:44:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020822/SRX5020822.05_summits.bed INFO @ Sun, 02 Jun 2019 21:44:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (582 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。