Job ID = 1292950 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,810,147 reads read : 10,810,147 reads written : 10,810,147 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: 00:02:16 10810147 reads; of these: 10810147 (100.00%) were unpaired; of these: 3739693 (34.59%) aligned 0 times 5872680 (54.33%) aligned exactly 1 time 1197774 (11.08%) aligned >1 times 65.41% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 638402 / 7070454 = 0.0903 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 21:12:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.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 21:12:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:12:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:12:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.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 21:12:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:12:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:12:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.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 21:12:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:12:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:12:58: 1000000 INFO @ Sun, 02 Jun 2019 21:13:00: 1000000 INFO @ Sun, 02 Jun 2019 21:13:00: 1000000 INFO @ Sun, 02 Jun 2019 21:13:06: 2000000 INFO @ Sun, 02 Jun 2019 21:13:10: 2000000 INFO @ Sun, 02 Jun 2019 21:13:10: 2000000 INFO @ Sun, 02 Jun 2019 21:13:15: 3000000 INFO @ Sun, 02 Jun 2019 21:13:20: 3000000 INFO @ Sun, 02 Jun 2019 21:13:21: 3000000 INFO @ Sun, 02 Jun 2019 21:13:23: 4000000 INFO @ Sun, 02 Jun 2019 21:13:30: 4000000 INFO @ Sun, 02 Jun 2019 21:13:31: 4000000 INFO @ Sun, 02 Jun 2019 21:13:31: 5000000 INFO @ Sun, 02 Jun 2019 21:13:40: 6000000 INFO @ Sun, 02 Jun 2019 21:13:40: 5000000 INFO @ Sun, 02 Jun 2019 21:13:41: 5000000 INFO @ Sun, 02 Jun 2019 21:13:43: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:13:43: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:13:43: #1 total tags in treatment: 6432052 INFO @ Sun, 02 Jun 2019 21:13:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:13:43: #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 21:13:43: #1 tags after filtering in treatment: 6432052 INFO @ Sun, 02 Jun 2019 21:13:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:13:43: #1 finished! INFO @ Sun, 02 Jun 2019 21:13:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:13:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:13:44: #2 number of paired peaks: 339 WARNING @ Sun, 02 Jun 2019 21:13:44: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sun, 02 Jun 2019 21:13:44: start model_add_line... INFO @ Sun, 02 Jun 2019 21:13:44: start X-correlation... INFO @ Sun, 02 Jun 2019 21:13:44: end of X-cor INFO @ Sun, 02 Jun 2019 21:13:44: #2 finished! INFO @ Sun, 02 Jun 2019 21:13:44: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:13:44: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sun, 02 Jun 2019 21:13:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.20_model.r WARNING @ Sun, 02 Jun 2019 21:13:44: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:13:44: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sun, 02 Jun 2019 21:13:44: #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 21:13:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:13:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:13:49: 6000000 INFO @ Sun, 02 Jun 2019 21:13:51: 6000000 INFO @ Sun, 02 Jun 2019 21:13:53: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:13:53: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:13:53: #1 total tags in treatment: 6432052 INFO @ Sun, 02 Jun 2019 21:13:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:13:53: #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 21:13:54: #1 tags after filtering in treatment: 6432052 INFO @ Sun, 02 Jun 2019 21:13:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:13:54: #1 finished! INFO @ Sun, 02 Jun 2019 21:13:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:13:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:13:54: #2 number of paired peaks: 339 WARNING @ Sun, 02 Jun 2019 21:13:54: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sun, 02 Jun 2019 21:13:54: start model_add_line... INFO @ Sun, 02 Jun 2019 21:13:54: start X-correlation... INFO @ Sun, 02 Jun 2019 21:13:54: end of X-cor INFO @ Sun, 02 Jun 2019 21:13:54: #2 finished! INFO @ Sun, 02 Jun 2019 21:13:54: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:13:54: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sun, 02 Jun 2019 21:13:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.10_model.r WARNING @ Sun, 02 Jun 2019 21:13:54: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:13:54: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sun, 02 Jun 2019 21:13:54: #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 21:13:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:13:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:13:55: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:13:55: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:13:55: #1 total tags in treatment: 6432052 INFO @ Sun, 02 Jun 2019 21:13:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:13:55: #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 21:13:55: #1 tags after filtering in treatment: 6432052 INFO @ Sun, 02 Jun 2019 21:13:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:13:55: #1 finished! INFO @ Sun, 02 Jun 2019 21:13:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:13:55: #2 number of paired peaks: 339 WARNING @ Sun, 02 Jun 2019 21:13:55: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sun, 02 Jun 2019 21:13:55: start model_add_line... INFO @ Sun, 02 Jun 2019 21:13:55: start X-correlation... INFO @ Sun, 02 Jun 2019 21:13:55: end of X-cor INFO @ Sun, 02 Jun 2019 21:13:55: #2 finished! INFO @ Sun, 02 Jun 2019 21:13:55: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:13:55: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sun, 02 Jun 2019 21:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.05_model.r WARNING @ Sun, 02 Jun 2019 21:13:55: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:13:55: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sun, 02 Jun 2019 21:13:55: #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 21:13:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:14:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:14:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:14:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:14:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.20_summits.bed INFO @ Sun, 02 Jun 2019 21:14:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (126 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:14:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:14:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:14:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:14:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:14:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.10_summits.bed INFO @ Sun, 02 Jun 2019 21:14:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (294 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:14:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:14:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:14:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020735/SRX5020735.05_summits.bed INFO @ Sun, 02 Jun 2019 21:14:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (498 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。