Job ID = 1292994 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,036,313 reads read : 36,072,626 reads written : 18,036,313 reads 0-length : 18,036,313 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: 00:06:36 18036313 reads; of these: 18036313 (100.00%) were unpaired; of these: 1748419 (9.69%) aligned 0 times 13638467 (75.62%) aligned exactly 1 time 2649427 (14.69%) aligned >1 times 90.31% overall alignment rate Time searching: 00:06:36 Overall time: 00:06:36 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] 3005316 / 16287894 = 0.1845 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 21:35:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.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 21:35:11: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:35:11: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:35:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.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 21:35:11: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:35:11: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:35:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.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 21:35:11: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:35:11: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:35:18: 1000000 INFO @ Sun, 02 Jun 2019 21:35:19: 1000000 INFO @ Sun, 02 Jun 2019 21:35:20: 1000000 INFO @ Sun, 02 Jun 2019 21:35:25: 2000000 INFO @ Sun, 02 Jun 2019 21:35:27: 2000000 INFO @ Sun, 02 Jun 2019 21:35:27: 2000000 INFO @ Sun, 02 Jun 2019 21:35:31: 3000000 INFO @ Sun, 02 Jun 2019 21:35:34: 3000000 INFO @ Sun, 02 Jun 2019 21:35:35: 3000000 INFO @ Sun, 02 Jun 2019 21:35:38: 4000000 INFO @ Sun, 02 Jun 2019 21:35:41: 4000000 INFO @ Sun, 02 Jun 2019 21:35:42: 4000000 INFO @ Sun, 02 Jun 2019 21:35:45: 5000000 INFO @ Sun, 02 Jun 2019 21:35:48: 5000000 INFO @ Sun, 02 Jun 2019 21:35:50: 5000000 INFO @ Sun, 02 Jun 2019 21:35:51: 6000000 INFO @ Sun, 02 Jun 2019 21:35:55: 6000000 INFO @ Sun, 02 Jun 2019 21:35:57: 6000000 INFO @ Sun, 02 Jun 2019 21:35:58: 7000000 INFO @ Sun, 02 Jun 2019 21:36:03: 7000000 INFO @ Sun, 02 Jun 2019 21:36:04: 8000000 INFO @ Sun, 02 Jun 2019 21:36:05: 7000000 INFO @ Sun, 02 Jun 2019 21:36:10: 8000000 INFO @ Sun, 02 Jun 2019 21:36:11: 9000000 INFO @ Sun, 02 Jun 2019 21:36:12: 8000000 INFO @ Sun, 02 Jun 2019 21:36:17: 9000000 INFO @ Sun, 02 Jun 2019 21:36:19: 10000000 INFO @ Sun, 02 Jun 2019 21:36:20: 9000000 INFO @ Sun, 02 Jun 2019 21:36:25: 10000000 INFO @ Sun, 02 Jun 2019 21:36:27: 11000000 INFO @ Sun, 02 Jun 2019 21:36:28: 10000000 INFO @ Sun, 02 Jun 2019 21:36:32: 11000000 INFO @ Sun, 02 Jun 2019 21:36:33: 12000000 INFO @ Sun, 02 Jun 2019 21:36:35: 11000000 INFO @ Sun, 02 Jun 2019 21:36:39: 12000000 INFO @ Sun, 02 Jun 2019 21:36:40: 13000000 INFO @ Sun, 02 Jun 2019 21:36:42: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:36:42: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:36:42: #1 total tags in treatment: 13282578 INFO @ Sun, 02 Jun 2019 21:36:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:36:42: #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 21:36:42: #1 tags after filtering in treatment: 13282578 INFO @ Sun, 02 Jun 2019 21:36:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:36:42: #1 finished! INFO @ Sun, 02 Jun 2019 21:36:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:36:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:36:43: 12000000 INFO @ Sun, 02 Jun 2019 21:36:43: #2 number of paired peaks: 407 WARNING @ Sun, 02 Jun 2019 21:36:43: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Sun, 02 Jun 2019 21:36:43: start model_add_line... INFO @ Sun, 02 Jun 2019 21:36:43: start X-correlation... INFO @ Sun, 02 Jun 2019 21:36:43: end of X-cor INFO @ Sun, 02 Jun 2019 21:36:43: #2 finished! INFO @ Sun, 02 Jun 2019 21:36:43: #2 predicted fragment length is 88 bps INFO @ Sun, 02 Jun 2019 21:36:43: #2 alternative fragment length(s) may be 4,88 bps INFO @ Sun, 02 Jun 2019 21:36:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.10_model.r WARNING @ Sun, 02 Jun 2019 21:36:43: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:36:43: #2 You may need to consider one of the other alternative d(s): 4,88 WARNING @ Sun, 02 Jun 2019 21:36:43: #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 21:36:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:36:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:36:46: 13000000 INFO @ Sun, 02 Jun 2019 21:36:48: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:36:48: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:36:48: #1 total tags in treatment: 13282578 INFO @ Sun, 02 Jun 2019 21:36:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:36:48: #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 21:36:49: #1 tags after filtering in treatment: 13282578 INFO @ Sun, 02 Jun 2019 21:36:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:36:49: #1 finished! INFO @ Sun, 02 Jun 2019 21:36:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:36:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:36:50: #2 number of paired peaks: 407 WARNING @ Sun, 02 Jun 2019 21:36:50: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Sun, 02 Jun 2019 21:36:50: start model_add_line... INFO @ Sun, 02 Jun 2019 21:36:50: start X-correlation... INFO @ Sun, 02 Jun 2019 21:36:50: end of X-cor INFO @ Sun, 02 Jun 2019 21:36:50: #2 finished! INFO @ Sun, 02 Jun 2019 21:36:50: #2 predicted fragment length is 88 bps INFO @ Sun, 02 Jun 2019 21:36:50: #2 alternative fragment length(s) may be 4,88 bps INFO @ Sun, 02 Jun 2019 21:36:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.05_model.r WARNING @ Sun, 02 Jun 2019 21:36:50: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:36:50: #2 You may need to consider one of the other alternative d(s): 4,88 WARNING @ Sun, 02 Jun 2019 21:36:50: #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 21:36:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:36:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:36:50: 13000000 INFO @ Sun, 02 Jun 2019 21:36:52: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:36:52: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:36:52: #1 total tags in treatment: 13282578 INFO @ Sun, 02 Jun 2019 21:36:52: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:36:52: #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 21:36:53: #1 tags after filtering in treatment: 13282578 INFO @ Sun, 02 Jun 2019 21:36:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:36:53: #1 finished! INFO @ Sun, 02 Jun 2019 21:36:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:36:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:36:54: #2 number of paired peaks: 407 WARNING @ Sun, 02 Jun 2019 21:36:54: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Sun, 02 Jun 2019 21:36:54: start model_add_line... INFO @ Sun, 02 Jun 2019 21:36:54: start X-correlation... INFO @ Sun, 02 Jun 2019 21:36:54: end of X-cor INFO @ Sun, 02 Jun 2019 21:36:54: #2 finished! INFO @ Sun, 02 Jun 2019 21:36:54: #2 predicted fragment length is 88 bps INFO @ Sun, 02 Jun 2019 21:36:54: #2 alternative fragment length(s) may be 4,88 bps INFO @ Sun, 02 Jun 2019 21:36:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.20_model.r WARNING @ Sun, 02 Jun 2019 21:36:54: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:36:54: #2 You may need to consider one of the other alternative d(s): 4,88 WARNING @ Sun, 02 Jun 2019 21:36:54: #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 21:36:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:36:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:37:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:37:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:37:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:37:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:37:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:37:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.10_summits.bed INFO @ Sun, 02 Jun 2019 21:37:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (565 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:37:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:37:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:37:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.05_summits.bed INFO @ Sun, 02 Jun 2019 21:37:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1021 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:37:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:37:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:37:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020769/SRX5020769.20_summits.bed INFO @ Sun, 02 Jun 2019 21:37:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (308 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。