Job ID = 2590167 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,970,231 reads read : 22,970,231 reads written : 22,970,231 rm: cannot remove ‘[DSE]RR*’: 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: 00:05:24 22970231 reads; of these: 22970231 (100.00%) were unpaired; of these: 2517629 (10.96%) aligned 0 times 16805823 (73.16%) aligned exactly 1 time 3646779 (15.88%) aligned >1 times 89.04% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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 12 files... [bam_rmdupse_core] 2297357 / 20452602 = 0.1123 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 @ Mon, 12 Aug 2019 20:14:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.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 @ Mon, 12 Aug 2019 20:14:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:14:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:14:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.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 @ Mon, 12 Aug 2019 20:14:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:14:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:14:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.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 @ Mon, 12 Aug 2019 20:14:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:14:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:14:20: 1000000 INFO @ Mon, 12 Aug 2019 20:14:21: 1000000 INFO @ Mon, 12 Aug 2019 20:14:21: 1000000 INFO @ Mon, 12 Aug 2019 20:14:27: 2000000 INFO @ Mon, 12 Aug 2019 20:14:28: 2000000 INFO @ Mon, 12 Aug 2019 20:14:29: 2000000 INFO @ Mon, 12 Aug 2019 20:14:34: 3000000 INFO @ Mon, 12 Aug 2019 20:14:36: 3000000 INFO @ Mon, 12 Aug 2019 20:14:37: 3000000 INFO @ Mon, 12 Aug 2019 20:14:41: 4000000 INFO @ Mon, 12 Aug 2019 20:14:45: 4000000 INFO @ Mon, 12 Aug 2019 20:14:45: 4000000 INFO @ Mon, 12 Aug 2019 20:14:47: 5000000 INFO @ Mon, 12 Aug 2019 20:14:53: 5000000 INFO @ Mon, 12 Aug 2019 20:14:53: 5000000 INFO @ Mon, 12 Aug 2019 20:14:54: 6000000 INFO @ Mon, 12 Aug 2019 20:15:00: 7000000 INFO @ Mon, 12 Aug 2019 20:15:01: 6000000 INFO @ Mon, 12 Aug 2019 20:15:01: 6000000 INFO @ Mon, 12 Aug 2019 20:15:07: 8000000 INFO @ Mon, 12 Aug 2019 20:15:09: 7000000 INFO @ Mon, 12 Aug 2019 20:15:09: 7000000 INFO @ Mon, 12 Aug 2019 20:15:14: 9000000 INFO @ Mon, 12 Aug 2019 20:15:17: 8000000 INFO @ Mon, 12 Aug 2019 20:15:18: 8000000 INFO @ Mon, 12 Aug 2019 20:15:20: 10000000 INFO @ Mon, 12 Aug 2019 20:15:24: 9000000 INFO @ Mon, 12 Aug 2019 20:15:26: 9000000 INFO @ Mon, 12 Aug 2019 20:15:27: 11000000 INFO @ Mon, 12 Aug 2019 20:15:32: 10000000 INFO @ Mon, 12 Aug 2019 20:15:33: 12000000 INFO @ Mon, 12 Aug 2019 20:15:34: 10000000 INFO @ Mon, 12 Aug 2019 20:15:40: 11000000 INFO @ Mon, 12 Aug 2019 20:15:41: 13000000 INFO @ Mon, 12 Aug 2019 20:15:42: 11000000 INFO @ Mon, 12 Aug 2019 20:15:47: 14000000 INFO @ Mon, 12 Aug 2019 20:15:48: 12000000 INFO @ Mon, 12 Aug 2019 20:15:50: 12000000 INFO @ Mon, 12 Aug 2019 20:15:54: 15000000 INFO @ Mon, 12 Aug 2019 20:15:55: 13000000 INFO @ Mon, 12 Aug 2019 20:15:57: 13000000 INFO @ Mon, 12 Aug 2019 20:16:01: 16000000 INFO @ Mon, 12 Aug 2019 20:16:03: 14000000 INFO @ Mon, 12 Aug 2019 20:16:05: 14000000 INFO @ Mon, 12 Aug 2019 20:16:08: 17000000 INFO @ Mon, 12 Aug 2019 20:16:11: 15000000 INFO @ Mon, 12 Aug 2019 20:16:14: 15000000 INFO @ Mon, 12 Aug 2019 20:16:17: 18000000 INFO @ Mon, 12 Aug 2019 20:16:18: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:16:18: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:16:18: #1 total tags in treatment: 18155245 INFO @ Mon, 12 Aug 2019 20:16:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:16:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:16:19: #1 tags after filtering in treatment: 18155245 INFO @ Mon, 12 Aug 2019 20:16:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:16:19: #1 finished! INFO @ Mon, 12 Aug 2019 20:16:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:16:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:16:19: 16000000 INFO @ Mon, 12 Aug 2019 20:16:20: #2 number of paired peaks: 259 WARNING @ Mon, 12 Aug 2019 20:16:20: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Mon, 12 Aug 2019 20:16:20: start model_add_line... INFO @ Mon, 12 Aug 2019 20:16:20: start X-correlation... INFO @ Mon, 12 Aug 2019 20:16:20: end of X-cor INFO @ Mon, 12 Aug 2019 20:16:20: #2 finished! INFO @ Mon, 12 Aug 2019 20:16:20: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 20:16:20: #2 alternative fragment length(s) may be 2,47 bps INFO @ Mon, 12 Aug 2019 20:16:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.20_model.r WARNING @ Mon, 12 Aug 2019 20:16:20: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:16:20: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Mon, 12 Aug 2019 20:16:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:16:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:16:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:16:22: 16000000 INFO @ Mon, 12 Aug 2019 20:16:27: 17000000 INFO @ Mon, 12 Aug 2019 20:16:30: 17000000 INFO @ Mon, 12 Aug 2019 20:16:35: 18000000 INFO @ Mon, 12 Aug 2019 20:16:37: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:16:37: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:16:37: #1 total tags in treatment: 18155245 INFO @ Mon, 12 Aug 2019 20:16:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:16:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:16:37: #1 tags after filtering in treatment: 18155245 INFO @ Mon, 12 Aug 2019 20:16:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:16:37: #1 finished! INFO @ Mon, 12 Aug 2019 20:16:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:16:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:16:38: #2 number of paired peaks: 259 WARNING @ Mon, 12 Aug 2019 20:16:38: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Mon, 12 Aug 2019 20:16:38: start model_add_line... INFO @ Mon, 12 Aug 2019 20:16:39: start X-correlation... INFO @ Mon, 12 Aug 2019 20:16:39: end of X-cor INFO @ Mon, 12 Aug 2019 20:16:39: #2 finished! INFO @ Mon, 12 Aug 2019 20:16:39: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 20:16:39: #2 alternative fragment length(s) may be 2,47 bps INFO @ Mon, 12 Aug 2019 20:16:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.10_model.r WARNING @ Mon, 12 Aug 2019 20:16:39: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:16:39: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Mon, 12 Aug 2019 20:16:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:16:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:16:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:16:39: 18000000 INFO @ Mon, 12 Aug 2019 20:16:40: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:16:40: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:16:40: #1 total tags in treatment: 18155245 INFO @ Mon, 12 Aug 2019 20:16:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:16:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:16:41: #1 tags after filtering in treatment: 18155245 INFO @ Mon, 12 Aug 2019 20:16:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:16:41: #1 finished! INFO @ Mon, 12 Aug 2019 20:16:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:16:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:16:42: #2 number of paired peaks: 259 WARNING @ Mon, 12 Aug 2019 20:16:42: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Mon, 12 Aug 2019 20:16:42: start model_add_line... INFO @ Mon, 12 Aug 2019 20:16:42: start X-correlation... INFO @ Mon, 12 Aug 2019 20:16:42: end of X-cor INFO @ Mon, 12 Aug 2019 20:16:42: #2 finished! INFO @ Mon, 12 Aug 2019 20:16:42: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 20:16:42: #2 alternative fragment length(s) may be 2,47 bps INFO @ Mon, 12 Aug 2019 20:16:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.05_model.r WARNING @ Mon, 12 Aug 2019 20:16:42: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:16:42: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Mon, 12 Aug 2019 20:16:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:16:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:16:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:17:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:17:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:17:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:17:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:17:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.20_summits.bed INFO @ Mon, 12 Aug 2019 20:17:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (178 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:17:25: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:17:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:17:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:17:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.10_summits.bed INFO @ Mon, 12 Aug 2019 20:17:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (464 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:17:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:17:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:17:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495041/SRX495041.05_summits.bed INFO @ Mon, 12 Aug 2019 20:17:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (771 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。