Job ID = 1292982 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,697,049 reads read : 67,394,098 reads written : 33,697,049 reads 0-length : 33,697,049 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: 00:07:56 33697049 reads; of these: 33697049 (100.00%) were unpaired; of these: 17246323 (51.18%) aligned 0 times 13568030 (40.26%) aligned exactly 1 time 2882696 (8.55%) aligned >1 times 48.82% overall alignment rate Time searching: 00:07:56 Overall time: 00:07:56 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] 3229646 / 16450726 = 0.1963 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 21:42:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.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 21:42:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:42:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.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 21:42:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:42:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.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 21:42:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:42:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:54: 1000000 INFO @ Sun, 02 Jun 2019 21:42:55: 1000000 INFO @ Sun, 02 Jun 2019 21:42:55: 1000000 INFO @ Sun, 02 Jun 2019 21:43:01: 2000000 INFO @ Sun, 02 Jun 2019 21:43:03: 2000000 INFO @ Sun, 02 Jun 2019 21:43:04: 2000000 INFO @ Sun, 02 Jun 2019 21:43:09: 3000000 INFO @ Sun, 02 Jun 2019 21:43:12: 3000000 INFO @ Sun, 02 Jun 2019 21:43:13: 3000000 INFO @ Sun, 02 Jun 2019 21:43:17: 4000000 INFO @ Sun, 02 Jun 2019 21:43:21: 4000000 INFO @ Sun, 02 Jun 2019 21:43:21: 4000000 INFO @ Sun, 02 Jun 2019 21:43:25: 5000000 INFO @ Sun, 02 Jun 2019 21:43:30: 5000000 INFO @ Sun, 02 Jun 2019 21:43:30: 5000000 INFO @ Sun, 02 Jun 2019 21:43:33: 6000000 INFO @ Sun, 02 Jun 2019 21:43:38: 6000000 INFO @ Sun, 02 Jun 2019 21:43:39: 6000000 INFO @ Sun, 02 Jun 2019 21:43:40: 7000000 INFO @ Sun, 02 Jun 2019 21:43:47: 7000000 INFO @ Sun, 02 Jun 2019 21:43:47: 7000000 INFO @ Sun, 02 Jun 2019 21:43:48: 8000000 INFO @ Sun, 02 Jun 2019 21:43:56: 8000000 INFO @ Sun, 02 Jun 2019 21:43:56: 8000000 INFO @ Sun, 02 Jun 2019 21:43:57: 9000000 INFO @ Sun, 02 Jun 2019 21:44:04: 9000000 INFO @ Sun, 02 Jun 2019 21:44:05: 9000000 INFO @ Sun, 02 Jun 2019 21:44:05: 10000000 INFO @ Sun, 02 Jun 2019 21:44:12: 11000000 INFO @ Sun, 02 Jun 2019 21:44:13: 10000000 INFO @ Sun, 02 Jun 2019 21:44:13: 10000000 INFO @ Sun, 02 Jun 2019 21:44:20: 12000000 INFO @ Sun, 02 Jun 2019 21:44:21: 11000000 INFO @ Sun, 02 Jun 2019 21:44:22: 11000000 INFO @ Sun, 02 Jun 2019 21:44:28: 13000000 INFO @ Sun, 02 Jun 2019 21:44:30: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:44:30: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:44:30: #1 total tags in treatment: 13221080 INFO @ Sun, 02 Jun 2019 21:44:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:44:30: #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 21:44:30: #1 tags after filtering in treatment: 13221080 INFO @ Sun, 02 Jun 2019 21:44:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:44:30: #1 finished! INFO @ Sun, 02 Jun 2019 21:44:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:44:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:44:30: 12000000 INFO @ Sun, 02 Jun 2019 21:44:31: 12000000 INFO @ Sun, 02 Jun 2019 21:44:31: #2 number of paired peaks: 420 WARNING @ Sun, 02 Jun 2019 21:44:31: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Sun, 02 Jun 2019 21:44:31: start model_add_line... INFO @ Sun, 02 Jun 2019 21:44:31: start X-correlation... INFO @ Sun, 02 Jun 2019 21:44:31: end of X-cor INFO @ Sun, 02 Jun 2019 21:44:31: #2 finished! INFO @ Sun, 02 Jun 2019 21:44:31: #2 predicted fragment length is 96 bps INFO @ Sun, 02 Jun 2019 21:44:31: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 02 Jun 2019 21:44:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.20_model.r WARNING @ Sun, 02 Jun 2019 21:44:31: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:44:31: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sun, 02 Jun 2019 21:44:31: #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 21:44:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:44:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:44:39: 13000000 INFO @ Sun, 02 Jun 2019 21:44:40: 13000000 INFO @ Sun, 02 Jun 2019 21:44:41: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:44:41: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:44:41: #1 total tags in treatment: 13221080 INFO @ Sun, 02 Jun 2019 21:44:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:44:41: #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 21:44:41: #1 tags after filtering in treatment: 13221080 INFO @ Sun, 02 Jun 2019 21:44:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:44:41: #1 finished! INFO @ Sun, 02 Jun 2019 21:44:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:44:42: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:44:42: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:44:42: #1 total tags in treatment: 13221080 INFO @ Sun, 02 Jun 2019 21:44:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:44:42: #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 21:44:42: #1 tags after filtering in treatment: 13221080 INFO @ Sun, 02 Jun 2019 21:44:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:44:42: #1 finished! INFO @ Sun, 02 Jun 2019 21:44:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:44:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:44:42: #2 number of paired peaks: 420 WARNING @ Sun, 02 Jun 2019 21:44:42: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Sun, 02 Jun 2019 21:44:42: start model_add_line... INFO @ Sun, 02 Jun 2019 21:44:42: start X-correlation... INFO @ Sun, 02 Jun 2019 21:44:42: end of X-cor INFO @ Sun, 02 Jun 2019 21:44:42: #2 finished! INFO @ Sun, 02 Jun 2019 21:44:42: #2 predicted fragment length is 96 bps INFO @ Sun, 02 Jun 2019 21:44:42: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 02 Jun 2019 21:44:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.05_model.r WARNING @ Sun, 02 Jun 2019 21:44:42: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:44:42: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sun, 02 Jun 2019 21:44:42: #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 21:44:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:44:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:44:43: #2 number of paired peaks: 420 WARNING @ Sun, 02 Jun 2019 21:44:43: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Sun, 02 Jun 2019 21:44:43: start model_add_line... INFO @ Sun, 02 Jun 2019 21:44:43: start X-correlation... INFO @ Sun, 02 Jun 2019 21:44:43: end of X-cor INFO @ Sun, 02 Jun 2019 21:44:43: #2 finished! INFO @ Sun, 02 Jun 2019 21:44:43: #2 predicted fragment length is 96 bps INFO @ Sun, 02 Jun 2019 21:44:43: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 02 Jun 2019 21:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.10_model.r WARNING @ Sun, 02 Jun 2019 21:44:43: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:44:43: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sun, 02 Jun 2019 21:44:43: #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 21:44:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:44:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:45:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:45:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:45:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:45:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:45:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:45:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.20_summits.bed INFO @ Sun, 02 Jun 2019 21:45:22: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (499 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:45:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:45:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:45:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.05_summits.bed INFO @ Sun, 02 Jun 2019 21:45:33: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1482 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:45:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:45:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:45:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020759/SRX5020759.10_summits.bed INFO @ Sun, 02 Jun 2019 21:45:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (853 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。