Job ID = 1291686 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,662,435 reads read : 21,662,435 reads written : 21,662,435 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: 00:05:18 21662435 reads; of these: 21662435 (100.00%) were unpaired; of these: 926977 (4.28%) aligned 0 times 17801263 (82.18%) aligned exactly 1 time 2934195 (13.55%) aligned >1 times 95.72% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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] 2174354 / 20735458 = 0.1049 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 16:27:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.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 16:27:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:27:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:27:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.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 16:27:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:27:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:27:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.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 16:27:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:27:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:27:53: 1000000 INFO @ Sun, 02 Jun 2019 16:27:53: 1000000 INFO @ Sun, 02 Jun 2019 16:27:55: 1000000 INFO @ Sun, 02 Jun 2019 16:28:00: 2000000 INFO @ Sun, 02 Jun 2019 16:28:01: 2000000 INFO @ Sun, 02 Jun 2019 16:28:04: 2000000 INFO @ Sun, 02 Jun 2019 16:28:08: 3000000 INFO @ Sun, 02 Jun 2019 16:28:09: 3000000 INFO @ Sun, 02 Jun 2019 16:28:13: 3000000 INFO @ Sun, 02 Jun 2019 16:28:15: 4000000 INFO @ Sun, 02 Jun 2019 16:28:17: 4000000 INFO @ Sun, 02 Jun 2019 16:28:22: 5000000 INFO @ Sun, 02 Jun 2019 16:28:23: 4000000 INFO @ Sun, 02 Jun 2019 16:28:25: 5000000 INFO @ Sun, 02 Jun 2019 16:28:29: 6000000 INFO @ Sun, 02 Jun 2019 16:28:32: 5000000 INFO @ Sun, 02 Jun 2019 16:28:33: 6000000 INFO @ Sun, 02 Jun 2019 16:28:37: 7000000 INFO @ Sun, 02 Jun 2019 16:28:41: 7000000 INFO @ Sun, 02 Jun 2019 16:28:41: 6000000 INFO @ Sun, 02 Jun 2019 16:28:44: 8000000 INFO @ Sun, 02 Jun 2019 16:28:48: 8000000 INFO @ Sun, 02 Jun 2019 16:28:50: 7000000 INFO @ Sun, 02 Jun 2019 16:28:51: 9000000 INFO @ Sun, 02 Jun 2019 16:28:56: 9000000 INFO @ Sun, 02 Jun 2019 16:28:58: 10000000 INFO @ Sun, 02 Jun 2019 16:28:59: 8000000 INFO @ Sun, 02 Jun 2019 16:29:04: 10000000 INFO @ Sun, 02 Jun 2019 16:29:06: 11000000 INFO @ Sun, 02 Jun 2019 16:29:07: 9000000 INFO @ Sun, 02 Jun 2019 16:29:12: 11000000 INFO @ Sun, 02 Jun 2019 16:29:13: 12000000 INFO @ Sun, 02 Jun 2019 16:29:16: 10000000 INFO @ Sun, 02 Jun 2019 16:29:19: 12000000 INFO @ Sun, 02 Jun 2019 16:29:20: 13000000 INFO @ Sun, 02 Jun 2019 16:29:25: 11000000 INFO @ Sun, 02 Jun 2019 16:29:27: 13000000 INFO @ Sun, 02 Jun 2019 16:29:27: 14000000 INFO @ Sun, 02 Jun 2019 16:29:33: 12000000 INFO @ Sun, 02 Jun 2019 16:29:34: 15000000 INFO @ Sun, 02 Jun 2019 16:29:34: 14000000 INFO @ Sun, 02 Jun 2019 16:29:41: 16000000 INFO @ Sun, 02 Jun 2019 16:29:42: 15000000 INFO @ Sun, 02 Jun 2019 16:29:42: 13000000 INFO @ Sun, 02 Jun 2019 16:29:48: 17000000 INFO @ Sun, 02 Jun 2019 16:29:49: 16000000 INFO @ Sun, 02 Jun 2019 16:29:51: 14000000 INFO @ Sun, 02 Jun 2019 16:29:55: 18000000 INFO @ Sun, 02 Jun 2019 16:29:58: 17000000 INFO @ Sun, 02 Jun 2019 16:29:59: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:29:59: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:29:59: #1 total tags in treatment: 18561104 INFO @ Sun, 02 Jun 2019 16:29:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:29:59: #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 16:29:59: 15000000 INFO @ Sun, 02 Jun 2019 16:30:00: #1 tags after filtering in treatment: 18561104 INFO @ Sun, 02 Jun 2019 16:30:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:30:00: #1 finished! INFO @ Sun, 02 Jun 2019 16:30:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:30:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:30:01: #2 number of paired peaks: 180 WARNING @ Sun, 02 Jun 2019 16:30:01: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sun, 02 Jun 2019 16:30:01: start model_add_line... INFO @ Sun, 02 Jun 2019 16:30:01: start X-correlation... INFO @ Sun, 02 Jun 2019 16:30:01: end of X-cor INFO @ Sun, 02 Jun 2019 16:30:01: #2 finished! INFO @ Sun, 02 Jun 2019 16:30:01: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 16:30:01: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 02 Jun 2019 16:30:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.20_model.r WARNING @ Sun, 02 Jun 2019 16:30:01: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:30:01: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 02 Jun 2019 16:30:01: #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 16:30:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:30:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:30:05: 18000000 INFO @ Sun, 02 Jun 2019 16:30:08: 16000000 INFO @ Sun, 02 Jun 2019 16:30:09: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:30:09: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:30:09: #1 total tags in treatment: 18561104 INFO @ Sun, 02 Jun 2019 16:30:09: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:30:09: #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 16:30:10: #1 tags after filtering in treatment: 18561104 INFO @ Sun, 02 Jun 2019 16:30:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:30:10: #1 finished! INFO @ Sun, 02 Jun 2019 16:30:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:30:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:30:11: #2 number of paired peaks: 180 WARNING @ Sun, 02 Jun 2019 16:30:11: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sun, 02 Jun 2019 16:30:11: start model_add_line... INFO @ Sun, 02 Jun 2019 16:30:11: start X-correlation... INFO @ Sun, 02 Jun 2019 16:30:11: end of X-cor INFO @ Sun, 02 Jun 2019 16:30:11: #2 finished! INFO @ Sun, 02 Jun 2019 16:30:11: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 16:30:11: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 02 Jun 2019 16:30:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.10_model.r WARNING @ Sun, 02 Jun 2019 16:30:11: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:30:11: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 02 Jun 2019 16:30:11: #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 16:30:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:30:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:30:16: 17000000 INFO @ Sun, 02 Jun 2019 16:30:25: 18000000 INFO @ Sun, 02 Jun 2019 16:30:29: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:30:29: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:30:29: #1 total tags in treatment: 18561104 INFO @ Sun, 02 Jun 2019 16:30:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:30:29: #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 16:30:30: #1 tags after filtering in treatment: 18561104 INFO @ Sun, 02 Jun 2019 16:30:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:30:30: #1 finished! INFO @ Sun, 02 Jun 2019 16:30:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:30:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:30:31: #2 number of paired peaks: 180 WARNING @ Sun, 02 Jun 2019 16:30:31: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sun, 02 Jun 2019 16:30:31: start model_add_line... INFO @ Sun, 02 Jun 2019 16:30:32: start X-correlation... INFO @ Sun, 02 Jun 2019 16:30:32: end of X-cor INFO @ Sun, 02 Jun 2019 16:30:32: #2 finished! INFO @ Sun, 02 Jun 2019 16:30:32: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 16:30:32: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 02 Jun 2019 16:30:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.05_model.r WARNING @ Sun, 02 Jun 2019 16:30:32: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:30:32: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 02 Jun 2019 16:30:32: #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 16:30:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:30:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:30:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:30:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:31:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:31:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:31:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.20_summits.bed INFO @ Sun, 02 Jun 2019 16:31:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:31:16: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:31:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:31:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:31:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.10_summits.bed INFO @ Sun, 02 Jun 2019 16:31:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (448 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:31:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:31:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:31:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216755/SRX216755.05_summits.bed INFO @ Sun, 02 Jun 2019 16:31:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (934 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。