Job ID = 2590048 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,642,022 reads read : 14,642,022 reads written : 14,642,022 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: 00:02:35 14642022 reads; of these: 14642022 (100.00%) were unpaired; of these: 5484556 (37.46%) aligned 0 times 7907450 (54.01%) aligned exactly 1 time 1250016 (8.54%) aligned >1 times 62.54% overall alignment rate Time searching: 00:02:35 Overall time: 00:02:35 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] 2444530 / 9157466 = 0.2669 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 19:27:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.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 19:27:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:27:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:27:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.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 19:27:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:27:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:27:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.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 19:27:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:27:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:27:26: 1000000 INFO @ Mon, 12 Aug 2019 19:27:27: 1000000 INFO @ Mon, 12 Aug 2019 19:27:28: 1000000 INFO @ Mon, 12 Aug 2019 19:27:33: 2000000 INFO @ Mon, 12 Aug 2019 19:27:34: 2000000 INFO @ Mon, 12 Aug 2019 19:27:36: 2000000 INFO @ Mon, 12 Aug 2019 19:27:40: 3000000 INFO @ Mon, 12 Aug 2019 19:27:41: 3000000 INFO @ Mon, 12 Aug 2019 19:27:44: 3000000 INFO @ Mon, 12 Aug 2019 19:27:47: 4000000 INFO @ Mon, 12 Aug 2019 19:27:48: 4000000 INFO @ Mon, 12 Aug 2019 19:27:52: 4000000 INFO @ Mon, 12 Aug 2019 19:27:54: 5000000 INFO @ Mon, 12 Aug 2019 19:27:55: 5000000 INFO @ Mon, 12 Aug 2019 19:28:00: 5000000 INFO @ Mon, 12 Aug 2019 19:28:01: 6000000 INFO @ Mon, 12 Aug 2019 19:28:02: 6000000 INFO @ Mon, 12 Aug 2019 19:28:06: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:28:06: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:28:06: #1 total tags in treatment: 6712936 INFO @ Mon, 12 Aug 2019 19:28:06: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:28:06: #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 19:28:06: #1 tags after filtering in treatment: 6712936 INFO @ Mon, 12 Aug 2019 19:28:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:28:06: #1 finished! INFO @ Mon, 12 Aug 2019 19:28:06: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:28:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:28:06: #2 number of paired peaks: 523 WARNING @ Mon, 12 Aug 2019 19:28:06: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Mon, 12 Aug 2019 19:28:06: start model_add_line... INFO @ Mon, 12 Aug 2019 19:28:06: start X-correlation... INFO @ Mon, 12 Aug 2019 19:28:06: end of X-cor INFO @ Mon, 12 Aug 2019 19:28:06: #2 finished! INFO @ Mon, 12 Aug 2019 19:28:06: #2 predicted fragment length is 148 bps INFO @ Mon, 12 Aug 2019 19:28:06: #2 alternative fragment length(s) may be 148 bps INFO @ Mon, 12 Aug 2019 19:28:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.05_model.r INFO @ Mon, 12 Aug 2019 19:28:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:28:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:28:07: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:28:07: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:28:07: #1 total tags in treatment: 6712936 INFO @ Mon, 12 Aug 2019 19:28:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:28:07: #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 19:28:07: #1 tags after filtering in treatment: 6712936 INFO @ Mon, 12 Aug 2019 19:28:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:28:07: #1 finished! INFO @ Mon, 12 Aug 2019 19:28:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:28:08: #2 number of paired peaks: 523 WARNING @ Mon, 12 Aug 2019 19:28:08: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Mon, 12 Aug 2019 19:28:08: start model_add_line... INFO @ Mon, 12 Aug 2019 19:28:08: start X-correlation... INFO @ Mon, 12 Aug 2019 19:28:08: end of X-cor INFO @ Mon, 12 Aug 2019 19:28:08: #2 finished! INFO @ Mon, 12 Aug 2019 19:28:08: #2 predicted fragment length is 148 bps INFO @ Mon, 12 Aug 2019 19:28:08: #2 alternative fragment length(s) may be 148 bps INFO @ Mon, 12 Aug 2019 19:28:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.10_model.r INFO @ Mon, 12 Aug 2019 19:28:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:28:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:28:08: 6000000 INFO @ Mon, 12 Aug 2019 19:28:13: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:28:13: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:28:13: #1 total tags in treatment: 6712936 INFO @ Mon, 12 Aug 2019 19:28:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:28:13: #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 19:28:13: #1 tags after filtering in treatment: 6712936 INFO @ Mon, 12 Aug 2019 19:28:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:28:13: #1 finished! INFO @ Mon, 12 Aug 2019 19:28:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:28:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:28:14: #2 number of paired peaks: 523 WARNING @ Mon, 12 Aug 2019 19:28:14: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Mon, 12 Aug 2019 19:28:14: start model_add_line... INFO @ Mon, 12 Aug 2019 19:28:14: start X-correlation... INFO @ Mon, 12 Aug 2019 19:28:14: end of X-cor INFO @ Mon, 12 Aug 2019 19:28:14: #2 finished! INFO @ Mon, 12 Aug 2019 19:28:14: #2 predicted fragment length is 148 bps INFO @ Mon, 12 Aug 2019 19:28:14: #2 alternative fragment length(s) may be 148 bps INFO @ Mon, 12 Aug 2019 19:28:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.20_model.r INFO @ Mon, 12 Aug 2019 19:28:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:28:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:28:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:28:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:28:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:28:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:28:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:28:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.05_summits.bed INFO @ Mon, 12 Aug 2019 19:28:36: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1585 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:28:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:28:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:28:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.10_summits.bed INFO @ Mon, 12 Aug 2019 19:28:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (671 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:28:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:28:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:28:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494892/SRX494892.20_summits.bed INFO @ Mon, 12 Aug 2019 19:28:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (252 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。