Job ID = 1292840 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,930,018 reads read : 18,930,018 reads written : 18,930,018 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: 00:03:40 18930018 reads; of these: 18930018 (100.00%) were unpaired; of these: 2656059 (14.03%) aligned 0 times 13795650 (72.88%) aligned exactly 1 time 2478309 (13.09%) aligned >1 times 85.97% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 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] 5323554 / 16273959 = 0.3271 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 21:07:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.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 21:07:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:07:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:07:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.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 21:07:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:07:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:07:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.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 21:07:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:07:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:07:58: 1000000 INFO @ Sun, 02 Jun 2019 21:07:58: 1000000 INFO @ Sun, 02 Jun 2019 21:08:00: 1000000 INFO @ Sun, 02 Jun 2019 21:08:07: 2000000 INFO @ Sun, 02 Jun 2019 21:08:07: 2000000 INFO @ Sun, 02 Jun 2019 21:08:11: 2000000 INFO @ Sun, 02 Jun 2019 21:08:16: 3000000 INFO @ Sun, 02 Jun 2019 21:08:16: 3000000 INFO @ Sun, 02 Jun 2019 21:08:21: 3000000 INFO @ Sun, 02 Jun 2019 21:08:25: 4000000 INFO @ Sun, 02 Jun 2019 21:08:25: 4000000 INFO @ Sun, 02 Jun 2019 21:08:31: 4000000 INFO @ Sun, 02 Jun 2019 21:08:34: 5000000 INFO @ Sun, 02 Jun 2019 21:08:34: 5000000 INFO @ Sun, 02 Jun 2019 21:08:42: 5000000 INFO @ Sun, 02 Jun 2019 21:08:43: 6000000 INFO @ Sun, 02 Jun 2019 21:08:44: 6000000 INFO @ Sun, 02 Jun 2019 21:08:53: 6000000 INFO @ Sun, 02 Jun 2019 21:08:53: 7000000 INFO @ Sun, 02 Jun 2019 21:08:53: 7000000 INFO @ Sun, 02 Jun 2019 21:09:03: 8000000 INFO @ Sun, 02 Jun 2019 21:09:03: 8000000 INFO @ Sun, 02 Jun 2019 21:09:05: 7000000 INFO @ Sun, 02 Jun 2019 21:09:12: 9000000 INFO @ Sun, 02 Jun 2019 21:09:13: 9000000 INFO @ Sun, 02 Jun 2019 21:09:16: 8000000 INFO @ Sun, 02 Jun 2019 21:09:21: 10000000 INFO @ Sun, 02 Jun 2019 21:09:22: 10000000 INFO @ Sun, 02 Jun 2019 21:09:27: 9000000 INFO @ Sun, 02 Jun 2019 21:09:29: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:09:29: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:09:29: #1 total tags in treatment: 10950405 INFO @ Sun, 02 Jun 2019 21:09:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:09:29: #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 21:09:29: #1 tags after filtering in treatment: 10950405 INFO @ Sun, 02 Jun 2019 21:09:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:09:29: #1 finished! INFO @ Sun, 02 Jun 2019 21:09:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:09:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:09:30: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:09:30: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:09:30: #1 total tags in treatment: 10950405 INFO @ Sun, 02 Jun 2019 21:09:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:09:30: #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 21:09:30: #1 tags after filtering in treatment: 10950405 INFO @ Sun, 02 Jun 2019 21:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:09:30: #1 finished! INFO @ Sun, 02 Jun 2019 21:09:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:09:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:09:31: #2 number of paired peaks: 696 WARNING @ Sun, 02 Jun 2019 21:09:31: Fewer paired peaks (696) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 696 pairs to build model! INFO @ Sun, 02 Jun 2019 21:09:31: start model_add_line... INFO @ Sun, 02 Jun 2019 21:09:31: start X-correlation... INFO @ Sun, 02 Jun 2019 21:09:31: end of X-cor INFO @ Sun, 02 Jun 2019 21:09:31: #2 finished! INFO @ Sun, 02 Jun 2019 21:09:31: #2 predicted fragment length is 220 bps INFO @ Sun, 02 Jun 2019 21:09:31: #2 alternative fragment length(s) may be 220 bps INFO @ Sun, 02 Jun 2019 21:09:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.10_model.r INFO @ Sun, 02 Jun 2019 21:09:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:09:31: #2 number of paired peaks: 696 WARNING @ Sun, 02 Jun 2019 21:09:31: Fewer paired peaks (696) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 696 pairs to build model! INFO @ Sun, 02 Jun 2019 21:09:31: start model_add_line... INFO @ Sun, 02 Jun 2019 21:09:31: start X-correlation... INFO @ Sun, 02 Jun 2019 21:09:31: end of X-cor INFO @ Sun, 02 Jun 2019 21:09:31: #2 finished! INFO @ Sun, 02 Jun 2019 21:09:31: #2 predicted fragment length is 220 bps INFO @ Sun, 02 Jun 2019 21:09:31: #2 alternative fragment length(s) may be 220 bps INFO @ Sun, 02 Jun 2019 21:09:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.05_model.r INFO @ Sun, 02 Jun 2019 21:09:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:09:37: 10000000 INFO @ Sun, 02 Jun 2019 21:09:46: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:09:46: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:09:46: #1 total tags in treatment: 10950405 INFO @ Sun, 02 Jun 2019 21:09:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:09:46: #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 21:09:46: #1 tags after filtering in treatment: 10950405 INFO @ Sun, 02 Jun 2019 21:09:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:09:46: #1 finished! INFO @ Sun, 02 Jun 2019 21:09:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:09:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:09:47: #2 number of paired peaks: 696 WARNING @ Sun, 02 Jun 2019 21:09:47: Fewer paired peaks (696) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 696 pairs to build model! INFO @ Sun, 02 Jun 2019 21:09:47: start model_add_line... INFO @ Sun, 02 Jun 2019 21:09:48: start X-correlation... INFO @ Sun, 02 Jun 2019 21:09:48: end of X-cor INFO @ Sun, 02 Jun 2019 21:09:48: #2 finished! INFO @ Sun, 02 Jun 2019 21:09:48: #2 predicted fragment length is 220 bps INFO @ Sun, 02 Jun 2019 21:09:48: #2 alternative fragment length(s) may be 220 bps INFO @ Sun, 02 Jun 2019 21:09:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.20_model.r INFO @ Sun, 02 Jun 2019 21:09:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:09:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:10:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:10:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:10:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:10:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:10:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.10_summits.bed INFO @ Sun, 02 Jun 2019 21:10:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1783 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:10:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:10:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:10:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.05_summits.bed INFO @ Sun, 02 Jun 2019 21:10:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3170 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:10:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:10:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:10:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:10:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495076/SRX495076.20_summits.bed INFO @ Sun, 02 Jun 2019 21:10:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (957 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。