Job ID = 2589402 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,285,635 reads read : 4,285,635 reads written : 4,285,635 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR494580.sra.cache’: 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: 00:00:52 4285635 reads; of these: 4285635 (100.00%) were unpaired; of these: 186867 (4.36%) aligned 0 times 3446769 (80.43%) aligned exactly 1 time 651999 (15.21%) aligned >1 times 95.64% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 323930 / 4098768 = 0.0790 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 17:36:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.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 17:36:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:36:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:36:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.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 17:36:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:36:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:36:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.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 17:36:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:36:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:36:40: 1000000 INFO @ Mon, 12 Aug 2019 17:36:41: 1000000 INFO @ Mon, 12 Aug 2019 17:36:42: 1000000 INFO @ Mon, 12 Aug 2019 17:36:47: 2000000 INFO @ Mon, 12 Aug 2019 17:36:48: 2000000 INFO @ Mon, 12 Aug 2019 17:36:50: 2000000 INFO @ Mon, 12 Aug 2019 17:36:55: 3000000 INFO @ Mon, 12 Aug 2019 17:36:56: 3000000 INFO @ Mon, 12 Aug 2019 17:36:57: 3000000 INFO @ Mon, 12 Aug 2019 17:37:00: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:37:00: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:37:00: #1 total tags in treatment: 3774838 INFO @ Mon, 12 Aug 2019 17:37:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:37:00: #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 17:37:00: #1 tags after filtering in treatment: 3774838 INFO @ Mon, 12 Aug 2019 17:37:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:37:00: #1 finished! INFO @ Mon, 12 Aug 2019 17:37:00: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:37:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:37:00: #2 number of paired peaks: 826 WARNING @ Mon, 12 Aug 2019 17:37:00: Fewer paired peaks (826) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 826 pairs to build model! INFO @ Mon, 12 Aug 2019 17:37:00: start model_add_line... INFO @ Mon, 12 Aug 2019 17:37:00: start X-correlation... INFO @ Mon, 12 Aug 2019 17:37:00: end of X-cor INFO @ Mon, 12 Aug 2019 17:37:00: #2 finished! INFO @ Mon, 12 Aug 2019 17:37:00: #2 predicted fragment length is 147 bps INFO @ Mon, 12 Aug 2019 17:37:00: #2 alternative fragment length(s) may be 147 bps INFO @ Mon, 12 Aug 2019 17:37:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.05_model.r INFO @ Mon, 12 Aug 2019 17:37:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:37:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:37:01: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:37:01: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:37:01: #1 total tags in treatment: 3774838 INFO @ Mon, 12 Aug 2019 17:37:01: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:37:01: #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 17:37:01: #1 tags after filtering in treatment: 3774838 INFO @ Mon, 12 Aug 2019 17:37:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:37:01: #1 finished! INFO @ Mon, 12 Aug 2019 17:37:01: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:37:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:37:02: #2 number of paired peaks: 826 WARNING @ Mon, 12 Aug 2019 17:37:02: Fewer paired peaks (826) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 826 pairs to build model! INFO @ Mon, 12 Aug 2019 17:37:02: start model_add_line... INFO @ Mon, 12 Aug 2019 17:37:02: start X-correlation... INFO @ Mon, 12 Aug 2019 17:37:02: end of X-cor INFO @ Mon, 12 Aug 2019 17:37:02: #2 finished! INFO @ Mon, 12 Aug 2019 17:37:02: #2 predicted fragment length is 147 bps INFO @ Mon, 12 Aug 2019 17:37:02: #2 alternative fragment length(s) may be 147 bps INFO @ Mon, 12 Aug 2019 17:37:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.10_model.r INFO @ Mon, 12 Aug 2019 17:37:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:37:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:37:03: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:37:03: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:37:03: #1 total tags in treatment: 3774838 INFO @ Mon, 12 Aug 2019 17:37:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:37:03: #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 17:37:03: #1 tags after filtering in treatment: 3774838 INFO @ Mon, 12 Aug 2019 17:37:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:37:03: #1 finished! INFO @ Mon, 12 Aug 2019 17:37:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:37:03: #2 number of paired peaks: 826 WARNING @ Mon, 12 Aug 2019 17:37:03: Fewer paired peaks (826) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 826 pairs to build model! INFO @ Mon, 12 Aug 2019 17:37:03: start model_add_line... INFO @ Mon, 12 Aug 2019 17:37:03: start X-correlation... INFO @ Mon, 12 Aug 2019 17:37:03: end of X-cor INFO @ Mon, 12 Aug 2019 17:37:03: #2 finished! INFO @ Mon, 12 Aug 2019 17:37:03: #2 predicted fragment length is 147 bps INFO @ Mon, 12 Aug 2019 17:37:03: #2 alternative fragment length(s) may be 147 bps INFO @ Mon, 12 Aug 2019 17:37:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.20_model.r INFO @ Mon, 12 Aug 2019 17:37:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:37:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:37:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:37:15: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:37:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:37:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:37:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.05_summits.bed INFO @ Mon, 12 Aug 2019 17:37:18: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1690 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:37:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:37:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:37:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.10_summits.bed INFO @ Mon, 12 Aug 2019 17:37:19: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1095 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:37:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:37:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:37:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX146419/SRX146419.20_summits.bed INFO @ Mon, 12 Aug 2019 17:37:21: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (682 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。