Job ID = 2589127 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,320,973 reads read : 1,320,973 reads written : 1,320,973 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107313.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: 00:00:16 1320973 reads; of these: 1320973 (100.00%) were unpaired; of these: 281750 (21.33%) aligned 0 times 894082 (67.68%) aligned exactly 1 time 145141 (10.99%) aligned >1 times 78.67% overall alignment rate Time searching: 00:00:16 Overall time: 00:00:16 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] 38865 / 1039223 = 0.0374 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 16:57:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.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 16:57:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 16:57:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 16:57:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.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 16:57:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 16:57:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 16:57:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.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 16:57:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 16:57:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 16:57:39: 1000000 INFO @ Mon, 12 Aug 2019 16:57:39: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 16:57:39: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 16:57:39: #1 total tags in treatment: 1000358 INFO @ Mon, 12 Aug 2019 16:57:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 16:57:39: #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 16:57:39: #1 tags after filtering in treatment: 1000358 INFO @ Mon, 12 Aug 2019 16:57:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 16:57:39: #1 finished! INFO @ Mon, 12 Aug 2019 16:57:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 16:57:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 16:57:39: #2 number of paired peaks: 390 WARNING @ Mon, 12 Aug 2019 16:57:39: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Mon, 12 Aug 2019 16:57:39: start model_add_line... INFO @ Mon, 12 Aug 2019 16:57:39: start X-correlation... INFO @ Mon, 12 Aug 2019 16:57:39: end of X-cor INFO @ Mon, 12 Aug 2019 16:57:39: #2 finished! INFO @ Mon, 12 Aug 2019 16:57:39: #2 predicted fragment length is 148 bps INFO @ Mon, 12 Aug 2019 16:57:39: #2 alternative fragment length(s) may be 123,148 bps INFO @ Mon, 12 Aug 2019 16:57:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.05_model.r INFO @ Mon, 12 Aug 2019 16:57:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 16:57:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 16:57:41: 1000000 INFO @ Mon, 12 Aug 2019 16:57:42: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 16:57:42: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 16:57:42: #1 total tags in treatment: 1000358 INFO @ Mon, 12 Aug 2019 16:57:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 16:57:42: #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 16:57:42: #1 tags after filtering in treatment: 1000358 INFO @ Mon, 12 Aug 2019 16:57:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 16:57:42: #1 finished! INFO @ Mon, 12 Aug 2019 16:57:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 16:57:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 16:57:42: 1000000 INFO @ Mon, 12 Aug 2019 16:57:42: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 16:57:42: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 16:57:42: #1 total tags in treatment: 1000358 INFO @ Mon, 12 Aug 2019 16:57:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 16:57:42: #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 16:57:42: #1 tags after filtering in treatment: 1000358 INFO @ Mon, 12 Aug 2019 16:57:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 16:57:42: #1 finished! INFO @ Mon, 12 Aug 2019 16:57:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 16:57:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 16:57:42: #2 number of paired peaks: 390 WARNING @ Mon, 12 Aug 2019 16:57:42: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Mon, 12 Aug 2019 16:57:42: start model_add_line... INFO @ Mon, 12 Aug 2019 16:57:42: start X-correlation... INFO @ Mon, 12 Aug 2019 16:57:42: end of X-cor INFO @ Mon, 12 Aug 2019 16:57:42: #2 finished! INFO @ Mon, 12 Aug 2019 16:57:42: #2 predicted fragment length is 148 bps INFO @ Mon, 12 Aug 2019 16:57:42: #2 alternative fragment length(s) may be 123,148 bps INFO @ Mon, 12 Aug 2019 16:57:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.20_model.r INFO @ Mon, 12 Aug 2019 16:57:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 16:57:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 16:57:42: #2 number of paired peaks: 390 WARNING @ Mon, 12 Aug 2019 16:57:42: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Mon, 12 Aug 2019 16:57:42: start model_add_line... INFO @ Mon, 12 Aug 2019 16:57:42: start X-correlation... INFO @ Mon, 12 Aug 2019 16:57:42: end of X-cor INFO @ Mon, 12 Aug 2019 16:57:42: #2 finished! INFO @ Mon, 12 Aug 2019 16:57:42: #2 predicted fragment length is 148 bps INFO @ Mon, 12 Aug 2019 16:57:42: #2 alternative fragment length(s) may be 123,148 bps INFO @ Mon, 12 Aug 2019 16:57:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.10_model.r INFO @ Mon, 12 Aug 2019 16:57:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 16:57:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 16:57:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 16:57:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.05_peaks.xls INFO @ Mon, 12 Aug 2019 16:57:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 16:57:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.05_summits.bed INFO @ Mon, 12 Aug 2019 16:57:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (278 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 16:57:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 16:57:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 16:57:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.20_peaks.xls INFO @ Mon, 12 Aug 2019 16:57:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 16:57:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.20_summits.bed INFO @ Mon, 12 Aug 2019 16:57:46: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 16:57:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.10_peaks.xls INFO @ Mon, 12 Aug 2019 16:57:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 16:57:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043856/SRX043856.10_summits.bed INFO @ Mon, 12 Aug 2019 16:57:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (58 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。