Job ID = 2589677 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,218,214 reads read : 5,218,214 reads written : 5,218,214 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947277.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: 00:00:40 5218214 reads; of these: 5218214 (100.00%) were unpaired; of these: 3344577 (64.09%) aligned 0 times 1568083 (30.05%) aligned exactly 1 time 305554 (5.86%) aligned >1 times 35.91% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 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_rmdupse_core] 265668 / 1873637 = 0.1418 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 18:13:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.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 18:13:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:13:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:13:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.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 18:13:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:13:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:13:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.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 18:13:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:13:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:14:02: 1000000 INFO @ Mon, 12 Aug 2019 18:14:03: 1000000 INFO @ Mon, 12 Aug 2019 18:14:05: 1000000 INFO @ Mon, 12 Aug 2019 18:14:06: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:14:06: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:14:06: #1 total tags in treatment: 1607969 INFO @ Mon, 12 Aug 2019 18:14:06: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:14:06: #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 18:14:06: #1 tags after filtering in treatment: 1607969 INFO @ Mon, 12 Aug 2019 18:14:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:14:06: #1 finished! INFO @ Mon, 12 Aug 2019 18:14:06: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:14:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:14:06: #2 number of paired peaks: 427 WARNING @ Mon, 12 Aug 2019 18:14:06: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Mon, 12 Aug 2019 18:14:06: start model_add_line... INFO @ Mon, 12 Aug 2019 18:14:06: start X-correlation... INFO @ Mon, 12 Aug 2019 18:14:06: end of X-cor INFO @ Mon, 12 Aug 2019 18:14:06: #2 finished! INFO @ Mon, 12 Aug 2019 18:14:06: #2 predicted fragment length is 105 bps INFO @ Mon, 12 Aug 2019 18:14:06: #2 alternative fragment length(s) may be 38,105 bps INFO @ Mon, 12 Aug 2019 18:14:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.05_model.r INFO @ Mon, 12 Aug 2019 18:14:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:14:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:14:07: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:14:07: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:14:07: #1 total tags in treatment: 1607969 INFO @ Mon, 12 Aug 2019 18:14:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:14:07: #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 18:14:07: #1 tags after filtering in treatment: 1607969 INFO @ Mon, 12 Aug 2019 18:14:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:14:07: #1 finished! INFO @ Mon, 12 Aug 2019 18:14:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:14:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:14:07: #2 number of paired peaks: 427 WARNING @ Mon, 12 Aug 2019 18:14:07: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Mon, 12 Aug 2019 18:14:07: start model_add_line... INFO @ Mon, 12 Aug 2019 18:14:07: start X-correlation... INFO @ Mon, 12 Aug 2019 18:14:07: end of X-cor INFO @ Mon, 12 Aug 2019 18:14:07: #2 finished! INFO @ Mon, 12 Aug 2019 18:14:07: #2 predicted fragment length is 105 bps INFO @ Mon, 12 Aug 2019 18:14:07: #2 alternative fragment length(s) may be 38,105 bps INFO @ Mon, 12 Aug 2019 18:14:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.10_model.r INFO @ Mon, 12 Aug 2019 18:14:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:14:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:14:09: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:14:09: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:14:09: #1 total tags in treatment: 1607969 INFO @ Mon, 12 Aug 2019 18:14:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:14:09: #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 18:14:09: #1 tags after filtering in treatment: 1607969 INFO @ Mon, 12 Aug 2019 18:14:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:14:09: #1 finished! INFO @ Mon, 12 Aug 2019 18:14:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:14:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:14:09: #2 number of paired peaks: 427 WARNING @ Mon, 12 Aug 2019 18:14:09: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Mon, 12 Aug 2019 18:14:09: start model_add_line... INFO @ Mon, 12 Aug 2019 18:14:09: start X-correlation... INFO @ Mon, 12 Aug 2019 18:14:09: end of X-cor INFO @ Mon, 12 Aug 2019 18:14:09: #2 finished! INFO @ Mon, 12 Aug 2019 18:14:09: #2 predicted fragment length is 105 bps INFO @ Mon, 12 Aug 2019 18:14:09: #2 alternative fragment length(s) may be 38,105 bps INFO @ Mon, 12 Aug 2019 18:14:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.20_model.r INFO @ Mon, 12 Aug 2019 18:14:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:14:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:14:11: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:14:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:14:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:14:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:14:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.05_summits.bed INFO @ Mon, 12 Aug 2019 18:14:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (431 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:14:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:14:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:14:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.10_summits.bed INFO @ Mon, 12 Aug 2019 18:14:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:14:15: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:14:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:14:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:14:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331054/SRX331054.20_summits.bed INFO @ Mon, 12 Aug 2019 18:14:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (44 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。