Job ID = 1291843 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,440,591 reads read : 17,440,591 reads written : 17,440,591 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: 00:03:14 17440591 reads; of these: 17440591 (100.00%) were unpaired; of these: 2956372 (16.95%) aligned 0 times 11862785 (68.02%) aligned exactly 1 time 2621434 (15.03%) aligned >1 times 83.05% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 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] 9964649 / 14484219 = 0.6880 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 16:47:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.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 16:47:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:47:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:47:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.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 16:47:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:47:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:47:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.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 16:47:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:47:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:47:20: 1000000 INFO @ Sun, 02 Jun 2019 16:47:20: 1000000 INFO @ Sun, 02 Jun 2019 16:47:22: 1000000 INFO @ Sun, 02 Jun 2019 16:47:28: 2000000 INFO @ Sun, 02 Jun 2019 16:47:28: 2000000 INFO @ Sun, 02 Jun 2019 16:47:30: 2000000 INFO @ Sun, 02 Jun 2019 16:47:35: 3000000 INFO @ Sun, 02 Jun 2019 16:47:35: 3000000 INFO @ Sun, 02 Jun 2019 16:47:38: 3000000 INFO @ Sun, 02 Jun 2019 16:47:43: 4000000 INFO @ Sun, 02 Jun 2019 16:47:43: 4000000 INFO @ Sun, 02 Jun 2019 16:47:46: 4000000 INFO @ Sun, 02 Jun 2019 16:47:47: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:47:47: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:47:47: #1 total tags in treatment: 4519570 INFO @ Sun, 02 Jun 2019 16:47:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:47:47: #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 16:47:47: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:47:47: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:47:47: #1 total tags in treatment: 4519570 INFO @ Sun, 02 Jun 2019 16:47:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:47:47: #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 16:47:47: #1 tags after filtering in treatment: 4519570 INFO @ Sun, 02 Jun 2019 16:47:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:47:47: #1 finished! INFO @ Sun, 02 Jun 2019 16:47:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:47:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:47:47: #1 tags after filtering in treatment: 4519570 INFO @ Sun, 02 Jun 2019 16:47:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:47:47: #1 finished! INFO @ Sun, 02 Jun 2019 16:47:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:47:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:47:47: #2 number of paired peaks: 841 WARNING @ Sun, 02 Jun 2019 16:47:47: Fewer paired peaks (841) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 841 pairs to build model! INFO @ Sun, 02 Jun 2019 16:47:47: start model_add_line... INFO @ Sun, 02 Jun 2019 16:47:47: #2 number of paired peaks: 841 WARNING @ Sun, 02 Jun 2019 16:47:47: Fewer paired peaks (841) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 841 pairs to build model! INFO @ Sun, 02 Jun 2019 16:47:47: start model_add_line... INFO @ Sun, 02 Jun 2019 16:47:47: start X-correlation... INFO @ Sun, 02 Jun 2019 16:47:47: start X-correlation... INFO @ Sun, 02 Jun 2019 16:47:47: end of X-cor INFO @ Sun, 02 Jun 2019 16:47:47: #2 finished! INFO @ Sun, 02 Jun 2019 16:47:47: #2 predicted fragment length is 134 bps INFO @ Sun, 02 Jun 2019 16:47:47: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 02 Jun 2019 16:47:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.05_model.r INFO @ Sun, 02 Jun 2019 16:47:47: end of X-cor INFO @ Sun, 02 Jun 2019 16:47:47: #2 finished! INFO @ Sun, 02 Jun 2019 16:47:47: #2 predicted fragment length is 134 bps INFO @ Sun, 02 Jun 2019 16:47:47: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 02 Jun 2019 16:47:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.10_model.r INFO @ Sun, 02 Jun 2019 16:47:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:47:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:47:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:47:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:47:50: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:47:50: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:47:50: #1 total tags in treatment: 4519570 INFO @ Sun, 02 Jun 2019 16:47:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:47:50: #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 16:47:50: #1 tags after filtering in treatment: 4519570 INFO @ Sun, 02 Jun 2019 16:47:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:47:50: #1 finished! INFO @ Sun, 02 Jun 2019 16:47:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:47:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:47:51: #2 number of paired peaks: 841 WARNING @ Sun, 02 Jun 2019 16:47:51: Fewer paired peaks (841) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 841 pairs to build model! INFO @ Sun, 02 Jun 2019 16:47:51: start model_add_line... INFO @ Sun, 02 Jun 2019 16:47:51: start X-correlation... INFO @ Sun, 02 Jun 2019 16:47:51: end of X-cor INFO @ Sun, 02 Jun 2019 16:47:51: #2 finished! INFO @ Sun, 02 Jun 2019 16:47:51: #2 predicted fragment length is 134 bps INFO @ Sun, 02 Jun 2019 16:47:51: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 02 Jun 2019 16:47:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.20_model.r INFO @ Sun, 02 Jun 2019 16:47:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:47:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:48:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:48:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:48:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:48:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:48:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:48:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.10_summits.bed INFO @ Sun, 02 Jun 2019 16:48:09: Done! INFO @ Sun, 02 Jun 2019 16:48:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:48:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:48:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.05_summits.bed INFO @ Sun, 02 Jun 2019 16:48:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (975 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1992 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:48:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:48:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:48:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257679/SRX257679.20_summits.bed INFO @ Sun, 02 Jun 2019 16:48:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (413 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。