Job ID = 2007653 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,672,115 reads read : 1,672,115 reads written : 1,672,115 spots read : 1,600,852 reads read : 1,600,852 reads written : 1,600,852 spots read : 1,749,891 reads read : 1,749,891 reads written : 1,749,891 spots read : 1,588,586 reads read : 1,588,586 reads written : 1,588,586 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529806.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529807.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529808.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: 00:01:37 6611444 reads; of these: 6611444 (100.00%) were unpaired; of these: 233769 (3.54%) aligned 0 times 5085530 (76.92%) aligned exactly 1 time 1292145 (19.54%) aligned >1 times 96.46% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 6251365 / 6377675 = 0.9802 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 @ Fri, 05 Jul 2019 16:17:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 16:17:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:17:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:17:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 16:17:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:17:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:17:42: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:17:42: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:17:42: #1 total tags in treatment: 126310 INFO @ Fri, 05 Jul 2019 16:17:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:17:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:17:42: #1 tags after filtering in treatment: 126310 INFO @ Fri, 05 Jul 2019 16:17:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:17:42: #1 finished! INFO @ Fri, 05 Jul 2019 16:17:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:17:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:17:42: #2 number of paired peaks: 361 WARNING @ Fri, 05 Jul 2019 16:17:42: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Fri, 05 Jul 2019 16:17:42: start model_add_line... INFO @ Fri, 05 Jul 2019 16:17:42: start X-correlation... INFO @ Fri, 05 Jul 2019 16:17:42: end of X-cor INFO @ Fri, 05 Jul 2019 16:17:42: #2 finished! INFO @ Fri, 05 Jul 2019 16:17:42: #2 predicted fragment length is 105 bps INFO @ Fri, 05 Jul 2019 16:17:42: #2 alternative fragment length(s) may be 25,70,105,135,166,199,229,273,303,365,406,429,464,476,524,568 bps INFO @ Fri, 05 Jul 2019 16:17:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.05_model.r WARNING @ Fri, 05 Jul 2019 16:17:42: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:17:42: #2 You may need to consider one of the other alternative d(s): 25,70,105,135,166,199,229,273,303,365,406,429,464,476,524,568 WARNING @ Fri, 05 Jul 2019 16:17:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:17:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:17:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:17:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:17:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:17:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:17:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.05_summits.bed INFO @ Fri, 05 Jul 2019 16:17:43: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (40 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:17:43: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:17:43: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:17:43: #1 total tags in treatment: 126310 INFO @ Fri, 05 Jul 2019 16:17:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:17:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:17:43: #1 tags after filtering in treatment: 126310 INFO @ Fri, 05 Jul 2019 16:17:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:17:43: #1 finished! INFO @ Fri, 05 Jul 2019 16:17:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:17:43: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:17:43: #2 number of paired peaks: 361 WARNING @ Fri, 05 Jul 2019 16:17:43: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Fri, 05 Jul 2019 16:17:43: start model_add_line... INFO @ Fri, 05 Jul 2019 16:17:43: start X-correlation... INFO @ Fri, 05 Jul 2019 16:17:43: end of X-cor INFO @ Fri, 05 Jul 2019 16:17:43: #2 finished! INFO @ Fri, 05 Jul 2019 16:17:43: #2 predicted fragment length is 105 bps INFO @ Fri, 05 Jul 2019 16:17:43: #2 alternative fragment length(s) may be 25,70,105,135,166,199,229,273,303,365,406,429,464,476,524,568 bps INFO @ Fri, 05 Jul 2019 16:17:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.10_model.r WARNING @ Fri, 05 Jul 2019 16:17:43: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:17:43: #2 You may need to consider one of the other alternative d(s): 25,70,105,135,166,199,229,273,303,365,406,429,464,476,524,568 WARNING @ Fri, 05 Jul 2019 16:17:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:17:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:17:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:17:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 16:17:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:17:43: #1 read treatment tags... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:17:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:17:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:17:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:17:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.10_summits.bed INFO @ Fri, 05 Jul 2019 16:17:44: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:17:44: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:17:44: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:17:44: #1 total tags in treatment: 126310 INFO @ Fri, 05 Jul 2019 16:17:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:17:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:17:44: #1 tags after filtering in treatment: 126310 INFO @ Fri, 05 Jul 2019 16:17:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:17:44: #1 finished! INFO @ Fri, 05 Jul 2019 16:17:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:17:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:17:44: #2 number of paired peaks: 361 WARNING @ Fri, 05 Jul 2019 16:17:44: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Fri, 05 Jul 2019 16:17:44: start model_add_line... INFO @ Fri, 05 Jul 2019 16:17:44: start X-correlation... INFO @ Fri, 05 Jul 2019 16:17:44: end of X-cor INFO @ Fri, 05 Jul 2019 16:17:44: #2 finished! INFO @ Fri, 05 Jul 2019 16:17:44: #2 predicted fragment length is 105 bps INFO @ Fri, 05 Jul 2019 16:17:44: #2 alternative fragment length(s) may be 25,70,105,135,166,199,229,273,303,365,406,429,464,476,524,568 bps INFO @ Fri, 05 Jul 2019 16:17:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.20_model.r WARNING @ Fri, 05 Jul 2019 16:17:44: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:17:44: #2 You may need to consider one of the other alternative d(s): 25,70,105,135,166,199,229,273,303,365,406,429,464,476,524,568 WARNING @ Fri, 05 Jul 2019 16:17:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:17:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:17:44: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:17:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:17:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:17:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:17:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548247/ERX2548247.20_summits.bed INFO @ Fri, 05 Jul 2019 16:17:45: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling