Job ID = 2006287 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,270,977 reads read : 1,270,977 reads written : 1,270,977 spots read : 1,224,677 reads read : 1,224,677 reads written : 1,224,677 spots read : 1,253,122 reads read : 1,253,122 reads written : 1,253,122 spots read : 1,276,519 reads read : 1,276,519 reads written : 1,276,519 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529434.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529436.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529437.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: 00:02:33 5025295 reads; of these: 5025295 (100.00%) were unpaired; of these: 165088 (3.29%) aligned 0 times 4135983 (82.30%) aligned exactly 1 time 724224 (14.41%) aligned >1 times 96.71% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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] 4793655 / 4860207 = 0.9863 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 15:25:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.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 15:25:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:25:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:25:12: #1 tag size is determined as 138 bps INFO @ Fri, 05 Jul 2019 15:25:12: #1 tag size = 138 INFO @ Fri, 05 Jul 2019 15:25:12: #1 total tags in treatment: 66552 INFO @ Fri, 05 Jul 2019 15:25:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:25:12: #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 15:25:12: #1 tags after filtering in treatment: 66552 INFO @ Fri, 05 Jul 2019 15:25:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:25:12: #1 finished! INFO @ Fri, 05 Jul 2019 15:25:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:25:12: #2 number of paired peaks: 271 WARNING @ Fri, 05 Jul 2019 15:25:12: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Fri, 05 Jul 2019 15:25:12: start model_add_line... INFO @ Fri, 05 Jul 2019 15:25:12: start X-correlation... INFO @ Fri, 05 Jul 2019 15:25:12: end of X-cor INFO @ Fri, 05 Jul 2019 15:25:12: #2 finished! INFO @ Fri, 05 Jul 2019 15:25:12: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 15:25:12: #2 alternative fragment length(s) may be 99,128,513,543 bps INFO @ Fri, 05 Jul 2019 15:25:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.05_model.r WARNING @ Fri, 05 Jul 2019 15:25:12: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:25:12: #2 You may need to consider one of the other alternative d(s): 99,128,513,543 WARNING @ Fri, 05 Jul 2019 15:25:12: #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 15:25:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:25:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:25:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.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 15:25:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:25:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:25:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:25:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.05_summits.bed INFO @ Fri, 05 Jul 2019 15:25:12: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:25:13: #1 tag size is determined as 138 bps INFO @ Fri, 05 Jul 2019 15:25:13: #1 tag size = 138 INFO @ Fri, 05 Jul 2019 15:25:13: #1 total tags in treatment: 66552 INFO @ Fri, 05 Jul 2019 15:25:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:25:13: #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 15:25:13: #1 tags after filtering in treatment: 66552 INFO @ Fri, 05 Jul 2019 15:25:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:25:13: #1 finished! INFO @ Fri, 05 Jul 2019 15:25:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:25:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:25:13: #2 number of paired peaks: 271 WARNING @ Fri, 05 Jul 2019 15:25:13: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Fri, 05 Jul 2019 15:25:13: start model_add_line... INFO @ Fri, 05 Jul 2019 15:25:13: start X-correlation... INFO @ Fri, 05 Jul 2019 15:25:13: end of X-cor INFO @ Fri, 05 Jul 2019 15:25:13: #2 finished! INFO @ Fri, 05 Jul 2019 15:25:13: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 15:25:13: #2 alternative fragment length(s) may be 99,128,513,543 bps INFO @ Fri, 05 Jul 2019 15:25:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.10_model.r WARNING @ Fri, 05 Jul 2019 15:25:13: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:25:13: #2 You may need to consider one of the other alternative d(s): 99,128,513,543 WARNING @ Fri, 05 Jul 2019 15:25:13: #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 15:25:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:25:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:25:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.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 15:25:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:25:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:25:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:25:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:25:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:25:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.10_summits.bed INFO @ Fri, 05 Jul 2019 15:25:13: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:25:14: #1 tag size is determined as 138 bps INFO @ Fri, 05 Jul 2019 15:25:14: #1 tag size = 138 INFO @ Fri, 05 Jul 2019 15:25:14: #1 total tags in treatment: 66552 INFO @ Fri, 05 Jul 2019 15:25:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:25:14: #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 15:25:14: #1 tags after filtering in treatment: 66552 INFO @ Fri, 05 Jul 2019 15:25:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:25:14: #1 finished! INFO @ Fri, 05 Jul 2019 15:25:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:25:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:25:14: #2 number of paired peaks: 271 WARNING @ Fri, 05 Jul 2019 15:25:14: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Fri, 05 Jul 2019 15:25:14: start model_add_line... INFO @ Fri, 05 Jul 2019 15:25:14: start X-correlation... INFO @ Fri, 05 Jul 2019 15:25:14: end of X-cor INFO @ Fri, 05 Jul 2019 15:25:14: #2 finished! INFO @ Fri, 05 Jul 2019 15:25:14: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 15:25:14: #2 alternative fragment length(s) may be 99,128,513,543 bps INFO @ Fri, 05 Jul 2019 15:25:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.20_model.r WARNING @ Fri, 05 Jul 2019 15:25:14: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:25:14: #2 You may need to consider one of the other alternative d(s): 99,128,513,543 WARNING @ Fri, 05 Jul 2019 15:25:14: #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 15:25:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:25:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:25:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:25:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:25:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:25:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548136/ERX2548136.20_summits.bed INFO @ Fri, 05 Jul 2019 15:25:14: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling