Job ID = 2007595 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,365,996 reads read : 2,365,996 reads written : 2,365,996 spots read : 2,275,582 reads read : 2,275,582 reads written : 2,275,582 spots read : 2,337,262 reads read : 2,337,262 reads written : 2,337,262 spots read : 2,361,180 reads read : 2,361,180 reads written : 2,361,180 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529722.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529723.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529724.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529725.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: 00:04:23 9340020 reads; of these: 9340020 (100.00%) were unpaired; of these: 307904 (3.30%) aligned 0 times 7499967 (80.30%) aligned exactly 1 time 1532149 (16.40%) aligned >1 times 96.70% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:23 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_sort_core] merging from 8 files... [bam_rmdupse_core] 8925276 / 9032116 = 0.9882 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 16:12:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.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 16:12:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:12:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:12:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.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 16:12:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:12:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:12:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.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 16:12:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:12:38: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:12:39: #1 tag size is determined as 143 bps INFO @ Fri, 05 Jul 2019 16:12:39: #1 tag size = 143 INFO @ Fri, 05 Jul 2019 16:12:39: #1 total tags in treatment: 106840 INFO @ Fri, 05 Jul 2019 16:12:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:12:39: #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 16:12:39: #1 tags after filtering in treatment: 106840 INFO @ Fri, 05 Jul 2019 16:12:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:12:39: #1 finished! INFO @ Fri, 05 Jul 2019 16:12:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:12:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:12:39: #1 tag size is determined as 143 bps INFO @ Fri, 05 Jul 2019 16:12:39: #1 tag size = 143 INFO @ Fri, 05 Jul 2019 16:12:39: #1 total tags in treatment: 106840 INFO @ Fri, 05 Jul 2019 16:12:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:12:39: #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 16:12:39: #1 tags after filtering in treatment: 106840 INFO @ Fri, 05 Jul 2019 16:12:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:12:39: #1 finished! INFO @ Fri, 05 Jul 2019 16:12:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:12:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:12:39: #2 number of paired peaks: 325 WARNING @ Fri, 05 Jul 2019 16:12:39: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Fri, 05 Jul 2019 16:12:39: start model_add_line... INFO @ Fri, 05 Jul 2019 16:12:39: #1 tag size is determined as 143 bps INFO @ Fri, 05 Jul 2019 16:12:39: #1 tag size = 143 INFO @ Fri, 05 Jul 2019 16:12:39: start X-correlation... INFO @ Fri, 05 Jul 2019 16:12:39: #1 total tags in treatment: 106840 INFO @ Fri, 05 Jul 2019 16:12:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:12:39: #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 16:12:39: #1 tags after filtering in treatment: 106840 INFO @ Fri, 05 Jul 2019 16:12:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:12:39: #1 finished! INFO @ Fri, 05 Jul 2019 16:12:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:12:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:12:39: #2 number of paired peaks: 325 WARNING @ Fri, 05 Jul 2019 16:12:39: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Fri, 05 Jul 2019 16:12:39: end of X-cor INFO @ Fri, 05 Jul 2019 16:12:39: start model_add_line... INFO @ Fri, 05 Jul 2019 16:12:39: #2 finished! INFO @ Fri, 05 Jul 2019 16:12:39: #2 predicted fragment length is 106 bps INFO @ Fri, 05 Jul 2019 16:12:39: #2 alternative fragment length(s) may be 106,501,535 bps INFO @ Fri, 05 Jul 2019 16:12:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.05_model.r INFO @ Fri, 05 Jul 2019 16:12:39: start X-correlation... WARNING @ Fri, 05 Jul 2019 16:12:39: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:12:39: #2 You may need to consider one of the other alternative d(s): 106,501,535 WARNING @ Fri, 05 Jul 2019 16:12:39: #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 16:12:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:12:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:12:39: #2 number of paired peaks: 325 WARNING @ Fri, 05 Jul 2019 16:12:39: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Fri, 05 Jul 2019 16:12:39: start model_add_line... INFO @ Fri, 05 Jul 2019 16:12:39: start X-correlation... INFO @ Fri, 05 Jul 2019 16:12:39: end of X-cor INFO @ Fri, 05 Jul 2019 16:12:39: #2 finished! INFO @ Fri, 05 Jul 2019 16:12:39: #2 predicted fragment length is 106 bps INFO @ Fri, 05 Jul 2019 16:12:39: #2 alternative fragment length(s) may be 106,501,535 bps INFO @ Fri, 05 Jul 2019 16:12:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.10_model.r WARNING @ Fri, 05 Jul 2019 16:12:39: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:12:39: #2 You may need to consider one of the other alternative d(s): 106,501,535 WARNING @ Fri, 05 Jul 2019 16:12:39: #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 16:12:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:12:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:12:39: end of X-cor INFO @ Fri, 05 Jul 2019 16:12:39: #2 finished! INFO @ Fri, 05 Jul 2019 16:12:39: #2 predicted fragment length is 106 bps INFO @ Fri, 05 Jul 2019 16:12:39: #2 alternative fragment length(s) may be 106,501,535 bps INFO @ Fri, 05 Jul 2019 16:12:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.20_model.r WARNING @ Fri, 05 Jul 2019 16:12:39: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:12:39: #2 You may need to consider one of the other alternative d(s): 106,501,535 WARNING @ Fri, 05 Jul 2019 16:12:39: #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 16:12:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:12:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:12:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:12:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:12:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:12:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:12:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:12:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.05_summits.bed INFO @ Fri, 05 Jul 2019 16:12:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:12:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:12:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:12:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:12:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.20_summits.bed INFO @ Fri, 05 Jul 2019 16:12:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548220/ERX2548220.10_summits.bed INFO @ Fri, 05 Jul 2019 16:12:40: Done! INFO @ Fri, 05 Jul 2019 16:12:40: Done! INFO @ Fri, 05 Jul 2019 16:12:40: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 5 millis pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 2 millis pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (54 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling