Job ID = 2006286 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 946,789 reads read : 946,789 reads written : 946,789 spots read : 901,436 reads read : 901,436 reads written : 901,436 spots read : 921,832 reads read : 921,832 reads written : 921,832 spots read : 938,309 reads read : 938,309 reads written : 938,309 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529430.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529431.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529432.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529433.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: 00:02:38 3708366 reads; of these: 3708366 (100.00%) were unpaired; of these: 123962 (3.34%) aligned 0 times 3040337 (81.99%) aligned exactly 1 time 544067 (14.67%) aligned >1 times 96.66% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 3531580 / 3584404 = 0.9853 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 15:24:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.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 15:24:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:24:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:24:04: #1 tag size is determined as 135 bps INFO @ Fri, 05 Jul 2019 15:24:04: #1 tag size = 135 INFO @ Fri, 05 Jul 2019 15:24:04: #1 total tags in treatment: 52824 INFO @ Fri, 05 Jul 2019 15:24:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:24:04: #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 15:24:04: #1 tags after filtering in treatment: 52824 INFO @ Fri, 05 Jul 2019 15:24:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:24:04: #1 finished! INFO @ Fri, 05 Jul 2019 15:24:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:24:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:24:04: #2 number of paired peaks: 210 WARNING @ Fri, 05 Jul 2019 15:24:04: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Fri, 05 Jul 2019 15:24:04: start model_add_line... INFO @ Fri, 05 Jul 2019 15:24:04: start X-correlation... INFO @ Fri, 05 Jul 2019 15:24:04: end of X-cor INFO @ Fri, 05 Jul 2019 15:24:04: #2 finished! INFO @ Fri, 05 Jul 2019 15:24:04: #2 predicted fragment length is 170 bps INFO @ Fri, 05 Jul 2019 15:24:04: #2 alternative fragment length(s) may be 4,117,137,170,211,233,441,483,520,542,562,583 bps INFO @ Fri, 05 Jul 2019 15:24:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.05_model.r WARNING @ Fri, 05 Jul 2019 15:24:04: #2 Since the d (170) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:24:04: #2 You may need to consider one of the other alternative d(s): 4,117,137,170,211,233,441,483,520,542,562,583 WARNING @ Fri, 05 Jul 2019 15:24:04: #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 15:24:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:24:04: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:24:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:24:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:24:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:24:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.05_summits.bed INFO @ Fri, 05 Jul 2019 15:24:05: Done! INFO @ Fri, 05 Jul 2019 15:24:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.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 15:24:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:24:05: #1 read treatment tags... pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (34 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:24:05: #1 tag size is determined as 135 bps INFO @ Fri, 05 Jul 2019 15:24:05: #1 tag size = 135 INFO @ Fri, 05 Jul 2019 15:24:05: #1 total tags in treatment: 52824 INFO @ Fri, 05 Jul 2019 15:24:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:24:05: #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 15:24:05: #1 tags after filtering in treatment: 52824 INFO @ Fri, 05 Jul 2019 15:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:24:05: #1 finished! INFO @ Fri, 05 Jul 2019 15:24:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:24:05: #2 number of paired peaks: 210 WARNING @ Fri, 05 Jul 2019 15:24:05: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Fri, 05 Jul 2019 15:24:05: start model_add_line... INFO @ Fri, 05 Jul 2019 15:24:05: start X-correlation... INFO @ Fri, 05 Jul 2019 15:24:05: end of X-cor INFO @ Fri, 05 Jul 2019 15:24:05: #2 finished! INFO @ Fri, 05 Jul 2019 15:24:05: #2 predicted fragment length is 170 bps INFO @ Fri, 05 Jul 2019 15:24:05: #2 alternative fragment length(s) may be 4,117,137,170,211,233,441,483,520,542,562,583 bps INFO @ Fri, 05 Jul 2019 15:24:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.10_model.r WARNING @ Fri, 05 Jul 2019 15:24:05: #2 Since the d (170) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:24:05: #2 You may need to consider one of the other alternative d(s): 4,117,137,170,211,233,441,483,520,542,562,583 WARNING @ Fri, 05 Jul 2019 15:24:05: #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 15:24:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:24:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:24:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:24:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:24:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:24:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.10_summits.bed INFO @ Fri, 05 Jul 2019 15:24:06: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:24:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.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 15:24:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:24:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:24:06: #1 tag size is determined as 135 bps INFO @ Fri, 05 Jul 2019 15:24:06: #1 tag size = 135 INFO @ Fri, 05 Jul 2019 15:24:06: #1 total tags in treatment: 52824 INFO @ Fri, 05 Jul 2019 15:24:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:24:06: #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 15:24:06: #1 tags after filtering in treatment: 52824 INFO @ Fri, 05 Jul 2019 15:24:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:24:06: #1 finished! INFO @ Fri, 05 Jul 2019 15:24:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:24:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:24:06: #2 number of paired peaks: 210 WARNING @ Fri, 05 Jul 2019 15:24:06: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Fri, 05 Jul 2019 15:24:06: start model_add_line... INFO @ Fri, 05 Jul 2019 15:24:06: start X-correlation... INFO @ Fri, 05 Jul 2019 15:24:06: end of X-cor INFO @ Fri, 05 Jul 2019 15:24:06: #2 finished! INFO @ Fri, 05 Jul 2019 15:24:06: #2 predicted fragment length is 170 bps INFO @ Fri, 05 Jul 2019 15:24:06: #2 alternative fragment length(s) may be 4,117,137,170,211,233,441,483,520,542,562,583 bps INFO @ Fri, 05 Jul 2019 15:24:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.20_model.r WARNING @ Fri, 05 Jul 2019 15:24:06: #2 Since the d (170) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:24:06: #2 You may need to consider one of the other alternative d(s): 4,117,137,170,211,233,441,483,520,542,562,583 WARNING @ Fri, 05 Jul 2019 15:24:06: #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 15:24:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:24:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:24:06: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:24:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:24:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:24:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548135/ERX2548135.20_summits.bed INFO @ Fri, 05 Jul 2019 15:24:07: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling