Job ID = 2007631 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,718,453 reads read : 2,718,453 reads written : 2,718,453 spots read : 2,592,639 reads read : 2,592,639 reads written : 2,592,639 spots read : 2,562,303 reads read : 2,562,303 reads written : 2,562,303 spots read : 2,704,658 reads read : 2,704,658 reads written : 2,704,658 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529750.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529752.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529753.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: 00:05:35 10578053 reads; of these: 10578053 (100.00%) were unpaired; of these: 457696 (4.33%) aligned 0 times 8433126 (79.72%) aligned exactly 1 time 1687231 (15.95%) aligned >1 times 95.67% overall alignment rate Time searching: 00:05:36 Overall time: 00:05:36 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] 10002884 / 10120357 = 0.9884 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 16:18:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.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 16:18:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:18:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:19:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.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 16:19:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:19:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:19:01: #1 tag size is determined as 131 bps INFO @ Fri, 05 Jul 2019 16:19:01: #1 tag size = 131 INFO @ Fri, 05 Jul 2019 16:19:01: #1 total tags in treatment: 117473 INFO @ Fri, 05 Jul 2019 16:19:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:19:01: #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 16:19:01: #1 tags after filtering in treatment: 117473 INFO @ Fri, 05 Jul 2019 16:19:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:19:01: #1 finished! INFO @ Fri, 05 Jul 2019 16:19:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:19:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:19:01: #2 number of paired peaks: 321 WARNING @ Fri, 05 Jul 2019 16:19:01: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Fri, 05 Jul 2019 16:19:01: start model_add_line... INFO @ Fri, 05 Jul 2019 16:19:01: start X-correlation... INFO @ Fri, 05 Jul 2019 16:19:01: end of X-cor INFO @ Fri, 05 Jul 2019 16:19:01: #2 finished! INFO @ Fri, 05 Jul 2019 16:19:01: #2 predicted fragment length is 183 bps INFO @ Fri, 05 Jul 2019 16:19:01: #2 alternative fragment length(s) may be 103,126,153,183,211,271,343,438,473,528,551,583 bps INFO @ Fri, 05 Jul 2019 16:19:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.05_model.r WARNING @ Fri, 05 Jul 2019 16:19:01: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:19:01: #2 You may need to consider one of the other alternative d(s): 103,126,153,183,211,271,343,438,473,528,551,583 WARNING @ Fri, 05 Jul 2019 16:19:01: #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 16:19:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:19:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:19:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.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 16:19:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:19:01: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:19:01: #1 tag size is determined as 131 bps INFO @ Fri, 05 Jul 2019 16:19:01: #1 tag size = 131 INFO @ Fri, 05 Jul 2019 16:19:01: #1 total tags in treatment: 117473 INFO @ Fri, 05 Jul 2019 16:19:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:19:01: #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 16:19:01: #1 tags after filtering in treatment: 117473 INFO @ Fri, 05 Jul 2019 16:19:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:19:01: #1 finished! INFO @ Fri, 05 Jul 2019 16:19:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:19:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:19:01: #2 number of paired peaks: 321 WARNING @ Fri, 05 Jul 2019 16:19:01: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Fri, 05 Jul 2019 16:19:01: start model_add_line... INFO @ Fri, 05 Jul 2019 16:19:01: start X-correlation... INFO @ Fri, 05 Jul 2019 16:19:01: end of X-cor INFO @ Fri, 05 Jul 2019 16:19:01: #2 finished! INFO @ Fri, 05 Jul 2019 16:19:01: #2 predicted fragment length is 183 bps INFO @ Fri, 05 Jul 2019 16:19:01: #2 alternative fragment length(s) may be 103,126,153,183,211,271,343,438,473,528,551,583 bps INFO @ Fri, 05 Jul 2019 16:19:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.10_model.r WARNING @ Fri, 05 Jul 2019 16:19:01: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:19:01: #2 You may need to consider one of the other alternative d(s): 103,126,153,183,211,271,343,438,473,528,551,583 WARNING @ Fri, 05 Jul 2019 16:19:01: #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 16:19:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:19:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:19:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:19:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:19:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:19:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.05_summits.bed INFO @ Fri, 05 Jul 2019 16:19:01: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 16:19:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:19:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:19:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:19:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.10_summits.bed INFO @ Fri, 05 Jul 2019 16:19:02: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:19:02: #1 tag size is determined as 131 bps INFO @ Fri, 05 Jul 2019 16:19:02: #1 tag size = 131 INFO @ Fri, 05 Jul 2019 16:19:02: #1 total tags in treatment: 117473 INFO @ Fri, 05 Jul 2019 16:19:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:19:02: #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 16:19:02: #1 tags after filtering in treatment: 117473 INFO @ Fri, 05 Jul 2019 16:19:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:19:02: #1 finished! INFO @ Fri, 05 Jul 2019 16:19:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:19:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:19:02: #2 number of paired peaks: 321 WARNING @ Fri, 05 Jul 2019 16:19:02: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Fri, 05 Jul 2019 16:19:02: start model_add_line... INFO @ Fri, 05 Jul 2019 16:19:02: start X-correlation... INFO @ Fri, 05 Jul 2019 16:19:02: end of X-cor INFO @ Fri, 05 Jul 2019 16:19:02: #2 finished! INFO @ Fri, 05 Jul 2019 16:19:02: #2 predicted fragment length is 183 bps INFO @ Fri, 05 Jul 2019 16:19:02: #2 alternative fragment length(s) may be 103,126,153,183,211,271,343,438,473,528,551,583 bps INFO @ Fri, 05 Jul 2019 16:19:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.20_model.r WARNING @ Fri, 05 Jul 2019 16:19:02: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:19:02: #2 You may need to consider one of the other alternative d(s): 103,126,153,183,211,271,343,438,473,528,551,583 WARNING @ Fri, 05 Jul 2019 16:19:02: #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 16:19:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:19:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:19:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:19:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:19:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:19:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548233/ERX2548233.20_summits.bed INFO @ Fri, 05 Jul 2019 16:19:03: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。