Job ID = 2007599 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,022,025 reads read : 3,022,025 reads written : 3,022,025 spots read : 2,931,889 reads read : 2,931,889 reads written : 2,931,889 spots read : 3,035,054 reads read : 3,035,054 reads written : 3,035,054 spots read : 2,827,115 reads read : 2,827,115 reads written : 2,827,115 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529728.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529730.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529731.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: 00:08:08 11816083 reads; of these: 11816083 (100.00%) were unpaired; of these: 870895 (7.37%) aligned 0 times 9027289 (76.40%) aligned exactly 1 time 1917899 (16.23%) aligned >1 times 92.63% overall alignment rate Time searching: 00:08:08 Overall time: 00:08:08 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] 10732427 / 10945188 = 0.9806 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 16:24:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.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 16:24:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:24:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:24:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.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 16:24:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:24:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:24:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.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 16:24:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:24:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:24:02: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:24:02: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:24:02: #1 total tags in treatment: 212761 INFO @ Fri, 05 Jul 2019 16:24:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:24:02: #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 16:24:02: #1 tags after filtering in treatment: 212761 INFO @ Fri, 05 Jul 2019 16:24:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:24:02: #1 finished! INFO @ Fri, 05 Jul 2019 16:24:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:24:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:24:02: #2 number of paired peaks: 517 WARNING @ Fri, 05 Jul 2019 16:24:02: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Fri, 05 Jul 2019 16:24:02: start model_add_line... INFO @ Fri, 05 Jul 2019 16:24:02: start X-correlation... INFO @ Fri, 05 Jul 2019 16:24:02: end of X-cor INFO @ Fri, 05 Jul 2019 16:24:02: #2 finished! INFO @ Fri, 05 Jul 2019 16:24:02: #2 predicted fragment length is 69 bps INFO @ Fri, 05 Jul 2019 16:24:02: #2 alternative fragment length(s) may be 69,186,214,304,419,478,491,562 bps INFO @ Fri, 05 Jul 2019 16:24:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.05_model.r WARNING @ Fri, 05 Jul 2019 16:24:02: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:24:02: #2 You may need to consider one of the other alternative d(s): 69,186,214,304,419,478,491,562 WARNING @ Fri, 05 Jul 2019 16:24:02: #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 16:24:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:24:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:24:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:24:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:24:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:24:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.05_summits.bed INFO @ Fri, 05 Jul 2019 16:24:03: Done! INFO @ Fri, 05 Jul 2019 16:24:03: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:24:03: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:24:03: #1 total tags in treatment: 212761 INFO @ Fri, 05 Jul 2019 16:24:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:24:03: #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 16:24:03: #1 tags after filtering in treatment: 212761 INFO @ Fri, 05 Jul 2019 16:24:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:24:03: #1 finished! INFO @ Fri, 05 Jul 2019 16:24:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:24:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:24:03: #2 number of paired peaks: 517 WARNING @ Fri, 05 Jul 2019 16:24:03: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Fri, 05 Jul 2019 16:24:03: start model_add_line... INFO @ Fri, 05 Jul 2019 16:24:03: start X-correlation... INFO @ Fri, 05 Jul 2019 16:24:03: end of X-cor INFO @ Fri, 05 Jul 2019 16:24:03: #2 finished! INFO @ Fri, 05 Jul 2019 16:24:03: #2 predicted fragment length is 69 bps INFO @ Fri, 05 Jul 2019 16:24:03: #2 alternative fragment length(s) may be 69,186,214,304,419,478,491,562 bps INFO @ Fri, 05 Jul 2019 16:24:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.10_model.r WARNING @ Fri, 05 Jul 2019 16:24:03: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:24:03: #2 You may need to consider one of the other alternative d(s): 69,186,214,304,419,478,491,562 WARNING @ Fri, 05 Jul 2019 16:24:03: #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 16:24:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:24:03: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (80 records, 4 fields): 5 millis BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:24:04: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:24:04: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:24:04: #1 total tags in treatment: 212761 INFO @ Fri, 05 Jul 2019 16:24:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:24:04: #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 16:24:04: #1 tags after filtering in treatment: 212761 INFO @ Fri, 05 Jul 2019 16:24:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:24:04: #1 finished! INFO @ Fri, 05 Jul 2019 16:24:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:24:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:24:04: #2 number of paired peaks: 517 WARNING @ Fri, 05 Jul 2019 16:24:04: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Fri, 05 Jul 2019 16:24:04: start model_add_line... INFO @ Fri, 05 Jul 2019 16:24:04: start X-correlation... INFO @ Fri, 05 Jul 2019 16:24:04: end of X-cor INFO @ Fri, 05 Jul 2019 16:24:04: #2 finished! INFO @ Fri, 05 Jul 2019 16:24:04: #2 predicted fragment length is 69 bps INFO @ Fri, 05 Jul 2019 16:24:04: #2 alternative fragment length(s) may be 69,186,214,304,419,478,491,562 bps INFO @ Fri, 05 Jul 2019 16:24:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.20_model.r WARNING @ Fri, 05 Jul 2019 16:24:04: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:24:04: #2 You may need to consider one of the other alternative d(s): 69,186,214,304,419,478,491,562 WARNING @ Fri, 05 Jul 2019 16:24:04: #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 16:24:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:24:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:24:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:24:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:24:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:24:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.10_summits.bed INFO @ Fri, 05 Jul 2019 16:24:04: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (31 records, 4 fields): 1 millis BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:24:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:24:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:24:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:24:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548223/ERX2548223.20_summits.bed INFO @ Fri, 05 Jul 2019 16:24:05: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling