Job ID = 2005885 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,251,336 reads read : 3,251,336 reads written : 3,251,336 spots read : 3,196,392 reads read : 3,196,392 reads written : 3,196,392 spots read : 3,178,086 reads read : 3,178,086 reads written : 3,178,086 spots read : 3,076,425 reads read : 3,076,425 reads written : 3,076,425 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529250.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529251.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529252.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529253.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: 00:06:06 12702239 reads; of these: 12702239 (100.00%) were unpaired; of these: 383532 (3.02%) aligned 0 times 10063420 (79.23%) aligned exactly 1 time 2255287 (17.76%) aligned >1 times 96.98% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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 12 files... [bam_rmdupse_core] 12013506 / 12318707 = 0.9752 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 15:03:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.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 15:03:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:03:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:03:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.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 15:03:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:03:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:03:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.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 15:03:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:03:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:03:11: #1 tag size is determined as 147 bps INFO @ Fri, 05 Jul 2019 15:03:11: #1 tag size = 147 INFO @ Fri, 05 Jul 2019 15:03:11: #1 total tags in treatment: 305201 INFO @ Fri, 05 Jul 2019 15:03:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:03:11: #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 15:03:11: #1 tags after filtering in treatment: 305201 INFO @ Fri, 05 Jul 2019 15:03:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:03:11: #1 finished! INFO @ Fri, 05 Jul 2019 15:03:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:03:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:03:11: #2 number of paired peaks: 314 WARNING @ Fri, 05 Jul 2019 15:03:11: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Fri, 05 Jul 2019 15:03:11: start model_add_line... INFO @ Fri, 05 Jul 2019 15:03:11: start X-correlation... INFO @ Fri, 05 Jul 2019 15:03:11: end of X-cor INFO @ Fri, 05 Jul 2019 15:03:11: #2 finished! INFO @ Fri, 05 Jul 2019 15:03:11: #2 predicted fragment length is 226 bps INFO @ Fri, 05 Jul 2019 15:03:11: #2 alternative fragment length(s) may be 4,91,122,163,188,226,255,283,573 bps INFO @ Fri, 05 Jul 2019 15:03:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.05_model.r WARNING @ Fri, 05 Jul 2019 15:03:11: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:03:11: #2 You may need to consider one of the other alternative d(s): 4,91,122,163,188,226,255,283,573 WARNING @ Fri, 05 Jul 2019 15:03:11: #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 15:03:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:03:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:03:13: #1 tag size is determined as 147 bps INFO @ Fri, 05 Jul 2019 15:03:13: #1 tag size = 147 INFO @ Fri, 05 Jul 2019 15:03:13: #1 total tags in treatment: 305201 INFO @ Fri, 05 Jul 2019 15:03:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:03:13: #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 15:03:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:03:13: #1 tags after filtering in treatment: 305201 INFO @ Fri, 05 Jul 2019 15:03:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:03:13: #1 finished! INFO @ Fri, 05 Jul 2019 15:03:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:03:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:03:13: #2 number of paired peaks: 314 WARNING @ Fri, 05 Jul 2019 15:03:13: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Fri, 05 Jul 2019 15:03:13: start model_add_line... INFO @ Fri, 05 Jul 2019 15:03:13: start X-correlation... INFO @ Fri, 05 Jul 2019 15:03:13: end of X-cor INFO @ Fri, 05 Jul 2019 15:03:13: #2 finished! INFO @ Fri, 05 Jul 2019 15:03:13: #2 predicted fragment length is 226 bps INFO @ Fri, 05 Jul 2019 15:03:13: #2 alternative fragment length(s) may be 4,91,122,163,188,226,255,283,573 bps INFO @ Fri, 05 Jul 2019 15:03:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.10_model.r WARNING @ Fri, 05 Jul 2019 15:03:13: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:03:13: #2 You may need to consider one of the other alternative d(s): 4,91,122,163,188,226,255,283,573 WARNING @ Fri, 05 Jul 2019 15:03:13: #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 15:03:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:03:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:03:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:03:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:03:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.05_summits.bed INFO @ Fri, 05 Jul 2019 15:03:13: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (106 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:03:14: #1 tag size is determined as 147 bps INFO @ Fri, 05 Jul 2019 15:03:14: #1 tag size = 147 INFO @ Fri, 05 Jul 2019 15:03:14: #1 total tags in treatment: 305201 INFO @ Fri, 05 Jul 2019 15:03:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:03:14: #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 15:03:14: #1 tags after filtering in treatment: 305201 INFO @ Fri, 05 Jul 2019 15:03:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:03:14: #1 finished! INFO @ Fri, 05 Jul 2019 15:03:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:03:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:03:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:03:14: #2 number of paired peaks: 314 WARNING @ Fri, 05 Jul 2019 15:03:14: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Fri, 05 Jul 2019 15:03:14: start model_add_line... INFO @ Fri, 05 Jul 2019 15:03:14: start X-correlation... INFO @ Fri, 05 Jul 2019 15:03:14: end of X-cor INFO @ Fri, 05 Jul 2019 15:03:14: #2 finished! INFO @ Fri, 05 Jul 2019 15:03:14: #2 predicted fragment length is 226 bps INFO @ Fri, 05 Jul 2019 15:03:14: #2 alternative fragment length(s) may be 4,91,122,163,188,226,255,283,573 bps INFO @ Fri, 05 Jul 2019 15:03:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.20_model.r WARNING @ Fri, 05 Jul 2019 15:03:14: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:03:14: #2 You may need to consider one of the other alternative d(s): 4,91,122,163,188,226,255,283,573 WARNING @ Fri, 05 Jul 2019 15:03:14: #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 15:03:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:03:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:03:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:03:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:03:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.10_summits.bed INFO @ Fri, 05 Jul 2019 15:03:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (47 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:03:16: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 15:03:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:03:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:03:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548084/ERX2548084.20_summits.bed INFO @ Fri, 05 Jul 2019 15:03:16: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 6 millis BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling