Job ID = 2007580 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,386,344 reads read : 3,386,344 reads written : 3,386,344 spots read : 3,294,038 reads read : 3,294,038 reads written : 3,294,038 spots read : 3,403,445 reads read : 3,403,445 reads written : 3,403,445 spots read : 3,158,394 reads read : 3,158,394 reads written : 3,158,394 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529674.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529676.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529677.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: 00:04:13 13242221 reads; of these: 13242221 (100.00%) were unpaired; of these: 1493176 (11.28%) aligned 0 times 10060137 (75.97%) aligned exactly 1 time 1688908 (12.75%) aligned >1 times 88.72% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 11277433 / 11749045 = 0.9599 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 16:13:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.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 16:13:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:13:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:13:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.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 16:13:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:13:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:13:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.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 16:13:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:13:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:13:07: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:13:07: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:13:07: #1 total tags in treatment: 471612 INFO @ Fri, 05 Jul 2019 16:13:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:13:07: #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 16:13:07: #1 tags after filtering in treatment: 471612 INFO @ Fri, 05 Jul 2019 16:13:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:13:07: #1 finished! INFO @ Fri, 05 Jul 2019 16:13:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:13:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:13:07: #2 number of paired peaks: 415 WARNING @ Fri, 05 Jul 2019 16:13:07: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Fri, 05 Jul 2019 16:13:07: start model_add_line... INFO @ Fri, 05 Jul 2019 16:13:07: start X-correlation... INFO @ Fri, 05 Jul 2019 16:13:07: end of X-cor INFO @ Fri, 05 Jul 2019 16:13:07: #2 finished! INFO @ Fri, 05 Jul 2019 16:13:07: #2 predicted fragment length is 66 bps INFO @ Fri, 05 Jul 2019 16:13:07: #2 alternative fragment length(s) may be 4,66,79,97,157,183,561 bps INFO @ Fri, 05 Jul 2019 16:13:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.05_model.r WARNING @ Fri, 05 Jul 2019 16:13:07: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:13:07: #2 You may need to consider one of the other alternative d(s): 4,66,79,97,157,183,561 WARNING @ Fri, 05 Jul 2019 16:13:07: #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 16:13:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:13:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:13:08: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:13:08: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:13:08: #1 total tags in treatment: 471612 INFO @ Fri, 05 Jul 2019 16:13:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:13:08: #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 16:13:08: #1 tags after filtering in treatment: 471612 INFO @ Fri, 05 Jul 2019 16:13:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:13:08: #1 finished! INFO @ Fri, 05 Jul 2019 16:13:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:13:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:13:08: #2 number of paired peaks: 415 WARNING @ Fri, 05 Jul 2019 16:13:08: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Fri, 05 Jul 2019 16:13:08: start model_add_line... INFO @ Fri, 05 Jul 2019 16:13:08: start X-correlation... INFO @ Fri, 05 Jul 2019 16:13:08: end of X-cor INFO @ Fri, 05 Jul 2019 16:13:08: #2 finished! INFO @ Fri, 05 Jul 2019 16:13:08: #2 predicted fragment length is 66 bps INFO @ Fri, 05 Jul 2019 16:13:08: #2 alternative fragment length(s) may be 4,66,79,97,157,183,561 bps INFO @ Fri, 05 Jul 2019 16:13:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.10_model.r WARNING @ Fri, 05 Jul 2019 16:13:08: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:13:08: #2 You may need to consider one of the other alternative d(s): 4,66,79,97,157,183,561 WARNING @ Fri, 05 Jul 2019 16:13:08: #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 16:13:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:13:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:13:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:13:09: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:13:09: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:13:09: #1 total tags in treatment: 471612 INFO @ Fri, 05 Jul 2019 16:13:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:13:09: #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 16:13:09: #1 tags after filtering in treatment: 471612 INFO @ Fri, 05 Jul 2019 16:13:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:13:09: #1 finished! INFO @ Fri, 05 Jul 2019 16:13:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:13:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:13:09: #2 number of paired peaks: 415 WARNING @ Fri, 05 Jul 2019 16:13:09: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Fri, 05 Jul 2019 16:13:09: start model_add_line... INFO @ Fri, 05 Jul 2019 16:13:09: start X-correlation... INFO @ Fri, 05 Jul 2019 16:13:09: end of X-cor INFO @ Fri, 05 Jul 2019 16:13:09: #2 finished! INFO @ Fri, 05 Jul 2019 16:13:09: #2 predicted fragment length is 66 bps INFO @ Fri, 05 Jul 2019 16:13:09: #2 alternative fragment length(s) may be 4,66,79,97,157,183,561 bps INFO @ Fri, 05 Jul 2019 16:13:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.20_model.r WARNING @ Fri, 05 Jul 2019 16:13:09: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:13:09: #2 You may need to consider one of the other alternative d(s): 4,66,79,97,157,183,561 WARNING @ Fri, 05 Jul 2019 16:13:09: #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 16:13:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:13:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:13:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:13:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:13:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.05_summits.bed INFO @ Fri, 05 Jul 2019 16:13:09: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (169 records, 4 fields): 5 millis INFO @ Fri, 05 Jul 2019 16:13:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:13:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:13:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:13:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.10_summits.bed INFO @ Fri, 05 Jul 2019 16:13:10: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (80 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 16:13:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:13:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:13:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:13:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548208/ERX2548208.20_summits.bed INFO @ Fri, 05 Jul 2019 16:13:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling