Job ID = 2006630 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,576,303 reads read : 1,576,303 reads written : 1,576,303 spots read : 1,499,293 reads read : 1,499,293 reads written : 1,499,293 spots read : 1,535,704 reads read : 1,535,704 reads written : 1,535,704 spots read : 1,509,293 reads read : 1,509,293 reads written : 1,509,293 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529554.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529555.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: 00:01:37 6120593 reads; of these: 6120593 (100.00%) were unpaired; of these: 286225 (4.68%) aligned 0 times 4922468 (80.42%) aligned exactly 1 time 911900 (14.90%) aligned >1 times 95.32% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 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] 5161294 / 5834368 = 0.8846 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 15:43:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.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 15:43:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:43:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:43:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.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 15:43:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:43:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:43:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.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 15:43:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:43:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:43:16: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:43:16: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:43:16: #1 total tags in treatment: 673074 INFO @ Fri, 05 Jul 2019 15:43:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:43:16: #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 15:43:16: #1 tags after filtering in treatment: 673074 INFO @ Fri, 05 Jul 2019 15:43:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:43:16: #1 finished! INFO @ Fri, 05 Jul 2019 15:43:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:43:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:43:16: #2 number of paired peaks: 124 WARNING @ Fri, 05 Jul 2019 15:43:16: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Fri, 05 Jul 2019 15:43:16: start model_add_line... INFO @ Fri, 05 Jul 2019 15:43:16: start X-correlation... INFO @ Fri, 05 Jul 2019 15:43:16: end of X-cor INFO @ Fri, 05 Jul 2019 15:43:16: #2 finished! INFO @ Fri, 05 Jul 2019 15:43:16: #2 predicted fragment length is 82 bps INFO @ Fri, 05 Jul 2019 15:43:16: #2 alternative fragment length(s) may be 2,16,59,82,131,138,165,219,239,415,510,532,568 bps INFO @ Fri, 05 Jul 2019 15:43:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.05_model.r WARNING @ Fri, 05 Jul 2019 15:43:16: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:43:16: #2 You may need to consider one of the other alternative d(s): 2,16,59,82,131,138,165,219,239,415,510,532,568 WARNING @ Fri, 05 Jul 2019 15:43:16: #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 15:43:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:43:16: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:43:16: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:43:16: #1 total tags in treatment: 673074 INFO @ Fri, 05 Jul 2019 15:43:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:43:16: #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 15:43:16: #1 tags after filtering in treatment: 673074 INFO @ Fri, 05 Jul 2019 15:43:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:43:16: #1 finished! INFO @ Fri, 05 Jul 2019 15:43:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:43:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:43:16: #2 number of paired peaks: 124 WARNING @ Fri, 05 Jul 2019 15:43:16: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Fri, 05 Jul 2019 15:43:16: start model_add_line... INFO @ Fri, 05 Jul 2019 15:43:16: start X-correlation... INFO @ Fri, 05 Jul 2019 15:43:16: end of X-cor INFO @ Fri, 05 Jul 2019 15:43:16: #2 finished! INFO @ Fri, 05 Jul 2019 15:43:16: #2 predicted fragment length is 82 bps INFO @ Fri, 05 Jul 2019 15:43:16: #2 alternative fragment length(s) may be 2,16,59,82,131,138,165,219,239,415,510,532,568 bps INFO @ Fri, 05 Jul 2019 15:43:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.10_model.r WARNING @ Fri, 05 Jul 2019 15:43:16: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:43:16: #2 You may need to consider one of the other alternative d(s): 2,16,59,82,131,138,165,219,239,415,510,532,568 WARNING @ Fri, 05 Jul 2019 15:43:16: #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 15:43:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:43:17: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:43:17: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:43:17: #1 total tags in treatment: 673074 INFO @ Fri, 05 Jul 2019 15:43:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:43:17: #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 15:43:17: #1 tags after filtering in treatment: 673074 INFO @ Fri, 05 Jul 2019 15:43:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:43:17: #1 finished! INFO @ Fri, 05 Jul 2019 15:43:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:43:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:43:17: #2 number of paired peaks: 124 WARNING @ Fri, 05 Jul 2019 15:43:17: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Fri, 05 Jul 2019 15:43:17: start model_add_line... INFO @ Fri, 05 Jul 2019 15:43:17: start X-correlation... INFO @ Fri, 05 Jul 2019 15:43:17: end of X-cor INFO @ Fri, 05 Jul 2019 15:43:17: #2 finished! INFO @ Fri, 05 Jul 2019 15:43:17: #2 predicted fragment length is 82 bps INFO @ Fri, 05 Jul 2019 15:43:17: #2 alternative fragment length(s) may be 2,16,59,82,131,138,165,219,239,415,510,532,568 bps INFO @ Fri, 05 Jul 2019 15:43:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.20_model.r WARNING @ Fri, 05 Jul 2019 15:43:17: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:43:17: #2 You may need to consider one of the other alternative d(s): 2,16,59,82,131,138,165,219,239,415,510,532,568 WARNING @ Fri, 05 Jul 2019 15:43:17: #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 15:43:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:43:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:43:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:43:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:43:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:43:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:43:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.05_summits.bed INFO @ Fri, 05 Jul 2019 15:43:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (65 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:43:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:43:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:43:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:43:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.10_summits.bed INFO @ Fri, 05 Jul 2019 15:43:19: Done! pass1 - making usageList (6 chroms): 8 millis pass2 - checking and writing primary data (10 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:43:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:43:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:43:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548172/ERX2548172.20_summits.bed INFO @ Fri, 05 Jul 2019 15:43:20: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。