Job ID = 2006304 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 915,759 reads read : 915,759 reads written : 915,759 spots read : 900,048 reads read : 900,048 reads written : 900,048 spots read : 893,592 reads read : 893,592 reads written : 893,592 spots read : 862,172 reads read : 862,172 reads written : 862,172 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529474.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529475.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529476.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: 00:01:38 3571571 reads; of these: 3571571 (100.00%) were unpaired; of these: 157394 (4.41%) aligned 0 times 2817775 (78.89%) aligned exactly 1 time 596402 (16.70%) aligned >1 times 95.59% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 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] 3331636 / 3414177 = 0.9758 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 15:36:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.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 15:36:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:36:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:36:35: #1 tag size is determined as 146 bps INFO @ Fri, 05 Jul 2019 15:36:35: #1 tag size = 146 INFO @ Fri, 05 Jul 2019 15:36:35: #1 total tags in treatment: 82541 INFO @ Fri, 05 Jul 2019 15:36:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:36:35: #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 15:36:35: #1 tags after filtering in treatment: 82541 INFO @ Fri, 05 Jul 2019 15:36:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:36:35: #1 finished! INFO @ Fri, 05 Jul 2019 15:36:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:36:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.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 15:36:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:36:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:36:35: #2 number of paired peaks: 216 WARNING @ Fri, 05 Jul 2019 15:36:35: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Fri, 05 Jul 2019 15:36:35: start model_add_line... INFO @ Fri, 05 Jul 2019 15:36:35: start X-correlation... INFO @ Fri, 05 Jul 2019 15:36:35: end of X-cor INFO @ Fri, 05 Jul 2019 15:36:35: #2 finished! INFO @ Fri, 05 Jul 2019 15:36:35: #2 predicted fragment length is 173 bps INFO @ Fri, 05 Jul 2019 15:36:35: #2 alternative fragment length(s) may be 133,154,173,234,407,472,509,539 bps INFO @ Fri, 05 Jul 2019 15:36:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.05_model.r WARNING @ Fri, 05 Jul 2019 15:36:35: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:36:35: #2 You may need to consider one of the other alternative d(s): 133,154,173,234,407,472,509,539 WARNING @ Fri, 05 Jul 2019 15:36:35: #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 15:36:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:36:35: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:36:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:36:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:36:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:36:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.05_summits.bed INFO @ Fri, 05 Jul 2019 15:36:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:36:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.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 15:36:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:36:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:36:36: #1 tag size is determined as 146 bps INFO @ Fri, 05 Jul 2019 15:36:36: #1 tag size = 146 INFO @ Fri, 05 Jul 2019 15:36:36: #1 total tags in treatment: 82541 INFO @ Fri, 05 Jul 2019 15:36:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:36:36: #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 15:36:36: #1 tags after filtering in treatment: 82541 INFO @ Fri, 05 Jul 2019 15:36:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:36:36: #1 finished! INFO @ Fri, 05 Jul 2019 15:36:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:36:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:36:36: #2 number of paired peaks: 216 WARNING @ Fri, 05 Jul 2019 15:36:36: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Fri, 05 Jul 2019 15:36:36: start model_add_line... INFO @ Fri, 05 Jul 2019 15:36:36: start X-correlation... INFO @ Fri, 05 Jul 2019 15:36:36: end of X-cor INFO @ Fri, 05 Jul 2019 15:36:36: #2 finished! INFO @ Fri, 05 Jul 2019 15:36:36: #2 predicted fragment length is 173 bps INFO @ Fri, 05 Jul 2019 15:36:36: #2 alternative fragment length(s) may be 133,154,173,234,407,472,509,539 bps INFO @ Fri, 05 Jul 2019 15:36:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.10_model.r WARNING @ Fri, 05 Jul 2019 15:36:36: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:36:36: #2 You may need to consider one of the other alternative d(s): 133,154,173,234,407,472,509,539 WARNING @ Fri, 05 Jul 2019 15:36:36: #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 15:36:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:36:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:36:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:36:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:36:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:36:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.10_summits.bed INFO @ Fri, 05 Jul 2019 15:36:37: Done! INFO @ Fri, 05 Jul 2019 15:36:37: #1 tag size is determined as 146 bps INFO @ Fri, 05 Jul 2019 15:36:37: #1 tag size = 146 INFO @ Fri, 05 Jul 2019 15:36:37: #1 total tags in treatment: 82541 INFO @ Fri, 05 Jul 2019 15:36:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:36:37: #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 15:36:37: #1 tags after filtering in treatment: 82541 INFO @ Fri, 05 Jul 2019 15:36:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:36:37: #1 finished! INFO @ Fri, 05 Jul 2019 15:36:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:36:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:36:37: #2 number of paired peaks: 216 WARNING @ Fri, 05 Jul 2019 15:36:37: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Fri, 05 Jul 2019 15:36:37: start model_add_line... INFO @ Fri, 05 Jul 2019 15:36:37: start X-correlation... INFO @ Fri, 05 Jul 2019 15:36:37: end of X-cor INFO @ Fri, 05 Jul 2019 15:36:37: #2 finished! INFO @ Fri, 05 Jul 2019 15:36:37: #2 predicted fragment length is 173 bps INFO @ Fri, 05 Jul 2019 15:36:37: #2 alternative fragment length(s) may be 133,154,173,234,407,472,509,539 bps INFO @ Fri, 05 Jul 2019 15:36:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.20_model.r WARNING @ Fri, 05 Jul 2019 15:36:37: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:36:37: #2 You may need to consider one of the other alternative d(s): 133,154,173,234,407,472,509,539 WARNING @ Fri, 05 Jul 2019 15:36:37: #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 15:36:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:36:37: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 15:36:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:36:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:36:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:36:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548152/ERX2548152.20_summits.bed INFO @ Fri, 05 Jul 2019 15:36:38: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 2 millis BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling