Job ID = 2590896 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,272,532 reads read : 13,272,532 reads written : 13,272,532 rm: cannot remove ‘[DSE]RR*’: 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: 00:02:36 13272532 reads; of these: 13272532 (100.00%) were unpaired; of these: 3269180 (24.63%) aligned 0 times 9569399 (72.10%) aligned exactly 1 time 433953 (3.27%) aligned >1 times 75.37% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 9667500 / 10003352 = 0.9664 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 @ Tue, 13 Aug 2019 00:00:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 13 Aug 2019 00:00:28: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:00:28: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:00:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 13 Aug 2019 00:00:29: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:00:29: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 13 Aug 2019 00:00:30: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:00:30: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:00:32: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:00:32: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:00:32: #1 total tags in treatment: 335852 INFO @ Tue, 13 Aug 2019 00:00:32: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:00:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:00:32: #1 tags after filtering in treatment: 335852 INFO @ Tue, 13 Aug 2019 00:00:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:00:32: #1 finished! INFO @ Tue, 13 Aug 2019 00:00:32: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:00:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:00:32: #2 number of paired peaks: 775 WARNING @ Tue, 13 Aug 2019 00:00:32: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Tue, 13 Aug 2019 00:00:32: start model_add_line... INFO @ Tue, 13 Aug 2019 00:00:32: start X-correlation... INFO @ Tue, 13 Aug 2019 00:00:32: end of X-cor INFO @ Tue, 13 Aug 2019 00:00:32: #2 finished! INFO @ Tue, 13 Aug 2019 00:00:32: #2 predicted fragment length is 50 bps INFO @ Tue, 13 Aug 2019 00:00:32: #2 alternative fragment length(s) may be 50 bps INFO @ Tue, 13 Aug 2019 00:00:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.05_model.r WARNING @ Tue, 13 Aug 2019 00:00:32: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:00:32: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Tue, 13 Aug 2019 00:00:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:00:32: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:00:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:00:32: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:00:32: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:00:32: #1 total tags in treatment: 335852 INFO @ Tue, 13 Aug 2019 00:00:32: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:00:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:00:32: #1 tags after filtering in treatment: 335852 INFO @ Tue, 13 Aug 2019 00:00:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:00:32: #1 finished! INFO @ Tue, 13 Aug 2019 00:00:32: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:00:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:00:32: #2 number of paired peaks: 775 WARNING @ Tue, 13 Aug 2019 00:00:32: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Tue, 13 Aug 2019 00:00:32: start model_add_line... INFO @ Tue, 13 Aug 2019 00:00:32: start X-correlation... INFO @ Tue, 13 Aug 2019 00:00:32: end of X-cor INFO @ Tue, 13 Aug 2019 00:00:32: #2 finished! INFO @ Tue, 13 Aug 2019 00:00:32: #2 predicted fragment length is 50 bps INFO @ Tue, 13 Aug 2019 00:00:32: #2 alternative fragment length(s) may be 50 bps INFO @ Tue, 13 Aug 2019 00:00:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.10_model.r WARNING @ Tue, 13 Aug 2019 00:00:32: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:00:32: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Tue, 13 Aug 2019 00:00:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:00:32: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:00:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:00:33: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 13 Aug 2019 00:00:33: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:00:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:00:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:00:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.05_summits.bed INFO @ Tue, 13 Aug 2019 00:00:33: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (436 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:00:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:00:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:00:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.10_summits.bed INFO @ Tue, 13 Aug 2019 00:00:33: Done! pass1 - making usageList (5 chroms): 2 millis pass2 - checking and writing primary data (330 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 13 Aug 2019 00:00:33: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:00:33: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:00:33: #1 total tags in treatment: 335852 INFO @ Tue, 13 Aug 2019 00:00:33: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:00:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:00:33: #1 tags after filtering in treatment: 335852 INFO @ Tue, 13 Aug 2019 00:00:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:00:33: #1 finished! INFO @ Tue, 13 Aug 2019 00:00:33: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:00:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:00:33: #2 number of paired peaks: 775 WARNING @ Tue, 13 Aug 2019 00:00:33: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Tue, 13 Aug 2019 00:00:33: start model_add_line... INFO @ Tue, 13 Aug 2019 00:00:33: start X-correlation... INFO @ Tue, 13 Aug 2019 00:00:34: end of X-cor INFO @ Tue, 13 Aug 2019 00:00:34: #2 finished! INFO @ Tue, 13 Aug 2019 00:00:34: #2 predicted fragment length is 50 bps INFO @ Tue, 13 Aug 2019 00:00:34: #2 alternative fragment length(s) may be 50 bps INFO @ Tue, 13 Aug 2019 00:00:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.20_model.r WARNING @ Tue, 13 Aug 2019 00:00:34: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:00:34: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Tue, 13 Aug 2019 00:00:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:00:34: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:00:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:00:35: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:00:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:00:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:00:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360578/SRX5360578.20_summits.bed INFO @ Tue, 13 Aug 2019 00:00:35: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 1 millis CompletedMACS2peakCalling