Job ID = 2590885 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,773,088 reads read : 1,773,088 reads written : 1,773,088 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: 00:00:21 1773088 reads; of these: 1773088 (100.00%) were unpaired; of these: 897617 (50.62%) aligned 0 times 832755 (46.97%) aligned exactly 1 time 42716 (2.41%) aligned >1 times 49.38% overall alignment rate Time searching: 00:00:21 Overall time: 00:00:21 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_rmdupse_core] 742332 / 875471 = 0.8479 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 @ Mon, 12 Aug 2019 23:51:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.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 @ Mon, 12 Aug 2019 23:51:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:51:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:51:02: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:51:02: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:51:02: #1 total tags in treatment: 133139 INFO @ Mon, 12 Aug 2019 23:51:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:51:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:51:02: #1 tags after filtering in treatment: 133138 INFO @ Mon, 12 Aug 2019 23:51:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:51:02: #1 finished! INFO @ Mon, 12 Aug 2019 23:51:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:51:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:51:02: #2 number of paired peaks: 253 WARNING @ Mon, 12 Aug 2019 23:51:02: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Mon, 12 Aug 2019 23:51:02: start model_add_line... INFO @ Mon, 12 Aug 2019 23:51:02: start X-correlation... INFO @ Mon, 12 Aug 2019 23:51:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.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 @ Mon, 12 Aug 2019 23:51:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:51:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:51:02: end of X-cor INFO @ Mon, 12 Aug 2019 23:51:02: #2 finished! INFO @ Mon, 12 Aug 2019 23:51:02: #2 predicted fragment length is 55 bps INFO @ Mon, 12 Aug 2019 23:51:02: #2 alternative fragment length(s) may be 55,152,174,308,417,451,483,569 bps INFO @ Mon, 12 Aug 2019 23:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.05_model.r WARNING @ Mon, 12 Aug 2019 23:51:02: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:51:02: #2 You may need to consider one of the other alternative d(s): 55,152,174,308,417,451,483,569 WARNING @ Mon, 12 Aug 2019 23:51:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:51:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:51:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.05_summits.bed INFO @ Mon, 12 Aug 2019 23:51:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (186 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 23:51:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:51:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:51:03: #1 total tags in treatment: 133139 INFO @ Mon, 12 Aug 2019 23:51:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:51:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:51:03: #1 tags after filtering in treatment: 133138 INFO @ Mon, 12 Aug 2019 23:51:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:51:03: #1 finished! INFO @ Mon, 12 Aug 2019 23:51:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:51:03: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Mon, 12 Aug 2019 23:51:03: #2 number of paired peaks: 253 WARNING @ Mon, 12 Aug 2019 23:51:03: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Mon, 12 Aug 2019 23:51:03: start model_add_line... INFO @ Mon, 12 Aug 2019 23:51:03: start X-correlation... INFO @ Mon, 12 Aug 2019 23:51:03: end of X-cor INFO @ Mon, 12 Aug 2019 23:51:03: #2 finished! INFO @ Mon, 12 Aug 2019 23:51:03: #2 predicted fragment length is 55 bps INFO @ Mon, 12 Aug 2019 23:51:03: #2 alternative fragment length(s) may be 55,152,174,308,417,451,483,569 bps INFO @ Mon, 12 Aug 2019 23:51:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.10_model.r INFO @ Mon, 12 Aug 2019 23:51:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.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 @ Mon, 12 Aug 2019 23:51:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:51:03: #1 read treatment tags... WARNING @ Mon, 12 Aug 2019 23:51:03: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:51:03: #2 You may need to consider one of the other alternative d(s): 55,152,174,308,417,451,483,569 WARNING @ Mon, 12 Aug 2019 23:51:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:51:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:51:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:51:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.10_summits.bed INFO @ Mon, 12 Aug 2019 23:51:03: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (125 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:51:04: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:51:04: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:51:04: #1 total tags in treatment: 133139 INFO @ Mon, 12 Aug 2019 23:51:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:51:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:51:04: #1 tags after filtering in treatment: 133138 INFO @ Mon, 12 Aug 2019 23:51:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:51:04: #1 finished! INFO @ Mon, 12 Aug 2019 23:51:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:51:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:51:04: #2 number of paired peaks: 253 WARNING @ Mon, 12 Aug 2019 23:51:04: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Mon, 12 Aug 2019 23:51:04: start model_add_line... INFO @ Mon, 12 Aug 2019 23:51:04: start X-correlation... INFO @ Mon, 12 Aug 2019 23:51:04: end of X-cor INFO @ Mon, 12 Aug 2019 23:51:04: #2 finished! INFO @ Mon, 12 Aug 2019 23:51:04: #2 predicted fragment length is 55 bps INFO @ Mon, 12 Aug 2019 23:51:04: #2 alternative fragment length(s) may be 55,152,174,308,417,451,483,569 bps INFO @ Mon, 12 Aug 2019 23:51:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.20_model.r WARNING @ Mon, 12 Aug 2019 23:51:04: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:51:04: #2 You may need to consider one of the other alternative d(s): 55,152,174,308,417,451,483,569 WARNING @ Mon, 12 Aug 2019 23:51:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:51:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:51:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:51:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360568/SRX5360568.20_summits.bed INFO @ Mon, 12 Aug 2019 23:51:04: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 2 millis CompletedMACS2peakCalling