Job ID = 2590876 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,228,130 reads read : 7,228,130 reads written : 7,228,130 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: 00:02:07 7228130 reads; of these: 7228130 (100.00%) were unpaired; of these: 440342 (6.09%) aligned 0 times 5421544 (75.01%) aligned exactly 1 time 1366244 (18.90%) aligned >1 times 93.91% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 3231707 / 6787788 = 0.4761 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 23:53:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.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 23:53:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:53:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:53:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.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 23:53:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:53:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:53:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.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 23:53:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:53:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:53:13: 1000000 INFO @ Mon, 12 Aug 2019 23:53:16: 1000000 INFO @ Mon, 12 Aug 2019 23:53:17: 1000000 INFO @ Mon, 12 Aug 2019 23:53:21: 2000000 INFO @ Mon, 12 Aug 2019 23:53:28: 2000000 INFO @ Mon, 12 Aug 2019 23:53:29: 2000000 INFO @ Mon, 12 Aug 2019 23:53:30: 3000000 INFO @ Mon, 12 Aug 2019 23:53:35: #1 tag size is determined as 44 bps INFO @ Mon, 12 Aug 2019 23:53:35: #1 tag size = 44 INFO @ Mon, 12 Aug 2019 23:53:35: #1 total tags in treatment: 3556081 INFO @ Mon, 12 Aug 2019 23:53:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:53:35: #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 23:53:35: #1 tags after filtering in treatment: 3556081 INFO @ Mon, 12 Aug 2019 23:53:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:53:35: #1 finished! INFO @ Mon, 12 Aug 2019 23:53:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:53:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:53:35: #2 number of paired peaks: 119 WARNING @ Mon, 12 Aug 2019 23:53:35: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Mon, 12 Aug 2019 23:53:35: start model_add_line... INFO @ Mon, 12 Aug 2019 23:53:35: start X-correlation... INFO @ Mon, 12 Aug 2019 23:53:35: end of X-cor INFO @ Mon, 12 Aug 2019 23:53:35: #2 finished! INFO @ Mon, 12 Aug 2019 23:53:35: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 23:53:35: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 12 Aug 2019 23:53:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.05_model.r WARNING @ Mon, 12 Aug 2019 23:53:35: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:53:35: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 12 Aug 2019 23:53:35: #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 23:53:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:53:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:53:39: 3000000 INFO @ Mon, 12 Aug 2019 23:53:40: 3000000 INFO @ Mon, 12 Aug 2019 23:53:45: #1 tag size is determined as 44 bps INFO @ Mon, 12 Aug 2019 23:53:45: #1 tag size = 44 INFO @ Mon, 12 Aug 2019 23:53:45: #1 total tags in treatment: 3556081 INFO @ Mon, 12 Aug 2019 23:53:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:53:45: #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 23:53:45: #1 tags after filtering in treatment: 3556081 INFO @ Mon, 12 Aug 2019 23:53:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:53:45: #1 finished! INFO @ Mon, 12 Aug 2019 23:53:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:53:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:53:45: #2 number of paired peaks: 119 WARNING @ Mon, 12 Aug 2019 23:53:45: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Mon, 12 Aug 2019 23:53:45: start model_add_line... INFO @ Mon, 12 Aug 2019 23:53:45: start X-correlation... INFO @ Mon, 12 Aug 2019 23:53:45: end of X-cor INFO @ Mon, 12 Aug 2019 23:53:45: #2 finished! INFO @ Mon, 12 Aug 2019 23:53:45: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 23:53:45: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 12 Aug 2019 23:53:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.10_model.r WARNING @ Mon, 12 Aug 2019 23:53:46: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:53:46: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 12 Aug 2019 23:53:46: #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 23:53:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:53:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:53:46: #1 tag size is determined as 44 bps INFO @ Mon, 12 Aug 2019 23:53:46: #1 tag size = 44 INFO @ Mon, 12 Aug 2019 23:53:46: #1 total tags in treatment: 3556081 INFO @ Mon, 12 Aug 2019 23:53:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:53:46: #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 23:53:46: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:53:46: #1 tags after filtering in treatment: 3556081 INFO @ Mon, 12 Aug 2019 23:53:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:53:46: #1 finished! INFO @ Mon, 12 Aug 2019 23:53:46: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:53:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:53:46: #2 number of paired peaks: 119 WARNING @ Mon, 12 Aug 2019 23:53:46: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Mon, 12 Aug 2019 23:53:46: start model_add_line... INFO @ Mon, 12 Aug 2019 23:53:46: start X-correlation... INFO @ Mon, 12 Aug 2019 23:53:46: end of X-cor INFO @ Mon, 12 Aug 2019 23:53:46: #2 finished! INFO @ Mon, 12 Aug 2019 23:53:46: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 23:53:46: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 12 Aug 2019 23:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.20_model.r WARNING @ Mon, 12 Aug 2019 23:53:46: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:53:46: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 12 Aug 2019 23:53:46: #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 23:53:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:53:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:53:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:53:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:53:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.05_summits.bed INFO @ Mon, 12 Aug 2019 23:53:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (224 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:53:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:53:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:54:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:54:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:54:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.10_summits.bed INFO @ Mon, 12 Aug 2019 23:54:02: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (91 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:54:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:54:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:54:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507394/SRX507394.20_summits.bed INFO @ Mon, 12 Aug 2019 23:54:02: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (46 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。