Job ID = 2591023 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,722,589 reads read : 21,722,589 reads written : 21,722,589 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: 00:05:32 21722589 reads; of these: 21722589 (100.00%) were unpaired; of these: 13354490 (61.48%) aligned 0 times 4421737 (20.36%) aligned exactly 1 time 3946362 (18.17%) aligned >1 times 38.52% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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] 1855076 / 8368099 = 0.2217 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 00:52:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.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 00:52:07: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:52:07: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:52:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.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 00:52:07: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:52:07: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:52:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.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 00:52:08: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:52:08: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:52:14: 1000000 INFO @ Tue, 13 Aug 2019 00:52:14: 1000000 INFO @ Tue, 13 Aug 2019 00:52:16: 1000000 INFO @ Tue, 13 Aug 2019 00:52:21: 2000000 INFO @ Tue, 13 Aug 2019 00:52:21: 2000000 INFO @ Tue, 13 Aug 2019 00:52:24: 2000000 INFO @ Tue, 13 Aug 2019 00:52:27: 3000000 INFO @ Tue, 13 Aug 2019 00:52:28: 3000000 INFO @ Tue, 13 Aug 2019 00:52:32: 3000000 INFO @ Tue, 13 Aug 2019 00:52:34: 4000000 INFO @ Tue, 13 Aug 2019 00:52:35: 4000000 INFO @ Tue, 13 Aug 2019 00:52:40: 4000000 INFO @ Tue, 13 Aug 2019 00:52:41: 5000000 INFO @ Tue, 13 Aug 2019 00:52:41: 5000000 INFO @ Tue, 13 Aug 2019 00:52:48: 6000000 INFO @ Tue, 13 Aug 2019 00:52:48: 5000000 INFO @ Tue, 13 Aug 2019 00:52:48: 6000000 INFO @ Tue, 13 Aug 2019 00:52:51: #1 tag size is determined as 47 bps INFO @ Tue, 13 Aug 2019 00:52:51: #1 tag size = 47 INFO @ Tue, 13 Aug 2019 00:52:51: #1 total tags in treatment: 6513023 INFO @ Tue, 13 Aug 2019 00:52:51: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:52:51: #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 00:52:51: #1 tags after filtering in treatment: 6513023 INFO @ Tue, 13 Aug 2019 00:52:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:52:51: #1 finished! INFO @ Tue, 13 Aug 2019 00:52:51: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:52:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:52:52: #1 tag size is determined as 47 bps INFO @ Tue, 13 Aug 2019 00:52:52: #1 tag size = 47 INFO @ Tue, 13 Aug 2019 00:52:52: #1 total tags in treatment: 6513023 INFO @ Tue, 13 Aug 2019 00:52:52: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:52:52: #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 00:52:52: #1 tags after filtering in treatment: 6513023 INFO @ Tue, 13 Aug 2019 00:52:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:52:52: #1 finished! INFO @ Tue, 13 Aug 2019 00:52:52: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:52:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:52:52: #2 number of paired peaks: 226 WARNING @ Tue, 13 Aug 2019 00:52:52: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Tue, 13 Aug 2019 00:52:52: start model_add_line... INFO @ Tue, 13 Aug 2019 00:52:52: start X-correlation... INFO @ Tue, 13 Aug 2019 00:52:52: end of X-cor INFO @ Tue, 13 Aug 2019 00:52:52: #2 finished! INFO @ Tue, 13 Aug 2019 00:52:52: #2 predicted fragment length is 46 bps INFO @ Tue, 13 Aug 2019 00:52:52: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 13 Aug 2019 00:52:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.05_model.r WARNING @ Tue, 13 Aug 2019 00:52:52: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:52:52: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 13 Aug 2019 00:52:52: #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 00:52:52: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:52:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:52:53: #2 number of paired peaks: 226 WARNING @ Tue, 13 Aug 2019 00:52:53: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Tue, 13 Aug 2019 00:52:53: start model_add_line... INFO @ Tue, 13 Aug 2019 00:52:53: start X-correlation... INFO @ Tue, 13 Aug 2019 00:52:53: end of X-cor INFO @ Tue, 13 Aug 2019 00:52:53: #2 finished! INFO @ Tue, 13 Aug 2019 00:52:53: #2 predicted fragment length is 46 bps INFO @ Tue, 13 Aug 2019 00:52:53: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 13 Aug 2019 00:52:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.10_model.r WARNING @ Tue, 13 Aug 2019 00:52:53: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:52:53: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 13 Aug 2019 00:52:53: #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 00:52:53: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:52:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:52:56: 6000000 INFO @ Tue, 13 Aug 2019 00:53:00: #1 tag size is determined as 47 bps INFO @ Tue, 13 Aug 2019 00:53:00: #1 tag size = 47 INFO @ Tue, 13 Aug 2019 00:53:00: #1 total tags in treatment: 6513023 INFO @ Tue, 13 Aug 2019 00:53:00: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:53:00: #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 00:53:00: #1 tags after filtering in treatment: 6513023 INFO @ Tue, 13 Aug 2019 00:53:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:53:00: #1 finished! INFO @ Tue, 13 Aug 2019 00:53:00: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:53:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:53:01: #2 number of paired peaks: 226 WARNING @ Tue, 13 Aug 2019 00:53:01: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Tue, 13 Aug 2019 00:53:01: start model_add_line... INFO @ Tue, 13 Aug 2019 00:53:01: start X-correlation... INFO @ Tue, 13 Aug 2019 00:53:01: end of X-cor INFO @ Tue, 13 Aug 2019 00:53:01: #2 finished! INFO @ Tue, 13 Aug 2019 00:53:01: #2 predicted fragment length is 46 bps INFO @ Tue, 13 Aug 2019 00:53:01: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 13 Aug 2019 00:53:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.20_model.r WARNING @ Tue, 13 Aug 2019 00:53:01: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:53:01: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 13 Aug 2019 00:53:01: #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 00:53:01: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:53:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:53:11: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:53:11: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:53:20: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:53:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:53:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:53:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.05_summits.bed INFO @ Tue, 13 Aug 2019 00:53:20: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1126 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:53:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:53:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:53:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.10_summits.bed INFO @ Tue, 13 Aug 2019 00:53:21: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (795 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:53:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:53:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:53:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661500/SRX661500.20_summits.bed INFO @ Tue, 13 Aug 2019 00:53:29: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。