Job ID = 2590267 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,758,175 reads read : 4,758,175 reads written : 4,758,175 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR504789.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: 00:01:25 4758175 reads; of these: 4758175 (100.00%) were unpaired; of these: 258174 (5.43%) aligned 0 times 3227385 (67.83%) aligned exactly 1 time 1272616 (26.75%) aligned >1 times 94.57% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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] 322225 / 4500001 = 0.0716 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 20:21:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.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 20:21:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:21:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:21:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.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 20:21:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:21:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:21:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.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 20:21:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:21:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:21:59: 1000000 INFO @ Mon, 12 Aug 2019 20:22:00: 1000000 INFO @ Mon, 12 Aug 2019 20:22:02: 1000000 INFO @ Mon, 12 Aug 2019 20:22:07: 2000000 INFO @ Mon, 12 Aug 2019 20:22:08: 2000000 INFO @ Mon, 12 Aug 2019 20:22:11: 2000000 INFO @ Mon, 12 Aug 2019 20:22:14: 3000000 INFO @ Mon, 12 Aug 2019 20:22:15: 3000000 INFO @ Mon, 12 Aug 2019 20:22:20: 3000000 INFO @ Mon, 12 Aug 2019 20:22:21: 4000000 INFO @ Mon, 12 Aug 2019 20:22:23: 4000000 INFO @ Mon, 12 Aug 2019 20:22:23: #1 tag size is determined as 30 bps INFO @ Mon, 12 Aug 2019 20:22:23: #1 tag size = 30 INFO @ Mon, 12 Aug 2019 20:22:23: #1 total tags in treatment: 4177776 INFO @ Mon, 12 Aug 2019 20:22:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:22:23: #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 20:22:23: #1 tags after filtering in treatment: 4177776 INFO @ Mon, 12 Aug 2019 20:22:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:22:23: #1 finished! INFO @ Mon, 12 Aug 2019 20:22:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:22:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:22:23: #2 number of paired peaks: 776 WARNING @ Mon, 12 Aug 2019 20:22:23: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Mon, 12 Aug 2019 20:22:23: start model_add_line... INFO @ Mon, 12 Aug 2019 20:22:23: start X-correlation... INFO @ Mon, 12 Aug 2019 20:22:23: end of X-cor INFO @ Mon, 12 Aug 2019 20:22:23: #2 finished! INFO @ Mon, 12 Aug 2019 20:22:23: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 20:22:23: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 12 Aug 2019 20:22:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.05_model.r WARNING @ Mon, 12 Aug 2019 20:22:23: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:22:23: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 12 Aug 2019 20:22:23: #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 20:22:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:22:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:22:24: #1 tag size is determined as 30 bps INFO @ Mon, 12 Aug 2019 20:22:24: #1 tag size = 30 INFO @ Mon, 12 Aug 2019 20:22:24: #1 total tags in treatment: 4177776 INFO @ Mon, 12 Aug 2019 20:22:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:22:24: #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 20:22:24: #1 tags after filtering in treatment: 4177776 INFO @ Mon, 12 Aug 2019 20:22:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:22:24: #1 finished! INFO @ Mon, 12 Aug 2019 20:22:24: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:22:24: #2 number of paired peaks: 776 WARNING @ Mon, 12 Aug 2019 20:22:24: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Mon, 12 Aug 2019 20:22:24: start model_add_line... INFO @ Mon, 12 Aug 2019 20:22:24: start X-correlation... INFO @ Mon, 12 Aug 2019 20:22:24: end of X-cor INFO @ Mon, 12 Aug 2019 20:22:24: #2 finished! INFO @ Mon, 12 Aug 2019 20:22:24: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 20:22:24: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 12 Aug 2019 20:22:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.10_model.r WARNING @ Mon, 12 Aug 2019 20:22:25: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:22:25: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 12 Aug 2019 20:22:25: #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 20:22:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:22:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:22:29: 4000000 INFO @ Mon, 12 Aug 2019 20:22:30: #1 tag size is determined as 30 bps INFO @ Mon, 12 Aug 2019 20:22:30: #1 tag size = 30 INFO @ Mon, 12 Aug 2019 20:22:30: #1 total tags in treatment: 4177776 INFO @ Mon, 12 Aug 2019 20:22:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:22:30: #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 20:22:30: #1 tags after filtering in treatment: 4177776 INFO @ Mon, 12 Aug 2019 20:22:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:22:30: #1 finished! INFO @ Mon, 12 Aug 2019 20:22:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:22:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:22:31: #2 number of paired peaks: 776 WARNING @ Mon, 12 Aug 2019 20:22:31: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Mon, 12 Aug 2019 20:22:31: start model_add_line... INFO @ Mon, 12 Aug 2019 20:22:31: start X-correlation... INFO @ Mon, 12 Aug 2019 20:22:31: end of X-cor INFO @ Mon, 12 Aug 2019 20:22:31: #2 finished! INFO @ Mon, 12 Aug 2019 20:22:31: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 20:22:31: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 12 Aug 2019 20:22:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.20_model.r WARNING @ Mon, 12 Aug 2019 20:22:31: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:22:31: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 12 Aug 2019 20:22:31: #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 20:22:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:22:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:22:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:22:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:22:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:22:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:22:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.05_summits.bed INFO @ Mon, 12 Aug 2019 20:22:42: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1588 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:22:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:22:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:22:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.10_summits.bed INFO @ Mon, 12 Aug 2019 20:22:43: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (935 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:22:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:22:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:22:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151955/SRX151955.20_summits.bed INFO @ Mon, 12 Aug 2019 20:22:49: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (378 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。