Job ID = 2590972 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,661,038 reads read : 7,322,076 reads written : 3,661,038 reads 0-length : 3,661,038 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: 00:05:44 3661038 reads; of these: 3661038 (100.00%) were unpaired; of these: 792187 (21.64%) aligned 0 times 2055080 (56.13%) aligned exactly 1 time 813771 (22.23%) aligned >1 times 78.36% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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] 109519 / 2868851 = 0.0382 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 00:15:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.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 00:15:51: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:15:51: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:15:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.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 00:15:52: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:15:52: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:15:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.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 00:15:53: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:15:53: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:16:04: 1000000 INFO @ Tue, 13 Aug 2019 00:16:08: 1000000 INFO @ Tue, 13 Aug 2019 00:16:09: 1000000 INFO @ Tue, 13 Aug 2019 00:16:16: 2000000 INFO @ Tue, 13 Aug 2019 00:16:24: 2000000 INFO @ Tue, 13 Aug 2019 00:16:24: #1 tag size is determined as 151 bps INFO @ Tue, 13 Aug 2019 00:16:24: #1 tag size = 151 INFO @ Tue, 13 Aug 2019 00:16:24: #1 total tags in treatment: 2759332 INFO @ Tue, 13 Aug 2019 00:16:24: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:16:24: #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 00:16:24: #1 tags after filtering in treatment: 2759332 INFO @ Tue, 13 Aug 2019 00:16:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:16:24: #1 finished! INFO @ Tue, 13 Aug 2019 00:16:24: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:16:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:16:25: #2 number of paired peaks: 301 WARNING @ Tue, 13 Aug 2019 00:16:25: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Tue, 13 Aug 2019 00:16:25: start model_add_line... INFO @ Tue, 13 Aug 2019 00:16:25: start X-correlation... INFO @ Tue, 13 Aug 2019 00:16:25: end of X-cor INFO @ Tue, 13 Aug 2019 00:16:25: #2 finished! INFO @ Tue, 13 Aug 2019 00:16:25: #2 predicted fragment length is 138 bps INFO @ Tue, 13 Aug 2019 00:16:25: #2 alternative fragment length(s) may be 138 bps INFO @ Tue, 13 Aug 2019 00:16:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.10_model.r WARNING @ Tue, 13 Aug 2019 00:16:25: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:16:25: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Tue, 13 Aug 2019 00:16:25: #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 00:16:25: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:16:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:16:26: 2000000 INFO @ Tue, 13 Aug 2019 00:16:34: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:16:36: #1 tag size is determined as 151 bps INFO @ Tue, 13 Aug 2019 00:16:36: #1 tag size = 151 INFO @ Tue, 13 Aug 2019 00:16:36: #1 total tags in treatment: 2759332 INFO @ Tue, 13 Aug 2019 00:16:36: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:16:36: #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 00:16:36: #1 tags after filtering in treatment: 2759332 INFO @ Tue, 13 Aug 2019 00:16:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:16:36: #1 finished! INFO @ Tue, 13 Aug 2019 00:16:36: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:16:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:16:36: #2 number of paired peaks: 301 WARNING @ Tue, 13 Aug 2019 00:16:36: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Tue, 13 Aug 2019 00:16:36: start model_add_line... INFO @ Tue, 13 Aug 2019 00:16:36: start X-correlation... INFO @ Tue, 13 Aug 2019 00:16:36: end of X-cor INFO @ Tue, 13 Aug 2019 00:16:36: #2 finished! INFO @ Tue, 13 Aug 2019 00:16:36: #2 predicted fragment length is 138 bps INFO @ Tue, 13 Aug 2019 00:16:36: #2 alternative fragment length(s) may be 138 bps INFO @ Tue, 13 Aug 2019 00:16:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.20_model.r WARNING @ Tue, 13 Aug 2019 00:16:36: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:16:36: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Tue, 13 Aug 2019 00:16:36: #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 00:16:36: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:16:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:16:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:16:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:16:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.10_summits.bed INFO @ Tue, 13 Aug 2019 00:16:38: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:16:38: #1 tag size is determined as 151 bps INFO @ Tue, 13 Aug 2019 00:16:38: #1 tag size = 151 INFO @ Tue, 13 Aug 2019 00:16:38: #1 total tags in treatment: 2759332 INFO @ Tue, 13 Aug 2019 00:16:38: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:16:38: #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 00:16:38: #1 tags after filtering in treatment: 2759332 INFO @ Tue, 13 Aug 2019 00:16:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:16:38: #1 finished! INFO @ Tue, 13 Aug 2019 00:16:38: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:16:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:16:39: #2 number of paired peaks: 301 WARNING @ Tue, 13 Aug 2019 00:16:39: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Tue, 13 Aug 2019 00:16:39: start model_add_line... INFO @ Tue, 13 Aug 2019 00:16:39: start X-correlation... INFO @ Tue, 13 Aug 2019 00:16:39: end of X-cor INFO @ Tue, 13 Aug 2019 00:16:39: #2 finished! INFO @ Tue, 13 Aug 2019 00:16:39: #2 predicted fragment length is 138 bps INFO @ Tue, 13 Aug 2019 00:16:39: #2 alternative fragment length(s) may be 138 bps INFO @ Tue, 13 Aug 2019 00:16:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.05_model.r WARNING @ Tue, 13 Aug 2019 00:16:39: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:16:39: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Tue, 13 Aug 2019 00:16:39: #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 00:16:39: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:16:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:16:45: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:16:47: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:16:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:16:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:16:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.20_summits.bed INFO @ Tue, 13 Aug 2019 00:16:49: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (122 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:16:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:16:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:16:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5931376/SRX5931376.05_summits.bed INFO @ Tue, 13 Aug 2019 00:16:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (479 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。