Job ID = 2591021 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,135,694 reads read : 19,135,694 reads written : 19,135,694 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:09 19135694 reads; of these: 19135694 (100.00%) were unpaired; of these: 11999536 (62.71%) aligned 0 times 6019759 (31.46%) aligned exactly 1 time 1116399 (5.83%) aligned >1 times 37.29% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 5849320 / 7136158 = 0.8197 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 00:39:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.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 00:39:35: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:39:35: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:39:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.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 00:39:36: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:39:36: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:39:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.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 00:39:37: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:39:37: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:39:42: 1000000 INFO @ Tue, 13 Aug 2019 00:39:44: 1000000 INFO @ Tue, 13 Aug 2019 00:39:44: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:39:44: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:39:44: #1 total tags in treatment: 1286838 INFO @ Tue, 13 Aug 2019 00:39:44: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:39:44: #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 00:39:44: #1 tags after filtering in treatment: 1286838 INFO @ Tue, 13 Aug 2019 00:39:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:39:44: #1 finished! INFO @ Tue, 13 Aug 2019 00:39:44: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:39:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:39:44: 1000000 INFO @ Tue, 13 Aug 2019 00:39:44: #2 number of paired peaks: 1633 INFO @ Tue, 13 Aug 2019 00:39:44: start model_add_line... INFO @ Tue, 13 Aug 2019 00:39:44: start X-correlation... INFO @ Tue, 13 Aug 2019 00:39:44: end of X-cor INFO @ Tue, 13 Aug 2019 00:39:44: #2 finished! INFO @ Tue, 13 Aug 2019 00:39:44: #2 predicted fragment length is 53 bps INFO @ Tue, 13 Aug 2019 00:39:44: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 13 Aug 2019 00:39:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.05_model.r WARNING @ Tue, 13 Aug 2019 00:39:45: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:39:45: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 13 Aug 2019 00:39:45: #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 00:39:45: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:39:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:39:46: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:39:46: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:39:46: #1 total tags in treatment: 1286838 INFO @ Tue, 13 Aug 2019 00:39:46: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:39:46: #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 00:39:46: #1 tags after filtering in treatment: 1286838 INFO @ Tue, 13 Aug 2019 00:39:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:39:46: #1 finished! INFO @ Tue, 13 Aug 2019 00:39:46: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:39:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:39:46: #2 number of paired peaks: 1633 INFO @ Tue, 13 Aug 2019 00:39:46: start model_add_line... INFO @ Tue, 13 Aug 2019 00:39:46: start X-correlation... INFO @ Tue, 13 Aug 2019 00:39:46: end of X-cor INFO @ Tue, 13 Aug 2019 00:39:46: #2 finished! INFO @ Tue, 13 Aug 2019 00:39:46: #2 predicted fragment length is 53 bps INFO @ Tue, 13 Aug 2019 00:39:46: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 13 Aug 2019 00:39:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.10_model.r WARNING @ Tue, 13 Aug 2019 00:39:46: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:39:46: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 13 Aug 2019 00:39:46: #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 00:39:46: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:39:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:39:46: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:39:46: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:39:46: #1 total tags in treatment: 1286838 INFO @ Tue, 13 Aug 2019 00:39:46: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:39:46: #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 00:39:46: #1 tags after filtering in treatment: 1286838 INFO @ Tue, 13 Aug 2019 00:39:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:39:46: #1 finished! INFO @ Tue, 13 Aug 2019 00:39:46: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:39:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:39:47: #2 number of paired peaks: 1633 INFO @ Tue, 13 Aug 2019 00:39:47: start model_add_line... INFO @ Tue, 13 Aug 2019 00:39:47: start X-correlation... INFO @ Tue, 13 Aug 2019 00:39:47: end of X-cor INFO @ Tue, 13 Aug 2019 00:39:47: #2 finished! INFO @ Tue, 13 Aug 2019 00:39:47: #2 predicted fragment length is 53 bps INFO @ Tue, 13 Aug 2019 00:39:47: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 13 Aug 2019 00:39:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.20_model.r WARNING @ Tue, 13 Aug 2019 00:39:47: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:39:47: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 13 Aug 2019 00:39:47: #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 00:39:47: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:39:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:39:48: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:39:50: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:39:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:39:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:39:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.05_summits.bed INFO @ Tue, 13 Aug 2019 00:39:50: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1116 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:39:51: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:39:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:39:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:39:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.10_summits.bed INFO @ Tue, 13 Aug 2019 00:39:52: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (447 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:39:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:39:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:39:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661232/SRX661232.20_summits.bed INFO @ Tue, 13 Aug 2019 00:39:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (182 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。