Job ID = 2590903 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,158,394 reads read : 4,158,394 reads written : 4,158,394 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: 00:00:48 4158394 reads; of these: 4158394 (100.00%) were unpaired; of these: 3043883 (73.20%) aligned 0 times 960531 (23.10%) aligned exactly 1 time 153980 (3.70%) aligned >1 times 26.80% overall alignment rate Time searching: 00:00:48 Overall time: 00:00:48 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] 690568 / 1114511 = 0.6196 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 23:54:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.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 23:54:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:54:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:54:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.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 23:54:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:54:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:54:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.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 23:54:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:54:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:54:37: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:54:37: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:54:37: #1 total tags in treatment: 423943 INFO @ Mon, 12 Aug 2019 23:54:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:54:37: #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 23:54:37: #1 tags after filtering in treatment: 423943 INFO @ Mon, 12 Aug 2019 23:54:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:54:37: #1 finished! INFO @ Mon, 12 Aug 2019 23:54:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:54:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:54:37: #2 number of paired peaks: 1781 INFO @ Mon, 12 Aug 2019 23:54:37: start model_add_line... INFO @ Mon, 12 Aug 2019 23:54:37: start X-correlation... INFO @ Mon, 12 Aug 2019 23:54:37: end of X-cor INFO @ Mon, 12 Aug 2019 23:54:37: #2 finished! INFO @ Mon, 12 Aug 2019 23:54:37: #2 predicted fragment length is 55 bps INFO @ Mon, 12 Aug 2019 23:54:37: #2 alternative fragment length(s) may be 55,580 bps INFO @ Mon, 12 Aug 2019 23:54:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.05_model.r WARNING @ Mon, 12 Aug 2019 23:54:37: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:54:37: #2 You may need to consider one of the other alternative d(s): 55,580 WARNING @ Mon, 12 Aug 2019 23:54:37: #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 23:54:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:54:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:54:38: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:54:38: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:54:38: #1 total tags in treatment: 423943 INFO @ Mon, 12 Aug 2019 23:54:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:54:38: #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 23:54:38: #1 tags after filtering in treatment: 423943 INFO @ Mon, 12 Aug 2019 23:54:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:54:38: #1 finished! INFO @ Mon, 12 Aug 2019 23:54:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:54:38: #2 number of paired peaks: 1781 INFO @ Mon, 12 Aug 2019 23:54:38: start model_add_line... INFO @ Mon, 12 Aug 2019 23:54:38: start X-correlation... INFO @ Mon, 12 Aug 2019 23:54:38: end of X-cor INFO @ Mon, 12 Aug 2019 23:54:38: #2 finished! INFO @ Mon, 12 Aug 2019 23:54:38: #2 predicted fragment length is 55 bps INFO @ Mon, 12 Aug 2019 23:54:38: #2 alternative fragment length(s) may be 55,580 bps INFO @ Mon, 12 Aug 2019 23:54:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.10_model.r WARNING @ Mon, 12 Aug 2019 23:54:38: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:54:38: #2 You may need to consider one of the other alternative d(s): 55,580 WARNING @ Mon, 12 Aug 2019 23:54:38: #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 23:54:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:54:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:54:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:54:38: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:54:38: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:54:38: #1 total tags in treatment: 423943 INFO @ Mon, 12 Aug 2019 23:54:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:54:38: #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 23:54:38: #1 tags after filtering in treatment: 423943 INFO @ Mon, 12 Aug 2019 23:54:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:54:38: #1 finished! INFO @ Mon, 12 Aug 2019 23:54:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:54:39: #2 number of paired peaks: 1781 INFO @ Mon, 12 Aug 2019 23:54:39: start model_add_line... INFO @ Mon, 12 Aug 2019 23:54:39: start X-correlation... INFO @ Mon, 12 Aug 2019 23:54:39: end of X-cor INFO @ Mon, 12 Aug 2019 23:54:39: #2 finished! INFO @ Mon, 12 Aug 2019 23:54:39: #2 predicted fragment length is 55 bps INFO @ Mon, 12 Aug 2019 23:54:39: #2 alternative fragment length(s) may be 55,580 bps INFO @ Mon, 12 Aug 2019 23:54:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.20_model.r WARNING @ Mon, 12 Aug 2019 23:54:39: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:54:39: #2 You may need to consider one of the other alternative d(s): 55,580 WARNING @ Mon, 12 Aug 2019 23:54:39: #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 23:54:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:54:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:54:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:54:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:54:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.05_summits.bed INFO @ Mon, 12 Aug 2019 23:54:39: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (272 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:54:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 12 Aug 2019 23:54:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:54:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:54:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:54:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.10_summits.bed INFO @ Mon, 12 Aug 2019 23:54:40: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (138 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360584/SRX5360584.20_summits.bed INFO @ Mon, 12 Aug 2019 23:54:41: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (71 records, 4 fields): 1 millis CompletedMACS2peakCalling