Job ID = 1293434 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 480,296 reads read : 480,296 reads written : 480,296 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:08 480296 reads; of these: 480296 (100.00%) were unpaired; of these: 60765 (12.65%) aligned 0 times 310215 (64.59%) aligned exactly 1 time 109316 (22.76%) aligned >1 times 87.35% overall alignment rate Time searching: 00:00:08 Overall time: 00:00:08 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] 40214 / 419531 = 0.0959 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 @ Sun, 02 Jun 2019 23:47:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.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 @ Sun, 02 Jun 2019 23:47:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:47:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:47:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.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 @ Sun, 02 Jun 2019 23:47:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:47:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:47:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.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 @ Sun, 02 Jun 2019 23:47:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:47:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:47:24: #1 tag size is determined as 27 bps INFO @ Sun, 02 Jun 2019 23:47:24: #1 tag size = 27 INFO @ Sun, 02 Jun 2019 23:47:24: #1 total tags in treatment: 379317 INFO @ Sun, 02 Jun 2019 23:47:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:47:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:47:24: #1 tags after filtering in treatment: 379317 INFO @ Sun, 02 Jun 2019 23:47:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:47:24: #1 finished! INFO @ Sun, 02 Jun 2019 23:47:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:47:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:47:24: #2 number of paired peaks: 1043 INFO @ Sun, 02 Jun 2019 23:47:24: start model_add_line... INFO @ Sun, 02 Jun 2019 23:47:24: start X-correlation... INFO @ Sun, 02 Jun 2019 23:47:24: end of X-cor INFO @ Sun, 02 Jun 2019 23:47:24: #2 finished! INFO @ Sun, 02 Jun 2019 23:47:24: #2 predicted fragment length is 32 bps INFO @ Sun, 02 Jun 2019 23:47:24: #2 alternative fragment length(s) may be 32 bps INFO @ Sun, 02 Jun 2019 23:47:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.10_model.r WARNING @ Sun, 02 Jun 2019 23:47:24: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:47:24: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Sun, 02 Jun 2019 23:47:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:47:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:47:24: #1 tag size is determined as 27 bps INFO @ Sun, 02 Jun 2019 23:47:24: #1 tag size = 27 INFO @ Sun, 02 Jun 2019 23:47:24: #1 total tags in treatment: 379317 INFO @ Sun, 02 Jun 2019 23:47:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:47:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:47:24: #1 tags after filtering in treatment: 379317 INFO @ Sun, 02 Jun 2019 23:47:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:47:24: #1 finished! INFO @ Sun, 02 Jun 2019 23:47:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:47:24: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 INFO @ Sun, 02 Jun 2019 23:47:24: #2 number of paired peaks: 1043 INFO @ Sun, 02 Jun 2019 23:47:24: start model_add_line... BigWig に変換中... INFO @ Sun, 02 Jun 2019 23:47:24: start X-correlation... INFO @ Sun, 02 Jun 2019 23:47:24: end of X-cor INFO @ Sun, 02 Jun 2019 23:47:24: #2 finished! INFO @ Sun, 02 Jun 2019 23:47:24: #2 predicted fragment length is 32 bps INFO @ Sun, 02 Jun 2019 23:47:24: #2 alternative fragment length(s) may be 32 bps INFO @ Sun, 02 Jun 2019 23:47:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.20_model.r WARNING @ Sun, 02 Jun 2019 23:47:24: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:47:24: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Sun, 02 Jun 2019 23:47:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:47:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:47:25: #1 tag size is determined as 27 bps INFO @ Sun, 02 Jun 2019 23:47:25: #1 tag size = 27 INFO @ Sun, 02 Jun 2019 23:47:25: #1 total tags in treatment: 379317 INFO @ Sun, 02 Jun 2019 23:47:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:47:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:47:25: #1 tags after filtering in treatment: 379317 INFO @ Sun, 02 Jun 2019 23:47:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:47:25: #1 finished! INFO @ Sun, 02 Jun 2019 23:47:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:47:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:47:25: #2 number of paired peaks: 1043 INFO @ Sun, 02 Jun 2019 23:47:25: start model_add_line... INFO @ Sun, 02 Jun 2019 23:47:25: start X-correlation... INFO @ Sun, 02 Jun 2019 23:47:25: end of X-cor INFO @ Sun, 02 Jun 2019 23:47:25: #2 finished! INFO @ Sun, 02 Jun 2019 23:47:25: #2 predicted fragment length is 32 bps INFO @ Sun, 02 Jun 2019 23:47:25: #2 alternative fragment length(s) may be 32 bps INFO @ Sun, 02 Jun 2019 23:47:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.05_model.r WARNING @ Sun, 02 Jun 2019 23:47:25: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:47:25: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Sun, 02 Jun 2019 23:47:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:47:25: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:47:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 02 Jun 2019 23:47:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:47:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:47:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:47:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:47:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.10_summits.bed INFO @ Sun, 02 Jun 2019 23:47:26: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (88 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:47:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:47:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:47:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:47:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.20_summits.bed INFO @ Sun, 02 Jun 2019 23:47:26: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:47:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:47:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:47:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX242717/ERX242717.05_summits.bed INFO @ Sun, 02 Jun 2019 23:47:26: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (283 records, 4 fields): 2 millis CompletedMACS2peakCalling