Job ID = 1294855 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,848,717 reads read : 6,848,717 reads written : 6,848,717 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: 00:01:54 6848717 reads; of these: 6848717 (100.00%) were unpaired; of these: 2711040 (39.58%) aligned 0 times 2593762 (37.87%) aligned exactly 1 time 1543915 (22.54%) aligned >1 times 60.42% overall alignment rate Time searching: 00:01:54 Overall time: 00:01:54 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] 165438 / 4137677 = 0.0400 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, 03 Jun 2019 10:29:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.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, 03 Jun 2019 10:29:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:29:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:29:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.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, 03 Jun 2019 10:29:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.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, 03 Jun 2019 10:29:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:29:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:29:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:29:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:29:15: 1000000 INFO @ Mon, 03 Jun 2019 10:29:16: 1000000 INFO @ Mon, 03 Jun 2019 10:29:16: 1000000 INFO @ Mon, 03 Jun 2019 10:29:22: 2000000 INFO @ Mon, 03 Jun 2019 10:29:23: 2000000 INFO @ Mon, 03 Jun 2019 10:29:23: 2000000 INFO @ Mon, 03 Jun 2019 10:29:29: 3000000 INFO @ Mon, 03 Jun 2019 10:29:31: 3000000 INFO @ Mon, 03 Jun 2019 10:29:31: 3000000 INFO @ Mon, 03 Jun 2019 10:29:35: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 10:29:35: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 10:29:35: #1 total tags in treatment: 3972239 INFO @ Mon, 03 Jun 2019 10:29:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:29:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 10:29:35: #1 tags after filtering in treatment: 3972239 INFO @ Mon, 03 Jun 2019 10:29:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:29:35: #1 finished! INFO @ Mon, 03 Jun 2019 10:29:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:29:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:29:36: #2 number of paired peaks: 617 WARNING @ Mon, 03 Jun 2019 10:29:36: Fewer paired peaks (617) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 617 pairs to build model! INFO @ Mon, 03 Jun 2019 10:29:36: start model_add_line... INFO @ Mon, 03 Jun 2019 10:29:36: start X-correlation... INFO @ Mon, 03 Jun 2019 10:29:36: end of X-cor INFO @ Mon, 03 Jun 2019 10:29:36: #2 finished! INFO @ Mon, 03 Jun 2019 10:29:36: #2 predicted fragment length is 40 bps INFO @ Mon, 03 Jun 2019 10:29:36: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 03 Jun 2019 10:29:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.20_model.r WARNING @ Mon, 03 Jun 2019 10:29:36: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:29:36: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 03 Jun 2019 10:29:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:29:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:29:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:29:38: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 10:29:38: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 10:29:38: #1 total tags in treatment: 3972239 INFO @ Mon, 03 Jun 2019 10:29:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:29:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 10:29:38: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 10:29:38: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 10:29:38: #1 total tags in treatment: 3972239 INFO @ Mon, 03 Jun 2019 10:29:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:29:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 10:29:38: #1 tags after filtering in treatment: 3972239 INFO @ Mon, 03 Jun 2019 10:29:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:29:38: #1 finished! INFO @ Mon, 03 Jun 2019 10:29:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:29:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:29:38: #1 tags after filtering in treatment: 3972239 INFO @ Mon, 03 Jun 2019 10:29:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:29:38: #1 finished! INFO @ Mon, 03 Jun 2019 10:29:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:29:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:29:38: #2 number of paired peaks: 617 WARNING @ Mon, 03 Jun 2019 10:29:38: Fewer paired peaks (617) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 617 pairs to build model! INFO @ Mon, 03 Jun 2019 10:29:38: start model_add_line... INFO @ Mon, 03 Jun 2019 10:29:38: #2 number of paired peaks: 617 WARNING @ Mon, 03 Jun 2019 10:29:38: Fewer paired peaks (617) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 617 pairs to build model! INFO @ Mon, 03 Jun 2019 10:29:38: start model_add_line... INFO @ Mon, 03 Jun 2019 10:29:38: start X-correlation... INFO @ Mon, 03 Jun 2019 10:29:38: start X-correlation... INFO @ Mon, 03 Jun 2019 10:29:38: end of X-cor INFO @ Mon, 03 Jun 2019 10:29:38: #2 finished! INFO @ Mon, 03 Jun 2019 10:29:38: #2 predicted fragment length is 40 bps INFO @ Mon, 03 Jun 2019 10:29:38: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 03 Jun 2019 10:29:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.05_model.r WARNING @ Mon, 03 Jun 2019 10:29:38: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:29:38: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 03 Jun 2019 10:29:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:29:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:29:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:29:38: end of X-cor INFO @ Mon, 03 Jun 2019 10:29:38: #2 finished! INFO @ Mon, 03 Jun 2019 10:29:38: #2 predicted fragment length is 40 bps INFO @ Mon, 03 Jun 2019 10:29:38: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 03 Jun 2019 10:29:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.10_model.r WARNING @ Mon, 03 Jun 2019 10:29:38: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:29:38: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 03 Jun 2019 10:29:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:29:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:29:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:29:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:29:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:29:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:29:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:29:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:29:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.20_summits.bed INFO @ Mon, 03 Jun 2019 10:29:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (603 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:29:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:29:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:29:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:29:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:29:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.10_summits.bed INFO @ Mon, 03 Jun 2019 10:29:56: Done! INFO @ Mon, 03 Jun 2019 10:29:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287948/SRX287948.05_summits.bed INFO @ Mon, 03 Jun 2019 10:29:56: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1033 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1490 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。