Job ID = 1295638 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,923,441 reads read : 8,923,441 reads written : 8,923,441 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:11 8923441 reads; of these: 8923441 (100.00%) were unpaired; of these: 839804 (9.41%) aligned 0 times 6765278 (75.81%) aligned exactly 1 time 1318359 (14.77%) aligned >1 times 90.59% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 6196142 / 8083637 = 0.7665 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 14:55:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.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 14:55:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:55:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:55:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.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 14:55:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:55:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:55:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.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 14:55:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:55:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:55:22: 1000000 INFO @ Mon, 03 Jun 2019 14:55:23: 1000000 INFO @ Mon, 03 Jun 2019 14:55:23: 1000000 INFO @ Mon, 03 Jun 2019 14:55:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 14:55:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 14:55:27: #1 total tags in treatment: 1887495 INFO @ Mon, 03 Jun 2019 14:55:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:55:27: #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 14:55:27: #1 tags after filtering in treatment: 1887495 INFO @ Mon, 03 Jun 2019 14:55:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:55:27: #1 finished! INFO @ Mon, 03 Jun 2019 14:55:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:55:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:55:27: #2 number of paired peaks: 433 WARNING @ Mon, 03 Jun 2019 14:55:27: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Mon, 03 Jun 2019 14:55:27: start model_add_line... INFO @ Mon, 03 Jun 2019 14:55:27: start X-correlation... INFO @ Mon, 03 Jun 2019 14:55:27: end of X-cor INFO @ Mon, 03 Jun 2019 14:55:27: #2 finished! INFO @ Mon, 03 Jun 2019 14:55:27: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 14:55:27: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 14:55:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.05_model.r WARNING @ Mon, 03 Jun 2019 14:55:27: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:55:27: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 14:55:27: #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 14:55:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:55:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:55:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 14:55:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 14:55:27: #1 total tags in treatment: 1887495 INFO @ Mon, 03 Jun 2019 14:55:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:55:27: #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 14:55:27: #1 tags after filtering in treatment: 1887495 INFO @ Mon, 03 Jun 2019 14:55:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:55:27: #1 finished! INFO @ Mon, 03 Jun 2019 14:55:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:55:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:55:28: #2 number of paired peaks: 433 WARNING @ Mon, 03 Jun 2019 14:55:28: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Mon, 03 Jun 2019 14:55:28: start model_add_line... INFO @ Mon, 03 Jun 2019 14:55:28: start X-correlation... INFO @ Mon, 03 Jun 2019 14:55:28: end of X-cor INFO @ Mon, 03 Jun 2019 14:55:28: #2 finished! INFO @ Mon, 03 Jun 2019 14:55:28: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 14:55:28: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 14:55:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.20_model.r WARNING @ Mon, 03 Jun 2019 14:55:28: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:55:28: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 14:55:28: #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 14:55:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:55:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:55:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 14:55:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 14:55:28: #1 total tags in treatment: 1887495 INFO @ Mon, 03 Jun 2019 14:55:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:55:28: #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 14:55:28: #1 tags after filtering in treatment: 1887495 INFO @ Mon, 03 Jun 2019 14:55:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:55:28: #1 finished! INFO @ Mon, 03 Jun 2019 14:55:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:55:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:55:28: #2 number of paired peaks: 433 WARNING @ Mon, 03 Jun 2019 14:55:28: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Mon, 03 Jun 2019 14:55:28: start model_add_line... INFO @ Mon, 03 Jun 2019 14:55:28: start X-correlation... INFO @ Mon, 03 Jun 2019 14:55:28: end of X-cor INFO @ Mon, 03 Jun 2019 14:55:28: #2 finished! INFO @ Mon, 03 Jun 2019 14:55:28: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 14:55:28: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 14:55:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.10_model.r WARNING @ Mon, 03 Jun 2019 14:55:28: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:55:28: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 14:55:28: #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 14:55:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:55:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:55:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:55:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:55:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:55:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:55:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:55:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.05_summits.bed INFO @ Mon, 03 Jun 2019 14:55:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (512 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:55:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:55:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:55:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.20_summits.bed INFO @ Mon, 03 Jun 2019 14:55:33: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:55:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:55:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:55:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX390503/SRX390503.10_summits.bed INFO @ Mon, 03 Jun 2019 14:55:34: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (273 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。