Job ID = 2591002 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,810,300 reads read : 29,810,300 reads written : 29,810,300 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: 00:10:41 29810300 reads; of these: 29810300 (100.00%) were unpaired; of these: 22930729 (76.92%) aligned 0 times 5045545 (16.93%) aligned exactly 1 time 1834026 (6.15%) aligned >1 times 23.08% overall alignment rate Time searching: 00:10:41 Overall time: 00:10:41 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] 5540883 / 6879571 = 0.8054 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 01:05:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.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 01:05:01: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:05:01: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:05:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.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 01:05:01: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:05:01: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:05:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.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 01:05:02: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:05:02: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:05:13: 1000000 INFO @ Tue, 13 Aug 2019 01:05:13: 1000000 INFO @ Tue, 13 Aug 2019 01:05:15: 1000000 INFO @ Tue, 13 Aug 2019 01:05:16: #1 tag size is determined as 100 bps INFO @ Tue, 13 Aug 2019 01:05:16: #1 tag size = 100 INFO @ Tue, 13 Aug 2019 01:05:16: #1 total tags in treatment: 1338688 INFO @ Tue, 13 Aug 2019 01:05:16: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:05:16: #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 01:05:16: #1 tags after filtering in treatment: 1338688 INFO @ Tue, 13 Aug 2019 01:05:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 01:05:16: #1 finished! INFO @ Tue, 13 Aug 2019 01:05:16: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:05:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:05:16: #2 number of paired peaks: 1783 INFO @ Tue, 13 Aug 2019 01:05:16: start model_add_line... INFO @ Tue, 13 Aug 2019 01:05:16: start X-correlation... INFO @ Tue, 13 Aug 2019 01:05:16: end of X-cor INFO @ Tue, 13 Aug 2019 01:05:16: #2 finished! INFO @ Tue, 13 Aug 2019 01:05:16: #2 predicted fragment length is 87 bps INFO @ Tue, 13 Aug 2019 01:05:16: #2 alternative fragment length(s) may be 87 bps INFO @ Tue, 13 Aug 2019 01:05:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.20_model.r WARNING @ Tue, 13 Aug 2019 01:05:16: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 01:05:16: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Tue, 13 Aug 2019 01:05:16: #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 01:05:16: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:05:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:05:17: #1 tag size is determined as 100 bps INFO @ Tue, 13 Aug 2019 01:05:17: #1 tag size = 100 INFO @ Tue, 13 Aug 2019 01:05:17: #1 total tags in treatment: 1338688 INFO @ Tue, 13 Aug 2019 01:05:17: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:05:17: #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 01:05:17: #1 tags after filtering in treatment: 1338688 INFO @ Tue, 13 Aug 2019 01:05:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 01:05:17: #1 finished! INFO @ Tue, 13 Aug 2019 01:05:17: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:05:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:05:17: #2 number of paired peaks: 1783 INFO @ Tue, 13 Aug 2019 01:05:17: start model_add_line... INFO @ Tue, 13 Aug 2019 01:05:17: start X-correlation... INFO @ Tue, 13 Aug 2019 01:05:17: end of X-cor INFO @ Tue, 13 Aug 2019 01:05:17: #2 finished! INFO @ Tue, 13 Aug 2019 01:05:17: #2 predicted fragment length is 87 bps INFO @ Tue, 13 Aug 2019 01:05:17: #2 alternative fragment length(s) may be 87 bps INFO @ Tue, 13 Aug 2019 01:05:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.10_model.r WARNING @ Tue, 13 Aug 2019 01:05:17: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 01:05:17: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Tue, 13 Aug 2019 01:05:17: #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 01:05:17: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:05:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:05:19: #1 tag size is determined as 100 bps INFO @ Tue, 13 Aug 2019 01:05:19: #1 tag size = 100 INFO @ Tue, 13 Aug 2019 01:05:19: #1 total tags in treatment: 1338688 INFO @ Tue, 13 Aug 2019 01:05:19: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:05:19: #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 01:05:19: #1 tags after filtering in treatment: 1338688 INFO @ Tue, 13 Aug 2019 01:05:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 01:05:19: #1 finished! INFO @ Tue, 13 Aug 2019 01:05:19: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:05:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:05:19: #2 number of paired peaks: 1783 INFO @ Tue, 13 Aug 2019 01:05:19: start model_add_line... INFO @ Tue, 13 Aug 2019 01:05:19: start X-correlation... INFO @ Tue, 13 Aug 2019 01:05:19: end of X-cor INFO @ Tue, 13 Aug 2019 01:05:19: #2 finished! INFO @ Tue, 13 Aug 2019 01:05:19: #2 predicted fragment length is 87 bps INFO @ Tue, 13 Aug 2019 01:05:19: #2 alternative fragment length(s) may be 87 bps INFO @ Tue, 13 Aug 2019 01:05:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.05_model.r WARNING @ Tue, 13 Aug 2019 01:05:19: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 01:05:19: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Tue, 13 Aug 2019 01:05:19: #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 01:05:19: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:05:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:05:20: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:05:21: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:05:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.20_peaks.xls INFO @ Tue, 13 Aug 2019 01:05:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:05:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.20_summits.bed INFO @ Tue, 13 Aug 2019 01:05:23: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (549 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:05:23: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:05:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.10_peaks.xls INFO @ Tue, 13 Aug 2019 01:05:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:05:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.10_summits.bed INFO @ Tue, 13 Aug 2019 01:05:24: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (793 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:05:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.05_peaks.xls INFO @ Tue, 13 Aug 2019 01:05:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:05:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645130/SRX645130.05_summits.bed INFO @ Tue, 13 Aug 2019 01:05:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1426 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。