Job ID = 1294467 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,840,701 reads read : 7,840,701 reads written : 7,840,701 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: 00:03:38 7840701 reads; of these: 7840701 (100.00%) were unpaired; of these: 310668 (3.96%) aligned 0 times 5174205 (65.99%) aligned exactly 1 time 2355828 (30.05%) aligned >1 times 96.04% overall alignment rate Time searching: 00:03:38 Overall time: 00:03:38 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] 965619 / 7530033 = 0.1282 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 08:18:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.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 08:18:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:18:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:18:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.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 08:18:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:18:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:18:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.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 08:18:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:18:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:18:14: 1000000 INFO @ Mon, 03 Jun 2019 08:18:15: 1000000 INFO @ Mon, 03 Jun 2019 08:18:15: 1000000 INFO @ Mon, 03 Jun 2019 08:18:22: 2000000 INFO @ Mon, 03 Jun 2019 08:18:24: 2000000 INFO @ Mon, 03 Jun 2019 08:18:25: 2000000 INFO @ Mon, 03 Jun 2019 08:18:30: 3000000 INFO @ Mon, 03 Jun 2019 08:18:33: 3000000 INFO @ Mon, 03 Jun 2019 08:18:35: 3000000 INFO @ Mon, 03 Jun 2019 08:18:37: 4000000 INFO @ Mon, 03 Jun 2019 08:18:42: 4000000 INFO @ Mon, 03 Jun 2019 08:18:45: 4000000 INFO @ Mon, 03 Jun 2019 08:18:45: 5000000 INFO @ Mon, 03 Jun 2019 08:18:52: 5000000 INFO @ Mon, 03 Jun 2019 08:18:55: 6000000 INFO @ Mon, 03 Jun 2019 08:18:55: 5000000 INFO @ Mon, 03 Jun 2019 08:19:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:19:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:19:01: #1 total tags in treatment: 6564414 INFO @ Mon, 03 Jun 2019 08:19:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:19:01: #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 08:19:01: #1 tags after filtering in treatment: 6564414 INFO @ Mon, 03 Jun 2019 08:19:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:19:01: #1 finished! INFO @ Mon, 03 Jun 2019 08:19:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:19:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:19:01: #2 number of paired peaks: 603 WARNING @ Mon, 03 Jun 2019 08:19:01: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Mon, 03 Jun 2019 08:19:01: start model_add_line... INFO @ Mon, 03 Jun 2019 08:19:01: start X-correlation... INFO @ Mon, 03 Jun 2019 08:19:01: end of X-cor INFO @ Mon, 03 Jun 2019 08:19:01: #2 finished! INFO @ Mon, 03 Jun 2019 08:19:01: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 08:19:01: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 08:19:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.10_model.r WARNING @ Mon, 03 Jun 2019 08:19:01: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:19:01: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 08:19:01: #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 08:19:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:19:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:19:02: 6000000 INFO @ Mon, 03 Jun 2019 08:19:06: 6000000 INFO @ Mon, 03 Jun 2019 08:19:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:19:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:19:07: #1 total tags in treatment: 6564414 INFO @ Mon, 03 Jun 2019 08:19:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:19:07: #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 08:19:08: #1 tags after filtering in treatment: 6564414 INFO @ Mon, 03 Jun 2019 08:19:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:19:08: #1 finished! INFO @ Mon, 03 Jun 2019 08:19:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:19:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:19:08: #2 number of paired peaks: 603 WARNING @ Mon, 03 Jun 2019 08:19:08: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Mon, 03 Jun 2019 08:19:08: start model_add_line... INFO @ Mon, 03 Jun 2019 08:19:08: start X-correlation... INFO @ Mon, 03 Jun 2019 08:19:08: end of X-cor INFO @ Mon, 03 Jun 2019 08:19:08: #2 finished! INFO @ Mon, 03 Jun 2019 08:19:08: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 08:19:08: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 08:19:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.20_model.r WARNING @ Mon, 03 Jun 2019 08:19:08: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:19:08: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 08:19:08: #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 08:19:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:19:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:19:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:19:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:19:11: #1 total tags in treatment: 6564414 INFO @ Mon, 03 Jun 2019 08:19:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:19:11: #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 08:19:12: #1 tags after filtering in treatment: 6564414 INFO @ Mon, 03 Jun 2019 08:19:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:19:12: #1 finished! INFO @ Mon, 03 Jun 2019 08:19:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:19:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:19:12: #2 number of paired peaks: 603 WARNING @ Mon, 03 Jun 2019 08:19:12: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Mon, 03 Jun 2019 08:19:12: start model_add_line... INFO @ Mon, 03 Jun 2019 08:19:12: start X-correlation... INFO @ Mon, 03 Jun 2019 08:19:12: end of X-cor INFO @ Mon, 03 Jun 2019 08:19:12: #2 finished! INFO @ Mon, 03 Jun 2019 08:19:12: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 08:19:12: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 08:19:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.05_model.r WARNING @ Mon, 03 Jun 2019 08:19:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:19:12: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 08:19:12: #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 08:19:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:19:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:19:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:19:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:19:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:19:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:19:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.10_summits.bed INFO @ Mon, 03 Jun 2019 08:19:30: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1566 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:19:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:19:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:19:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:19:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.20_summits.bed INFO @ Mon, 03 Jun 2019 08:19:36: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1171 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:19:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:19:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:19:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287668/SRX287668.05_summits.bed INFO @ Mon, 03 Jun 2019 08:19:41: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1863 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。