Job ID = 4178468 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,698,148 reads read : 3,396,296 reads written : 1,698,148 reads 0-length : 1,698,148 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: 00:00:01 Multiseed full-index search: 00:00:45 1698148 reads; of these: 1698148 (100.00%) were unpaired; of these: 574 (0.03%) aligned 0 times 1254123 (73.85%) aligned exactly 1 time 443451 (26.11%) aligned >1 times 99.97% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 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] 45739 / 1697574 = 0.0269 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:25:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.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 @ Thu, 05 Dec 2019 12:25:16: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:25:16: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:25:24: 1000000 INFO @ Thu, 05 Dec 2019 12:25:29: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:25:29: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:25:29: #1 total tags in treatment: 1651835 INFO @ Thu, 05 Dec 2019 12:25:29: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:25:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:25:29: #1 tags after filtering in treatment: 1651835 INFO @ Thu, 05 Dec 2019 12:25:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:25:29: #1 finished! INFO @ Thu, 05 Dec 2019 12:25:29: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:25:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:25:29: #2 number of paired peaks: 294 WARNING @ Thu, 05 Dec 2019 12:25:29: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Thu, 05 Dec 2019 12:25:29: start model_add_line... INFO @ Thu, 05 Dec 2019 12:25:29: start X-correlation... INFO @ Thu, 05 Dec 2019 12:25:29: end of X-cor INFO @ Thu, 05 Dec 2019 12:25:29: #2 finished! INFO @ Thu, 05 Dec 2019 12:25:29: #2 predicted fragment length is 52 bps INFO @ Thu, 05 Dec 2019 12:25:29: #2 alternative fragment length(s) may be 52,546,570,575 bps INFO @ Thu, 05 Dec 2019 12:25:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.05_model.r WARNING @ Thu, 05 Dec 2019 12:25:29: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:25:29: #2 You may need to consider one of the other alternative d(s): 52,546,570,575 WARNING @ Thu, 05 Dec 2019 12:25:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:25:29: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:25:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:25:34: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:25:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:25:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:25:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.05_summits.bed INFO @ Thu, 05 Dec 2019 12:25:37: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (159 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:25:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.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 @ Thu, 05 Dec 2019 12:25:45: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:25:45: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:25:53: 1000000 INFO @ Thu, 05 Dec 2019 12:25:58: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:25:58: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:25:58: #1 total tags in treatment: 1651835 INFO @ Thu, 05 Dec 2019 12:25:58: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:25:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:25:58: #1 tags after filtering in treatment: 1651835 INFO @ Thu, 05 Dec 2019 12:25:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:25:58: #1 finished! INFO @ Thu, 05 Dec 2019 12:25:58: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:25:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:25:58: #2 number of paired peaks: 294 WARNING @ Thu, 05 Dec 2019 12:25:58: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Thu, 05 Dec 2019 12:25:58: start model_add_line... INFO @ Thu, 05 Dec 2019 12:25:58: start X-correlation... INFO @ Thu, 05 Dec 2019 12:25:58: end of X-cor INFO @ Thu, 05 Dec 2019 12:25:58: #2 finished! INFO @ Thu, 05 Dec 2019 12:25:58: #2 predicted fragment length is 52 bps INFO @ Thu, 05 Dec 2019 12:25:58: #2 alternative fragment length(s) may be 52,546,570,575 bps INFO @ Thu, 05 Dec 2019 12:25:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.10_model.r WARNING @ Thu, 05 Dec 2019 12:25:58: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:25:58: #2 You may need to consider one of the other alternative d(s): 52,546,570,575 WARNING @ Thu, 05 Dec 2019 12:25:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:25:58: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:25:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:26:04: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:26:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.10_summits.bed INFO @ Thu, 05 Dec 2019 12:26:06: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (84 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:26:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.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 @ Thu, 05 Dec 2019 12:26:15: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:26:15: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:26:23: 1000000 INFO @ Thu, 05 Dec 2019 12:26:28: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:26:28: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:26:28: #1 total tags in treatment: 1651835 INFO @ Thu, 05 Dec 2019 12:26:28: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:26:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:26:28: #1 tags after filtering in treatment: 1651835 INFO @ Thu, 05 Dec 2019 12:26:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:26:28: #1 finished! INFO @ Thu, 05 Dec 2019 12:26:28: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:26:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:26:28: #2 number of paired peaks: 294 WARNING @ Thu, 05 Dec 2019 12:26:28: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Thu, 05 Dec 2019 12:26:28: start model_add_line... INFO @ Thu, 05 Dec 2019 12:26:28: start X-correlation... INFO @ Thu, 05 Dec 2019 12:26:28: end of X-cor INFO @ Thu, 05 Dec 2019 12:26:28: #2 finished! INFO @ Thu, 05 Dec 2019 12:26:28: #2 predicted fragment length is 52 bps INFO @ Thu, 05 Dec 2019 12:26:28: #2 alternative fragment length(s) may be 52,546,570,575 bps INFO @ Thu, 05 Dec 2019 12:26:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.20_model.r WARNING @ Thu, 05 Dec 2019 12:26:28: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:26:28: #2 You may need to consider one of the other alternative d(s): 52,546,570,575 WARNING @ Thu, 05 Dec 2019 12:26:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:26:28: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:26:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:26:34: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:26:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:26:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:26:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5515083/SRX5515083.20_summits.bed INFO @ Thu, 05 Dec 2019 12:26:36: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (53 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。