Job ID = 4303122 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,437,102 reads read : 4,437,102 reads written : 4,437,102 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1552267.sra.cache’: 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: 00:01:03 4437102 reads; of these: 4437102 (100.00%) were unpaired; of these: 446129 (10.05%) aligned 0 times 3466305 (78.12%) aligned exactly 1 time 524668 (11.82%) aligned >1 times 89.95% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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] 1608667 / 3990973 = 0.4031 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:47:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.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, 12 Dec 2019 00:47:01: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:47:01: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:47:07: 1000000 INFO @ Thu, 12 Dec 2019 00:47:14: 2000000 INFO @ Thu, 12 Dec 2019 00:47:16: #1 tag size is determined as 36 bps INFO @ Thu, 12 Dec 2019 00:47:16: #1 tag size = 36 INFO @ Thu, 12 Dec 2019 00:47:16: #1 total tags in treatment: 2382306 INFO @ Thu, 12 Dec 2019 00:47:16: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:47:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:47:16: #1 tags after filtering in treatment: 2382306 INFO @ Thu, 12 Dec 2019 00:47:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:47:16: #1 finished! INFO @ Thu, 12 Dec 2019 00:47:16: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:47:16: #2 number of paired peaks: 242 WARNING @ Thu, 12 Dec 2019 00:47:16: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Thu, 12 Dec 2019 00:47:16: start model_add_line... INFO @ Thu, 12 Dec 2019 00:47:16: start X-correlation... INFO @ Thu, 12 Dec 2019 00:47:16: end of X-cor INFO @ Thu, 12 Dec 2019 00:47:16: #2 finished! INFO @ Thu, 12 Dec 2019 00:47:16: #2 predicted fragment length is 39 bps INFO @ Thu, 12 Dec 2019 00:47:16: #2 alternative fragment length(s) may be 39 bps INFO @ Thu, 12 Dec 2019 00:47:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.05_model.r WARNING @ Thu, 12 Dec 2019 00:47:16: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:47:16: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Thu, 12 Dec 2019 00:47:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:47:16: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:47:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:47:24: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:47:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:47:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:47:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.05_summits.bed INFO @ Thu, 12 Dec 2019 00:47:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (443 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:47:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.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, 12 Dec 2019 00:47:30: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:47:30: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:47:37: 1000000 INFO @ Thu, 12 Dec 2019 00:47:44: 2000000 INFO @ Thu, 12 Dec 2019 00:47:47: #1 tag size is determined as 36 bps INFO @ Thu, 12 Dec 2019 00:47:47: #1 tag size = 36 INFO @ Thu, 12 Dec 2019 00:47:47: #1 total tags in treatment: 2382306 INFO @ Thu, 12 Dec 2019 00:47:47: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:47:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:47:47: #1 tags after filtering in treatment: 2382306 INFO @ Thu, 12 Dec 2019 00:47:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:47:47: #1 finished! INFO @ Thu, 12 Dec 2019 00:47:47: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:47:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:47:47: #2 number of paired peaks: 242 WARNING @ Thu, 12 Dec 2019 00:47:47: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Thu, 12 Dec 2019 00:47:47: start model_add_line... INFO @ Thu, 12 Dec 2019 00:47:47: start X-correlation... INFO @ Thu, 12 Dec 2019 00:47:48: end of X-cor INFO @ Thu, 12 Dec 2019 00:47:48: #2 finished! INFO @ Thu, 12 Dec 2019 00:47:48: #2 predicted fragment length is 39 bps INFO @ Thu, 12 Dec 2019 00:47:48: #2 alternative fragment length(s) may be 39 bps INFO @ Thu, 12 Dec 2019 00:47:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.10_model.r WARNING @ Thu, 12 Dec 2019 00:47:48: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:47:48: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Thu, 12 Dec 2019 00:47:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:47:48: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:47:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:47:55: #3 Call peaks for each chromosome... BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:47:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:47:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:47:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.10_summits.bed INFO @ Thu, 12 Dec 2019 00:47:59: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (206 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:48:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.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, 12 Dec 2019 00:48:00: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:48:00: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:48:08: 1000000 INFO @ Thu, 12 Dec 2019 00:48:16: 2000000 INFO @ Thu, 12 Dec 2019 00:48:19: #1 tag size is determined as 36 bps INFO @ Thu, 12 Dec 2019 00:48:19: #1 tag size = 36 INFO @ Thu, 12 Dec 2019 00:48:19: #1 total tags in treatment: 2382306 INFO @ Thu, 12 Dec 2019 00:48:19: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:48:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:48:19: #1 tags after filtering in treatment: 2382306 INFO @ Thu, 12 Dec 2019 00:48:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:48:19: #1 finished! INFO @ Thu, 12 Dec 2019 00:48:19: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:48:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:48:19: #2 number of paired peaks: 242 WARNING @ Thu, 12 Dec 2019 00:48:19: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Thu, 12 Dec 2019 00:48:19: start model_add_line... INFO @ Thu, 12 Dec 2019 00:48:19: start X-correlation... INFO @ Thu, 12 Dec 2019 00:48:19: end of X-cor INFO @ Thu, 12 Dec 2019 00:48:19: #2 finished! INFO @ Thu, 12 Dec 2019 00:48:19: #2 predicted fragment length is 39 bps INFO @ Thu, 12 Dec 2019 00:48:19: #2 alternative fragment length(s) may be 39 bps INFO @ Thu, 12 Dec 2019 00:48:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.20_model.r WARNING @ Thu, 12 Dec 2019 00:48:19: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:48:19: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Thu, 12 Dec 2019 00:48:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:48:19: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:48:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:48:26: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:48:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:48:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:48:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681798/SRX681798.20_summits.bed INFO @ Thu, 12 Dec 2019 00:48:30: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (116 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。