Job ID = 2589562 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,438,791 reads read : 6,438,791 reads written : 6,438,791 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR707569.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: 00:00:39 6438791 reads; of these: 6438791 (100.00%) were unpaired; of these: 4596198 (71.38%) aligned 0 times 1528946 (23.75%) aligned exactly 1 time 313647 (4.87%) aligned >1 times 28.62% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 290151 / 1842593 = 0.1575 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, 12 Aug 2019 17:58:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 17:58:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:58:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:58:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 17:58:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:58:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:58:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 17:58:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:58:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:58:22: 1000000 INFO @ Mon, 12 Aug 2019 17:58:23: 1000000 INFO @ Mon, 12 Aug 2019 17:58:25: 1000000 INFO @ Mon, 12 Aug 2019 17:58:27: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:58:27: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:58:27: #1 total tags in treatment: 1552442 INFO @ Mon, 12 Aug 2019 17:58:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:58:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:58:27: #1 tags after filtering in treatment: 1552442 INFO @ Mon, 12 Aug 2019 17:58:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:58:27: #1 finished! INFO @ Mon, 12 Aug 2019 17:58:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:58:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:58:27: #2 number of paired peaks: 485 WARNING @ Mon, 12 Aug 2019 17:58:27: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Mon, 12 Aug 2019 17:58:27: start model_add_line... INFO @ Mon, 12 Aug 2019 17:58:27: start X-correlation... INFO @ Mon, 12 Aug 2019 17:58:27: end of X-cor INFO @ Mon, 12 Aug 2019 17:58:27: #2 finished! INFO @ Mon, 12 Aug 2019 17:58:27: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 17:58:27: #2 alternative fragment length(s) may be 51,105,565 bps INFO @ Mon, 12 Aug 2019 17:58:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.05_model.r WARNING @ Mon, 12 Aug 2019 17:58:27: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:58:27: #2 You may need to consider one of the other alternative d(s): 51,105,565 WARNING @ Mon, 12 Aug 2019 17:58:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:58:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:58:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:58:27: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:58:27: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:58:27: #1 total tags in treatment: 1552442 INFO @ Mon, 12 Aug 2019 17:58:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:58:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:58:27: #1 tags after filtering in treatment: 1552442 INFO @ Mon, 12 Aug 2019 17:58:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:58:27: #1 finished! INFO @ Mon, 12 Aug 2019 17:58:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:58:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:58:27: #2 number of paired peaks: 485 WARNING @ Mon, 12 Aug 2019 17:58:27: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Mon, 12 Aug 2019 17:58:27: start model_add_line... INFO @ Mon, 12 Aug 2019 17:58:27: start X-correlation... INFO @ Mon, 12 Aug 2019 17:58:27: end of X-cor INFO @ Mon, 12 Aug 2019 17:58:27: #2 finished! INFO @ Mon, 12 Aug 2019 17:58:27: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 17:58:27: #2 alternative fragment length(s) may be 51,105,565 bps INFO @ Mon, 12 Aug 2019 17:58:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.10_model.r WARNING @ Mon, 12 Aug 2019 17:58:27: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:58:27: #2 You may need to consider one of the other alternative d(s): 51,105,565 WARNING @ Mon, 12 Aug 2019 17:58:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:58:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:58:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:58:29: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:58:29: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:58:29: #1 total tags in treatment: 1552442 INFO @ Mon, 12 Aug 2019 17:58:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:58:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:58:29: #1 tags after filtering in treatment: 1552442 INFO @ Mon, 12 Aug 2019 17:58:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:58:29: #1 finished! INFO @ Mon, 12 Aug 2019 17:58:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:58:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:58:29: #2 number of paired peaks: 485 WARNING @ Mon, 12 Aug 2019 17:58:29: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Mon, 12 Aug 2019 17:58:29: start model_add_line... INFO @ Mon, 12 Aug 2019 17:58:29: start X-correlation... INFO @ Mon, 12 Aug 2019 17:58:29: end of X-cor INFO @ Mon, 12 Aug 2019 17:58:29: #2 finished! INFO @ Mon, 12 Aug 2019 17:58:29: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 17:58:29: #2 alternative fragment length(s) may be 51,105,565 bps INFO @ Mon, 12 Aug 2019 17:58:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.20_model.r WARNING @ Mon, 12 Aug 2019 17:58:29: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:58:29: #2 You may need to consider one of the other alternative d(s): 51,105,565 WARNING @ Mon, 12 Aug 2019 17:58:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:58:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:58:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:58:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:58:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:58:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:58:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:58:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:58:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.05_summits.bed INFO @ Mon, 12 Aug 2019 17:58:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (359 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:58:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:58:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:58:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.10_summits.bed INFO @ Mon, 12 Aug 2019 17:58:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (118 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:58:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX234925/SRX234925.20_summits.bed INFO @ Mon, 12 Aug 2019 17:58:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (28 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。