Job ID = 2589460 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,197,141 reads read : 5,197,141 reads written : 5,197,141 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR496299.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: 00:00:44 5197141 reads; of these: 5197141 (100.00%) were unpaired; of these: 2424886 (46.66%) aligned 0 times 2337458 (44.98%) aligned exactly 1 time 434797 (8.37%) aligned >1 times 53.34% overall alignment rate Time searching: 00:00:44 Overall time: 00:00:44 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] 293332 / 2772255 = 0.1058 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 17:44:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.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 17:44:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:44:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:44:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.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 17:44:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:44:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:44:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.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 17:44:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:44:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:44:30: 1000000 INFO @ Mon, 12 Aug 2019 17:44:31: 1000000 INFO @ Mon, 12 Aug 2019 17:44:32: 1000000 INFO @ Mon, 12 Aug 2019 17:44:39: 2000000 INFO @ Mon, 12 Aug 2019 17:44:39: 2000000 INFO @ Mon, 12 Aug 2019 17:44:40: 2000000 INFO @ Mon, 12 Aug 2019 17:44:43: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:44:43: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:44:43: #1 total tags in treatment: 2478923 INFO @ Mon, 12 Aug 2019 17:44:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:44:43: #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 17:44:43: #1 tags after filtering in treatment: 2478923 INFO @ Mon, 12 Aug 2019 17:44:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:44:43: #1 finished! INFO @ Mon, 12 Aug 2019 17:44:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:44:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:44:43: #2 number of paired peaks: 446 WARNING @ Mon, 12 Aug 2019 17:44:43: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Mon, 12 Aug 2019 17:44:43: start model_add_line... INFO @ Mon, 12 Aug 2019 17:44:43: start X-correlation... INFO @ Mon, 12 Aug 2019 17:44:43: end of X-cor INFO @ Mon, 12 Aug 2019 17:44:43: #2 finished! INFO @ Mon, 12 Aug 2019 17:44:43: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 17:44:43: #2 alternative fragment length(s) may be 33,93,154,502,581,588 bps INFO @ Mon, 12 Aug 2019 17:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.05_model.r WARNING @ Mon, 12 Aug 2019 17:44:43: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:44:43: #2 You may need to consider one of the other alternative d(s): 33,93,154,502,581,588 WARNING @ Mon, 12 Aug 2019 17:44:43: #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 17:44:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:44:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:44:43: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:44:43: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:44:43: #1 total tags in treatment: 2478923 INFO @ Mon, 12 Aug 2019 17:44:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:44:43: #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 17:44:43: #1 tags after filtering in treatment: 2478923 INFO @ Mon, 12 Aug 2019 17:44:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:44:43: #1 finished! INFO @ Mon, 12 Aug 2019 17:44:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:44:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:44:44: #2 number of paired peaks: 446 WARNING @ Mon, 12 Aug 2019 17:44:44: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Mon, 12 Aug 2019 17:44:44: start model_add_line... INFO @ Mon, 12 Aug 2019 17:44:44: start X-correlation... INFO @ Mon, 12 Aug 2019 17:44:44: end of X-cor INFO @ Mon, 12 Aug 2019 17:44:44: #2 finished! INFO @ Mon, 12 Aug 2019 17:44:44: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 17:44:44: #2 alternative fragment length(s) may be 33,93,154,502,581,588 bps INFO @ Mon, 12 Aug 2019 17:44:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.10_model.r WARNING @ Mon, 12 Aug 2019 17:44:44: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:44:44: #2 You may need to consider one of the other alternative d(s): 33,93,154,502,581,588 WARNING @ Mon, 12 Aug 2019 17:44:44: #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 17:44:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:44:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:44:44: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:44:44: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:44:44: #1 total tags in treatment: 2478923 INFO @ Mon, 12 Aug 2019 17:44:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:44:44: #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 17:44:44: #1 tags after filtering in treatment: 2478923 INFO @ Mon, 12 Aug 2019 17:44:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:44:44: #1 finished! INFO @ Mon, 12 Aug 2019 17:44:44: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:44:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:44:44: #2 number of paired peaks: 446 WARNING @ Mon, 12 Aug 2019 17:44:44: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Mon, 12 Aug 2019 17:44:44: start model_add_line... INFO @ Mon, 12 Aug 2019 17:44:44: start X-correlation... INFO @ Mon, 12 Aug 2019 17:44:44: end of X-cor INFO @ Mon, 12 Aug 2019 17:44:44: #2 finished! INFO @ Mon, 12 Aug 2019 17:44:44: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 17:44:44: #2 alternative fragment length(s) may be 33,93,154,502,581,588 bps INFO @ Mon, 12 Aug 2019 17:44:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.20_model.r WARNING @ Mon, 12 Aug 2019 17:44:44: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:44:44: #2 You may need to consider one of the other alternative d(s): 33,93,154,502,581,588 WARNING @ Mon, 12 Aug 2019 17:44:44: #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 17:44:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:44:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:44:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:44:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:44:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:44:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:44:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:44:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.05_summits.bed INFO @ Mon, 12 Aug 2019 17:44:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (299 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.10_summits.bed INFO @ Mon, 12 Aug 2019 17:44:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (113 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:44:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:44:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:44:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX147622/SRX147622.20_summits.bed INFO @ Mon, 12 Aug 2019 17:44:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (18 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。