Job ID = 2589459 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,893,961 reads read : 4,893,961 reads written : 4,893,961 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR496298.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: 00:00:40 4893961 reads; of these: 4893961 (100.00%) were unpaired; of these: 2304527 (47.09%) aligned 0 times 2169577 (44.33%) aligned exactly 1 time 419857 (8.58%) aligned >1 times 52.91% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 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] 240001 / 2589434 = 0.0927 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 17:43:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.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 17:43:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:43:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:44:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.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 17:44:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:44:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:44:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.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 17:44:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:44:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:44:08: 1000000 INFO @ Mon, 12 Aug 2019 17:44:09: 1000000 INFO @ Mon, 12 Aug 2019 17:44:10: 1000000 INFO @ Mon, 12 Aug 2019 17:44:16: 2000000 INFO @ Mon, 12 Aug 2019 17:44:17: 2000000 INFO @ Mon, 12 Aug 2019 17:44:18: 2000000 INFO @ Mon, 12 Aug 2019 17:44:19: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:44:19: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:44:19: #1 total tags in treatment: 2349433 INFO @ Mon, 12 Aug 2019 17:44:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:44:19: #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 17:44:19: #1 tags after filtering in treatment: 2349433 INFO @ Mon, 12 Aug 2019 17:44:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:44:19: #1 finished! INFO @ Mon, 12 Aug 2019 17:44:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:44:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:44:19: #2 number of paired peaks: 477 WARNING @ Mon, 12 Aug 2019 17:44:19: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Mon, 12 Aug 2019 17:44:19: start model_add_line... INFO @ Mon, 12 Aug 2019 17:44:19: start X-correlation... INFO @ Mon, 12 Aug 2019 17:44:19: end of X-cor INFO @ Mon, 12 Aug 2019 17:44:19: #2 finished! INFO @ Mon, 12 Aug 2019 17:44:19: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 17:44:19: #2 alternative fragment length(s) may be 34,547,585 bps INFO @ Mon, 12 Aug 2019 17:44:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.05_model.r WARNING @ Mon, 12 Aug 2019 17:44:19: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:44:19: #2 You may need to consider one of the other alternative d(s): 34,547,585 WARNING @ Mon, 12 Aug 2019 17:44:19: #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 17:44:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:44:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:44:20: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:44:20: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:44:20: #1 total tags in treatment: 2349433 INFO @ Mon, 12 Aug 2019 17:44:20: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:44:20: #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 17:44:20: #1 tags after filtering in treatment: 2349433 INFO @ Mon, 12 Aug 2019 17:44:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:44:20: #1 finished! INFO @ Mon, 12 Aug 2019 17:44:20: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:44:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:44:20: #2 number of paired peaks: 477 WARNING @ Mon, 12 Aug 2019 17:44:20: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Mon, 12 Aug 2019 17:44:20: start model_add_line... INFO @ Mon, 12 Aug 2019 17:44:20: start X-correlation... INFO @ Mon, 12 Aug 2019 17:44:20: end of X-cor INFO @ Mon, 12 Aug 2019 17:44:20: #2 finished! INFO @ Mon, 12 Aug 2019 17:44:20: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 17:44:20: #2 alternative fragment length(s) may be 34,547,585 bps INFO @ Mon, 12 Aug 2019 17:44:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.10_model.r WARNING @ Mon, 12 Aug 2019 17:44:20: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:44:20: #2 You may need to consider one of the other alternative d(s): 34,547,585 WARNING @ Mon, 12 Aug 2019 17:44:20: #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 17:44:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:44:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:44:21: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:44:21: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:44:21: #1 total tags in treatment: 2349433 INFO @ Mon, 12 Aug 2019 17:44:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:44:21: #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 17:44:21: #1 tags after filtering in treatment: 2349433 INFO @ Mon, 12 Aug 2019 17:44:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:44:21: #1 finished! INFO @ Mon, 12 Aug 2019 17:44:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:44:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:44:21: #2 number of paired peaks: 477 WARNING @ Mon, 12 Aug 2019 17:44:21: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Mon, 12 Aug 2019 17:44:21: start model_add_line... INFO @ Mon, 12 Aug 2019 17:44:21: start X-correlation... INFO @ Mon, 12 Aug 2019 17:44:21: end of X-cor INFO @ Mon, 12 Aug 2019 17:44:21: #2 finished! INFO @ Mon, 12 Aug 2019 17:44:21: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 17:44:21: #2 alternative fragment length(s) may be 34,547,585 bps INFO @ Mon, 12 Aug 2019 17:44:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.20_model.r WARNING @ Mon, 12 Aug 2019 17:44:21: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:44:21: #2 You may need to consider one of the other alternative d(s): 34,547,585 WARNING @ Mon, 12 Aug 2019 17:44:21: #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 17:44:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:44:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:44:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:44:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:44:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:44:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:44:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:44:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.05_summits.bed INFO @ Mon, 12 Aug 2019 17:44:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (271 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:44:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:44:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:44:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.10_summits.bed INFO @ Mon, 12 Aug 2019 17:44:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (119 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:44:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:44:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:44:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX147621/SRX147621.20_summits.bed INFO @ Mon, 12 Aug 2019 17:44:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (16 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。