Job ID = 2589281 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,346,433 reads read : 6,346,433 reads written : 6,346,433 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR217355.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: 00:00:47 6346433 reads; of these: 6346433 (100.00%) were unpaired; of these: 3823830 (60.25%) aligned 0 times 2121903 (33.43%) aligned exactly 1 time 400700 (6.31%) aligned >1 times 39.75% overall alignment rate Time searching: 00:00:47 Overall time: 00:00:47 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] 269589 / 2522603 = 0.1069 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 17:19:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.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 17:19:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:19:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:19:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.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 17:19:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:19:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:19:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.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 17:19:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:19:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:19:44: 1000000 INFO @ Mon, 12 Aug 2019 17:19:45: 1000000 INFO @ Mon, 12 Aug 2019 17:19:48: 1000000 INFO @ Mon, 12 Aug 2019 17:19:53: 2000000 INFO @ Mon, 12 Aug 2019 17:19:54: 2000000 INFO @ Mon, 12 Aug 2019 17:19:55: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:19:55: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:19:55: #1 total tags in treatment: 2253014 INFO @ Mon, 12 Aug 2019 17:19:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:19:55: #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 17:19:55: #1 tags after filtering in treatment: 2253014 INFO @ Mon, 12 Aug 2019 17:19:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:19:55: #1 finished! INFO @ Mon, 12 Aug 2019 17:19:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:19:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:19:55: #2 number of paired peaks: 405 WARNING @ Mon, 12 Aug 2019 17:19:55: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Mon, 12 Aug 2019 17:19:55: start model_add_line... INFO @ Mon, 12 Aug 2019 17:19:55: start X-correlation... INFO @ Mon, 12 Aug 2019 17:19:55: end of X-cor INFO @ Mon, 12 Aug 2019 17:19:55: #2 finished! INFO @ Mon, 12 Aug 2019 17:19:55: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 17:19:55: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 12 Aug 2019 17:19:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.05_model.r WARNING @ Mon, 12 Aug 2019 17:19:55: #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 17:19:55: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 12 Aug 2019 17:19:55: #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 17:19:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:19:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:19:56: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:19:56: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:19:56: #1 total tags in treatment: 2253014 INFO @ Mon, 12 Aug 2019 17:19:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:19:56: #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 17:19:56: #1 tags after filtering in treatment: 2253014 INFO @ Mon, 12 Aug 2019 17:19:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:19:56: #1 finished! INFO @ Mon, 12 Aug 2019 17:19:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:19:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:19:56: #2 number of paired peaks: 405 WARNING @ Mon, 12 Aug 2019 17:19:56: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Mon, 12 Aug 2019 17:19:56: start model_add_line... INFO @ Mon, 12 Aug 2019 17:19:56: start X-correlation... INFO @ Mon, 12 Aug 2019 17:19:56: end of X-cor INFO @ Mon, 12 Aug 2019 17:19:56: #2 finished! INFO @ Mon, 12 Aug 2019 17:19:56: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 17:19:56: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 12 Aug 2019 17:19:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.10_model.r WARNING @ Mon, 12 Aug 2019 17:19:56: #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 17:19:56: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 12 Aug 2019 17:19:56: #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 17:19:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:19:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:19:58: 2000000 INFO @ Mon, 12 Aug 2019 17:20:00: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:20:00: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:20:00: #1 total tags in treatment: 2253014 INFO @ Mon, 12 Aug 2019 17:20:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:20:00: #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 17:20:00: #1 tags after filtering in treatment: 2253014 INFO @ Mon, 12 Aug 2019 17:20:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:20:00: #1 finished! INFO @ Mon, 12 Aug 2019 17:20:00: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:20:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:20:00: #2 number of paired peaks: 405 WARNING @ Mon, 12 Aug 2019 17:20:00: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Mon, 12 Aug 2019 17:20:00: start model_add_line... INFO @ Mon, 12 Aug 2019 17:20:00: start X-correlation... INFO @ Mon, 12 Aug 2019 17:20:00: end of X-cor INFO @ Mon, 12 Aug 2019 17:20:00: #2 finished! INFO @ Mon, 12 Aug 2019 17:20:00: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 17:20:00: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 12 Aug 2019 17:20:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.20_model.r WARNING @ Mon, 12 Aug 2019 17:20:00: #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 17:20:00: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 12 Aug 2019 17:20:00: #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 17:20:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:20:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:20:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:20:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:20:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:20:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:20:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.05_summits.bed INFO @ Mon, 12 Aug 2019 17:20:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (308 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:20:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:20:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:20:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.10_summits.bed INFO @ Mon, 12 Aug 2019 17:20:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (100 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:20:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:20:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:20:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:20:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065649/SRX065649.20_summits.bed INFO @ Mon, 12 Aug 2019 17:20:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (14 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。