Job ID = 2589268 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,310,923 reads read : 5,310,923 reads written : 5,310,923 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR217342.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: 00:00:26 5310923 reads; of these: 5310923 (100.00%) were unpaired; of these: 4173487 (78.58%) aligned 0 times 969452 (18.25%) aligned exactly 1 time 167984 (3.16%) aligned >1 times 21.42% overall alignment rate Time searching: 00:00:26 Overall time: 00:00:26 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] 62824 / 1137436 = 0.0552 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 17:17:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.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 17:17:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:17:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:17:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.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 17:17:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:17:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:17:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.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 17:17:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:17:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:17:21: 1000000 INFO @ Mon, 12 Aug 2019 17:17:21: 1000000 INFO @ Mon, 12 Aug 2019 17:17:21: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:17:21: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:17:21: #1 total tags in treatment: 1074612 INFO @ Mon, 12 Aug 2019 17:17:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:17:21: #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 17:17:21: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:17:21: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:17:21: #1 total tags in treatment: 1074612 INFO @ Mon, 12 Aug 2019 17:17:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:17:21: #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 17:17:21: #1 tags after filtering in treatment: 1074612 INFO @ Mon, 12 Aug 2019 17:17:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:17:21: #1 finished! INFO @ Mon, 12 Aug 2019 17:17:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:17:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:17:21: #1 tags after filtering in treatment: 1074612 INFO @ Mon, 12 Aug 2019 17:17:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:17:21: #1 finished! INFO @ Mon, 12 Aug 2019 17:17:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:17:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:17:21: #2 number of paired peaks: 890 WARNING @ Mon, 12 Aug 2019 17:17:21: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Mon, 12 Aug 2019 17:17:21: start model_add_line... INFO @ Mon, 12 Aug 2019 17:17:21: start X-correlation... INFO @ Mon, 12 Aug 2019 17:17:21: #2 number of paired peaks: 890 WARNING @ Mon, 12 Aug 2019 17:17:21: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Mon, 12 Aug 2019 17:17:21: start model_add_line... INFO @ Mon, 12 Aug 2019 17:17:21: end of X-cor INFO @ Mon, 12 Aug 2019 17:17:21: #2 finished! INFO @ Mon, 12 Aug 2019 17:17:21: #2 predicted fragment length is 115 bps INFO @ Mon, 12 Aug 2019 17:17:21: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 12 Aug 2019 17:17:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.10_model.r INFO @ Mon, 12 Aug 2019 17:17:21: start X-correlation... INFO @ Mon, 12 Aug 2019 17:17:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:17:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:17:21: end of X-cor INFO @ Mon, 12 Aug 2019 17:17:21: #2 finished! INFO @ Mon, 12 Aug 2019 17:17:21: #2 predicted fragment length is 115 bps INFO @ Mon, 12 Aug 2019 17:17:21: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 12 Aug 2019 17:17:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.05_model.r INFO @ Mon, 12 Aug 2019 17:17:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:17:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:17:23: 1000000 INFO @ Mon, 12 Aug 2019 17:17:23: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:17:23: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:17:23: #1 total tags in treatment: 1074612 INFO @ Mon, 12 Aug 2019 17:17:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:17:23: #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 17:17:23: #1 tags after filtering in treatment: 1074612 INFO @ Mon, 12 Aug 2019 17:17:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:17:23: #1 finished! INFO @ Mon, 12 Aug 2019 17:17:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:17:23: #2 number of paired peaks: 890 WARNING @ Mon, 12 Aug 2019 17:17:23: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Mon, 12 Aug 2019 17:17:23: start model_add_line... INFO @ Mon, 12 Aug 2019 17:17:23: start X-correlation... INFO @ Mon, 12 Aug 2019 17:17:23: end of X-cor INFO @ Mon, 12 Aug 2019 17:17:23: #2 finished! INFO @ Mon, 12 Aug 2019 17:17:23: #2 predicted fragment length is 115 bps INFO @ Mon, 12 Aug 2019 17:17:23: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 12 Aug 2019 17:17:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.20_model.r INFO @ Mon, 12 Aug 2019 17:17:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:17:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:17:25: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:17:25: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:17:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:17:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:17:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.05_summits.bed INFO @ Mon, 12 Aug 2019 17:17:27: Done! INFO @ Mon, 12 Aug 2019 17:17:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:17:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:17:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.10_summits.bed INFO @ Mon, 12 Aug 2019 17:17:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (314 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (96 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:17:27: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 17:17:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:17:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:17:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065636/SRX065636.20_summits.bed INFO @ Mon, 12 Aug 2019 17:17:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (21 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。