Job ID = 2589346 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,517,145 reads read : 9,517,145 reads written : 9,517,145 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR217427.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: 00:01:25 9517145 reads; of these: 9517145 (100.00%) were unpaired; of these: 4765326 (50.07%) aligned 0 times 3938261 (41.38%) aligned exactly 1 time 813558 (8.55%) aligned >1 times 49.93% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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] 608156 / 4751819 = 0.1280 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 17:29:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.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 17:29:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:29:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:30:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.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 17:30:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:30:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:30:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.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 17:30:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:30:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:30:06: 1000000 INFO @ Mon, 12 Aug 2019 17:30:07: 1000000 INFO @ Mon, 12 Aug 2019 17:30:08: 1000000 INFO @ Mon, 12 Aug 2019 17:30:14: 2000000 INFO @ Mon, 12 Aug 2019 17:30:14: 2000000 INFO @ Mon, 12 Aug 2019 17:30:15: 2000000 INFO @ Mon, 12 Aug 2019 17:30:21: 3000000 INFO @ Mon, 12 Aug 2019 17:30:22: 3000000 INFO @ Mon, 12 Aug 2019 17:30:22: 3000000 INFO @ Mon, 12 Aug 2019 17:30:27: 4000000 INFO @ Mon, 12 Aug 2019 17:30:28: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:30:28: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:30:28: #1 total tags in treatment: 4143663 INFO @ Mon, 12 Aug 2019 17:30:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:30:28: #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 17:30:28: #1 tags after filtering in treatment: 4143663 INFO @ Mon, 12 Aug 2019 17:30:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:30:28: #1 finished! INFO @ Mon, 12 Aug 2019 17:30:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:30:29: #2 number of paired peaks: 593 WARNING @ Mon, 12 Aug 2019 17:30:29: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Mon, 12 Aug 2019 17:30:29: start model_add_line... INFO @ Mon, 12 Aug 2019 17:30:29: start X-correlation... INFO @ Mon, 12 Aug 2019 17:30:29: end of X-cor INFO @ Mon, 12 Aug 2019 17:30:29: #2 finished! INFO @ Mon, 12 Aug 2019 17:30:29: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 17:30:29: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 12 Aug 2019 17:30:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.20_model.r INFO @ Mon, 12 Aug 2019 17:30:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:30:29: 4000000 INFO @ Mon, 12 Aug 2019 17:30:29: 4000000 INFO @ Mon, 12 Aug 2019 17:30:30: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:30:30: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:30:30: #1 total tags in treatment: 4143663 INFO @ Mon, 12 Aug 2019 17:30:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:30:30: #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 17:30:30: #1 tags after filtering in treatment: 4143663 INFO @ Mon, 12 Aug 2019 17:30:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:30:30: #1 finished! INFO @ Mon, 12 Aug 2019 17:30:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:30:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:30:30: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:30:30: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:30:30: #1 total tags in treatment: 4143663 INFO @ Mon, 12 Aug 2019 17:30:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:30:30: #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 17:30:30: #1 tags after filtering in treatment: 4143663 INFO @ Mon, 12 Aug 2019 17:30:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:30:30: #1 finished! INFO @ Mon, 12 Aug 2019 17:30:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:30:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:30:31: #2 number of paired peaks: 593 WARNING @ Mon, 12 Aug 2019 17:30:31: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Mon, 12 Aug 2019 17:30:31: start model_add_line... INFO @ Mon, 12 Aug 2019 17:30:31: start X-correlation... INFO @ Mon, 12 Aug 2019 17:30:31: end of X-cor INFO @ Mon, 12 Aug 2019 17:30:31: #2 finished! INFO @ Mon, 12 Aug 2019 17:30:31: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 17:30:31: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 12 Aug 2019 17:30:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.10_model.r INFO @ Mon, 12 Aug 2019 17:30:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:30:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:30:31: #2 number of paired peaks: 593 WARNING @ Mon, 12 Aug 2019 17:30:31: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Mon, 12 Aug 2019 17:30:31: start model_add_line... INFO @ Mon, 12 Aug 2019 17:30:31: start X-correlation... INFO @ Mon, 12 Aug 2019 17:30:31: end of X-cor INFO @ Mon, 12 Aug 2019 17:30:31: #2 finished! INFO @ Mon, 12 Aug 2019 17:30:31: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 17:30:31: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 12 Aug 2019 17:30:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.05_model.r INFO @ Mon, 12 Aug 2019 17:30:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:30:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:30:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:30:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:30:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:30:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:30:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:30:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.20_summits.bed INFO @ Mon, 12 Aug 2019 17:30:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (315 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:30:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:30:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:30:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.10_summits.bed INFO @ Mon, 12 Aug 2019 17:30:50: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (550 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:30:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:30:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:30:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065721/SRX065721.05_summits.bed INFO @ Mon, 12 Aug 2019 17:30:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (853 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。