Job ID = 2589495 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,486,474 reads read : 6,486,474 reads written : 6,486,474 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR573720.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: 00:00:58 6486474 reads; of these: 6486474 (100.00%) were unpaired; of these: 2117190 (32.64%) aligned 0 times 3961152 (61.07%) aligned exactly 1 time 408132 (6.29%) aligned >1 times 67.36% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 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] 681539 / 4369284 = 0.1560 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 17:50:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.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 17:50:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:50:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.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 17:50:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:50:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:50:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.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 17:50:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:50:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:50:16: 1000000 INFO @ Mon, 12 Aug 2019 17:50:17: 1000000 INFO @ Mon, 12 Aug 2019 17:50:19: 1000000 INFO @ Mon, 12 Aug 2019 17:50:23: 2000000 INFO @ Mon, 12 Aug 2019 17:50:24: 2000000 INFO @ Mon, 12 Aug 2019 17:50:27: 2000000 INFO @ Mon, 12 Aug 2019 17:50:30: 3000000 INFO @ Mon, 12 Aug 2019 17:50:31: 3000000 INFO @ Mon, 12 Aug 2019 17:50:35: 3000000 INFO @ Mon, 12 Aug 2019 17:50:35: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:50:35: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:50:35: #1 total tags in treatment: 3687745 INFO @ Mon, 12 Aug 2019 17:50:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:50:35: #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 17:50:35: #1 tags after filtering in treatment: 3687745 INFO @ Mon, 12 Aug 2019 17:50:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:50:35: #1 finished! INFO @ Mon, 12 Aug 2019 17:50:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:50:36: #2 number of paired peaks: 3250 INFO @ Mon, 12 Aug 2019 17:50:36: start model_add_line... INFO @ Mon, 12 Aug 2019 17:50:36: start X-correlation... INFO @ Mon, 12 Aug 2019 17:50:36: end of X-cor INFO @ Mon, 12 Aug 2019 17:50:36: #2 finished! INFO @ Mon, 12 Aug 2019 17:50:36: #2 predicted fragment length is 140 bps INFO @ Mon, 12 Aug 2019 17:50:36: #2 alternative fragment length(s) may be 4,140 bps INFO @ Mon, 12 Aug 2019 17:50:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.05_model.r INFO @ Mon, 12 Aug 2019 17:50:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:50:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:50:36: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:50:36: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:50:36: #1 total tags in treatment: 3687745 INFO @ Mon, 12 Aug 2019 17:50:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:50:36: #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 17:50:36: #1 tags after filtering in treatment: 3687745 INFO @ Mon, 12 Aug 2019 17:50:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:50:36: #1 finished! INFO @ Mon, 12 Aug 2019 17:50:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:50:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:50:37: #2 number of paired peaks: 3250 INFO @ Mon, 12 Aug 2019 17:50:37: start model_add_line... INFO @ Mon, 12 Aug 2019 17:50:37: start X-correlation... INFO @ Mon, 12 Aug 2019 17:50:37: end of X-cor INFO @ Mon, 12 Aug 2019 17:50:37: #2 finished! INFO @ Mon, 12 Aug 2019 17:50:37: #2 predicted fragment length is 140 bps INFO @ Mon, 12 Aug 2019 17:50:37: #2 alternative fragment length(s) may be 4,140 bps INFO @ Mon, 12 Aug 2019 17:50:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.10_model.r INFO @ Mon, 12 Aug 2019 17:50:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:50:40: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:50:40: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:50:40: #1 total tags in treatment: 3687745 INFO @ Mon, 12 Aug 2019 17:50:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:50:40: #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 17:50:40: #1 tags after filtering in treatment: 3687745 INFO @ Mon, 12 Aug 2019 17:50:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:50:40: #1 finished! INFO @ Mon, 12 Aug 2019 17:50:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:50:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:50:40: #2 number of paired peaks: 3250 INFO @ Mon, 12 Aug 2019 17:50:40: start model_add_line... INFO @ Mon, 12 Aug 2019 17:50:41: start X-correlation... INFO @ Mon, 12 Aug 2019 17:50:41: end of X-cor INFO @ Mon, 12 Aug 2019 17:50:41: #2 finished! INFO @ Mon, 12 Aug 2019 17:50:41: #2 predicted fragment length is 140 bps INFO @ Mon, 12 Aug 2019 17:50:41: #2 alternative fragment length(s) may be 4,140 bps INFO @ Mon, 12 Aug 2019 17:50:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.20_model.r INFO @ Mon, 12 Aug 2019 17:50:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:50:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:50:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:50:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:50:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.05_summits.bed INFO @ Mon, 12 Aug 2019 17:50:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3028 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:50:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:50:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:50:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.10_summits.bed INFO @ Mon, 12 Aug 2019 17:50:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1003 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:50:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:50:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:50:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX188614/SRX188614.20_summits.bed INFO @ Mon, 12 Aug 2019 17:50:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (251 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。