Job ID = 4303031 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,199,658 reads read : 8,199,658 reads written : 8,199,658 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947507.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: 00:01:10 8199658 reads; of these: 8199658 (100.00%) were unpaired; of these: 2781655 (33.92%) aligned 0 times 4708433 (57.42%) aligned exactly 1 time 709570 (8.65%) aligned >1 times 66.08% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 2139185 / 5418003 = 0.3948 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:33:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.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 @ Thu, 12 Dec 2019 00:33:58: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:33:58: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:34:05: 1000000 INFO @ Thu, 12 Dec 2019 00:34:12: 2000000 INFO @ Thu, 12 Dec 2019 00:34:19: 3000000 INFO @ Thu, 12 Dec 2019 00:34:21: #1 tag size is determined as 32 bps INFO @ Thu, 12 Dec 2019 00:34:21: #1 tag size = 32 INFO @ Thu, 12 Dec 2019 00:34:21: #1 total tags in treatment: 3278818 INFO @ Thu, 12 Dec 2019 00:34:21: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:34:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:34:21: #1 tags after filtering in treatment: 3278818 INFO @ Thu, 12 Dec 2019 00:34:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:34:21: #1 finished! INFO @ Thu, 12 Dec 2019 00:34:21: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:34:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:34:22: #2 number of paired peaks: 1736 INFO @ Thu, 12 Dec 2019 00:34:22: start model_add_line... INFO @ Thu, 12 Dec 2019 00:34:22: start X-correlation... INFO @ Thu, 12 Dec 2019 00:34:22: end of X-cor INFO @ Thu, 12 Dec 2019 00:34:22: #2 finished! INFO @ Thu, 12 Dec 2019 00:34:22: #2 predicted fragment length is 145 bps INFO @ Thu, 12 Dec 2019 00:34:22: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 12 Dec 2019 00:34:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.05_model.r INFO @ Thu, 12 Dec 2019 00:34:22: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:34:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:34:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.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 @ Thu, 12 Dec 2019 00:34:26: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:34:26: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:34:33: 1000000 INFO @ Thu, 12 Dec 2019 00:34:33: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:34:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:34:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:34:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.05_summits.bed INFO @ Thu, 12 Dec 2019 00:34:38: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (5021 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:34:39: 2000000 INFO @ Thu, 12 Dec 2019 00:34:46: 3000000 INFO @ Thu, 12 Dec 2019 00:34:48: #1 tag size is determined as 32 bps INFO @ Thu, 12 Dec 2019 00:34:48: #1 tag size = 32 INFO @ Thu, 12 Dec 2019 00:34:48: #1 total tags in treatment: 3278818 INFO @ Thu, 12 Dec 2019 00:34:48: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:34:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:34:48: #1 tags after filtering in treatment: 3278818 INFO @ Thu, 12 Dec 2019 00:34:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:34:48: #1 finished! INFO @ Thu, 12 Dec 2019 00:34:48: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:34:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:34:48: #2 number of paired peaks: 1736 INFO @ Thu, 12 Dec 2019 00:34:48: start model_add_line... INFO @ Thu, 12 Dec 2019 00:34:48: start X-correlation... INFO @ Thu, 12 Dec 2019 00:34:48: end of X-cor INFO @ Thu, 12 Dec 2019 00:34:48: #2 finished! INFO @ Thu, 12 Dec 2019 00:34:48: #2 predicted fragment length is 145 bps INFO @ Thu, 12 Dec 2019 00:34:48: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 12 Dec 2019 00:34:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.10_model.r INFO @ Thu, 12 Dec 2019 00:34:48: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:34:48: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:34:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.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 @ Thu, 12 Dec 2019 00:34:56: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:34:56: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:34:59: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:35:02: 1000000 INFO @ Thu, 12 Dec 2019 00:35:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:35:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:35:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.10_summits.bed INFO @ Thu, 12 Dec 2019 00:35:04: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3414 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:35:08: 2000000 INFO @ Thu, 12 Dec 2019 00:35:15: 3000000 INFO @ Thu, 12 Dec 2019 00:35:16: #1 tag size is determined as 32 bps INFO @ Thu, 12 Dec 2019 00:35:16: #1 tag size = 32 INFO @ Thu, 12 Dec 2019 00:35:16: #1 total tags in treatment: 3278818 INFO @ Thu, 12 Dec 2019 00:35:16: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:35:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:35:17: #1 tags after filtering in treatment: 3278818 INFO @ Thu, 12 Dec 2019 00:35:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:35:17: #1 finished! INFO @ Thu, 12 Dec 2019 00:35:17: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:35:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:35:17: #2 number of paired peaks: 1736 INFO @ Thu, 12 Dec 2019 00:35:17: start model_add_line... INFO @ Thu, 12 Dec 2019 00:35:17: start X-correlation... INFO @ Thu, 12 Dec 2019 00:35:17: end of X-cor INFO @ Thu, 12 Dec 2019 00:35:17: #2 finished! INFO @ Thu, 12 Dec 2019 00:35:17: #2 predicted fragment length is 145 bps INFO @ Thu, 12 Dec 2019 00:35:17: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 12 Dec 2019 00:35:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.20_model.r INFO @ Thu, 12 Dec 2019 00:35:17: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:35:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:35:28: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:35:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:35:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:35:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331272/SRX331272.20_summits.bed INFO @ Thu, 12 Dec 2019 00:35:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1700 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。