Job ID = 2640414 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,396,816 reads read : 27,396,816 reads written : 27,396,816 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR399330.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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:56 27396816 reads; of these: 27396816 (100.00%) were unpaired; of these: 20383872 (74.40%) aligned 0 times 5253621 (19.18%) aligned exactly 1 time 1759323 (6.42%) aligned >1 times 25.60% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 4260491 / 7012944 = 0.6075 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 16:30:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 16:30:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:30:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:30:15: 1000000 INFO @ Sat, 24 Aug 2019 16:30:22: 2000000 INFO @ Sat, 24 Aug 2019 16:30:28: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 16:30:28: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 16:30:28: #1 total tags in treatment: 2752453 INFO @ Sat, 24 Aug 2019 16:30:28: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:30:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:30:28: #1 tags after filtering in treatment: 2752156 INFO @ Sat, 24 Aug 2019 16:30:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:30:28: #1 finished! INFO @ Sat, 24 Aug 2019 16:30:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:30:32: #2 number of paired peaks: 81032 INFO @ Sat, 24 Aug 2019 16:30:32: start model_add_line... INFO @ Sat, 24 Aug 2019 16:30:32: start X-correlation... INFO @ Sat, 24 Aug 2019 16:30:32: end of X-cor INFO @ Sat, 24 Aug 2019 16:30:32: #2 finished! INFO @ Sat, 24 Aug 2019 16:30:32: #2 predicted fragment length is 79 bps INFO @ Sat, 24 Aug 2019 16:30:32: #2 alternative fragment length(s) may be 79 bps INFO @ Sat, 24 Aug 2019 16:30:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.05_model.r INFO @ Sat, 24 Aug 2019 16:30:32: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:30:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:30:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 16:30:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:30:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:30:41: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:30:45: 1000000 INFO @ Sat, 24 Aug 2019 16:30:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.05_peaks.xls INFO @ Sat, 24 Aug 2019 16:30:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:30:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.05_summits.bed INFO @ Sat, 24 Aug 2019 16:30:46: Done! pass1 - making usageList (57 chroms): 2 millis pass2 - checking and writing primary data (715 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 16:30:51: 2000000 INFO @ Sat, 24 Aug 2019 16:30:57: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 16:30:57: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 16:30:57: #1 total tags in treatment: 2752453 INFO @ Sat, 24 Aug 2019 16:30:57: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:30:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:30:57: #1 tags after filtering in treatment: 2752156 INFO @ Sat, 24 Aug 2019 16:30:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:30:57: #1 finished! INFO @ Sat, 24 Aug 2019 16:30:57: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:30:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:31:01: #2 number of paired peaks: 81032 INFO @ Sat, 24 Aug 2019 16:31:01: start model_add_line... INFO @ Sat, 24 Aug 2019 16:31:01: start X-correlation... INFO @ Sat, 24 Aug 2019 16:31:01: end of X-cor INFO @ Sat, 24 Aug 2019 16:31:01: #2 finished! INFO @ Sat, 24 Aug 2019 16:31:01: #2 predicted fragment length is 79 bps INFO @ Sat, 24 Aug 2019 16:31:01: #2 alternative fragment length(s) may be 79 bps INFO @ Sat, 24 Aug 2019 16:31:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.10_model.r INFO @ Sat, 24 Aug 2019 16:31:01: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:31:01: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Sat, 24 Aug 2019 16:31:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 16:31:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:31:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:31:11: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:31:14: 1000000 INFO @ Sat, 24 Aug 2019 16:31:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.10_peaks.xls INFO @ Sat, 24 Aug 2019 16:31:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:31:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.10_summits.bed INFO @ Sat, 24 Aug 2019 16:31:15: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (275 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 16:31:21: 2000000 INFO @ Sat, 24 Aug 2019 16:31:26: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 16:31:26: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 16:31:26: #1 total tags in treatment: 2752453 INFO @ Sat, 24 Aug 2019 16:31:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:31:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:31:26: #1 tags after filtering in treatment: 2752156 INFO @ Sat, 24 Aug 2019 16:31:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:31:26: #1 finished! INFO @ Sat, 24 Aug 2019 16:31:26: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:31:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:31:30: #2 number of paired peaks: 81032 INFO @ Sat, 24 Aug 2019 16:31:30: start model_add_line... INFO @ Sat, 24 Aug 2019 16:31:30: start X-correlation... INFO @ Sat, 24 Aug 2019 16:31:30: end of X-cor INFO @ Sat, 24 Aug 2019 16:31:30: #2 finished! INFO @ Sat, 24 Aug 2019 16:31:30: #2 predicted fragment length is 79 bps INFO @ Sat, 24 Aug 2019 16:31:30: #2 alternative fragment length(s) may be 79 bps INFO @ Sat, 24 Aug 2019 16:31:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.20_model.r INFO @ Sat, 24 Aug 2019 16:31:30: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:31:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:31:39: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:31:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.20_peaks.xls INFO @ Sat, 24 Aug 2019 16:31:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:31:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116052/SRX116052.20_summits.bed INFO @ Sat, 24 Aug 2019 16:31:44: Done! pass1 - making usageList (31 chroms): 2 millis pass2 - checking and writing primary data (89 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。