Job ID = 2589774 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,574,869 reads read : 2,574,869 reads written : 2,574,869 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947383.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: 00:00:19 2574869 reads; of these: 2574869 (100.00%) were unpaired; of these: 1022547 (39.71%) aligned 0 times 1356166 (52.67%) aligned exactly 1 time 196156 (7.62%) aligned >1 times 60.29% overall alignment rate Time searching: 00:00:19 Overall time: 00:00:19 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] 193684 / 1552322 = 0.1248 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 18:26:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.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 18:26:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:26:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:26:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.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 18:26:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:26:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:26:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.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 18:26:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:26:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:26:27: 1000000 INFO @ Mon, 12 Aug 2019 18:26:29: 1000000 INFO @ Mon, 12 Aug 2019 18:26:30: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:26:30: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:26:30: #1 total tags in treatment: 1358638 INFO @ Mon, 12 Aug 2019 18:26:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:26:30: #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 18:26:30: #1 tags after filtering in treatment: 1358638 INFO @ Mon, 12 Aug 2019 18:26:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:26:30: #1 finished! INFO @ Mon, 12 Aug 2019 18:26:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:26:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:26:30: #2 number of paired peaks: 2269 INFO @ Mon, 12 Aug 2019 18:26:30: start model_add_line... INFO @ Mon, 12 Aug 2019 18:26:30: start X-correlation... INFO @ Mon, 12 Aug 2019 18:26:30: end of X-cor INFO @ Mon, 12 Aug 2019 18:26:30: #2 finished! INFO @ Mon, 12 Aug 2019 18:26:30: #2 predicted fragment length is 175 bps INFO @ Mon, 12 Aug 2019 18:26:30: #2 alternative fragment length(s) may be 175 bps INFO @ Mon, 12 Aug 2019 18:26:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.05_model.r INFO @ Mon, 12 Aug 2019 18:26:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:26:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:26:31: 1000000 INFO @ Mon, 12 Aug 2019 18:26:32: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:26:32: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:26:32: #1 total tags in treatment: 1358638 INFO @ Mon, 12 Aug 2019 18:26:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:26:32: #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 18:26:32: #1 tags after filtering in treatment: 1358638 INFO @ Mon, 12 Aug 2019 18:26:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:26:32: #1 finished! INFO @ Mon, 12 Aug 2019 18:26:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:26:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:26:32: #2 number of paired peaks: 2269 INFO @ Mon, 12 Aug 2019 18:26:32: start model_add_line... INFO @ Mon, 12 Aug 2019 18:26:32: start X-correlation... INFO @ Mon, 12 Aug 2019 18:26:32: end of X-cor INFO @ Mon, 12 Aug 2019 18:26:32: #2 finished! INFO @ Mon, 12 Aug 2019 18:26:32: #2 predicted fragment length is 175 bps INFO @ Mon, 12 Aug 2019 18:26:32: #2 alternative fragment length(s) may be 175 bps INFO @ Mon, 12 Aug 2019 18:26:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.10_model.r INFO @ Mon, 12 Aug 2019 18:26:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:26:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:26:34: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:26:34: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:26:34: #1 total tags in treatment: 1358638 INFO @ Mon, 12 Aug 2019 18:26:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:26:34: #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 18:26:34: #1 tags after filtering in treatment: 1358638 INFO @ Mon, 12 Aug 2019 18:26:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:26:34: #1 finished! INFO @ Mon, 12 Aug 2019 18:26:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:26:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:26:34: #2 number of paired peaks: 2269 INFO @ Mon, 12 Aug 2019 18:26:34: start model_add_line... INFO @ Mon, 12 Aug 2019 18:26:34: start X-correlation... INFO @ Mon, 12 Aug 2019 18:26:34: end of X-cor INFO @ Mon, 12 Aug 2019 18:26:34: #2 finished! INFO @ Mon, 12 Aug 2019 18:26:34: #2 predicted fragment length is 175 bps INFO @ Mon, 12 Aug 2019 18:26:34: #2 alternative fragment length(s) may be 175 bps INFO @ Mon, 12 Aug 2019 18:26:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.20_model.r INFO @ Mon, 12 Aug 2019 18:26:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:26:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:26:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:26:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:26:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:26:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.05_summits.bed INFO @ Mon, 12 Aug 2019 18:26:37: Done! INFO @ Mon, 12 Aug 2019 18:26:37: #3 Call peaks for each chromosome... pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2763 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:26:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:26:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:26:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:26:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.10_summits.bed INFO @ Mon, 12 Aug 2019 18:26:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1302 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:26:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:26:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:26:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331152/SRX331152.20_summits.bed INFO @ Mon, 12 Aug 2019 18:26:41: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (427 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。