Job ID = 1292469 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,602,844 reads read : 8,602,844 reads written : 8,602,844 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:01:43 8602844 reads; of these: 8602844 (100.00%) were unpaired; of these: 242764 (2.82%) aligned 0 times 7183888 (83.51%) aligned exactly 1 time 1176192 (13.67%) aligned >1 times 97.18% overall alignment rate Time searching: 00:01:43 Overall time: 00:01:43 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] 608089 / 8360080 = 0.0727 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 @ Sun, 02 Jun 2019 19:09:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.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 @ Sun, 02 Jun 2019 19:09:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:09:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:09:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.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 @ Sun, 02 Jun 2019 19:09:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:09:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:09:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.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 @ Sun, 02 Jun 2019 19:09:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:09:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:09:30: 1000000 INFO @ Sun, 02 Jun 2019 19:09:30: 1000000 INFO @ Sun, 02 Jun 2019 19:09:30: 1000000 INFO @ Sun, 02 Jun 2019 19:09:37: 2000000 INFO @ Sun, 02 Jun 2019 19:09:38: 2000000 INFO @ Sun, 02 Jun 2019 19:09:38: 2000000 INFO @ Sun, 02 Jun 2019 19:09:45: 3000000 INFO @ Sun, 02 Jun 2019 19:09:45: 3000000 INFO @ Sun, 02 Jun 2019 19:09:46: 3000000 INFO @ Sun, 02 Jun 2019 19:09:52: 4000000 INFO @ Sun, 02 Jun 2019 19:09:53: 4000000 INFO @ Sun, 02 Jun 2019 19:09:53: 4000000 INFO @ Sun, 02 Jun 2019 19:10:00: 5000000 INFO @ Sun, 02 Jun 2019 19:10:01: 5000000 INFO @ Sun, 02 Jun 2019 19:10:01: 5000000 INFO @ Sun, 02 Jun 2019 19:10:08: 6000000 INFO @ Sun, 02 Jun 2019 19:10:08: 6000000 INFO @ Sun, 02 Jun 2019 19:10:09: 6000000 INFO @ Sun, 02 Jun 2019 19:10:15: 7000000 INFO @ Sun, 02 Jun 2019 19:10:16: 7000000 INFO @ Sun, 02 Jun 2019 19:10:17: 7000000 INFO @ Sun, 02 Jun 2019 19:10:21: #1 tag size is determined as 35 bps INFO @ Sun, 02 Jun 2019 19:10:21: #1 tag size = 35 INFO @ Sun, 02 Jun 2019 19:10:21: #1 total tags in treatment: 7751991 INFO @ Sun, 02 Jun 2019 19:10:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:10:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:10:21: #1 tags after filtering in treatment: 7751991 INFO @ Sun, 02 Jun 2019 19:10:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:10:21: #1 finished! INFO @ Sun, 02 Jun 2019 19:10:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:10:22: #1 tag size is determined as 35 bps INFO @ Sun, 02 Jun 2019 19:10:22: #1 tag size = 35 INFO @ Sun, 02 Jun 2019 19:10:22: #1 total tags in treatment: 7751991 INFO @ Sun, 02 Jun 2019 19:10:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:10:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:10:22: #2 number of paired peaks: 289 WARNING @ Sun, 02 Jun 2019 19:10:22: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Sun, 02 Jun 2019 19:10:22: start model_add_line... INFO @ Sun, 02 Jun 2019 19:10:22: start X-correlation... INFO @ Sun, 02 Jun 2019 19:10:22: #1 tags after filtering in treatment: 7751991 INFO @ Sun, 02 Jun 2019 19:10:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:10:22: #1 finished! INFO @ Sun, 02 Jun 2019 19:10:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:10:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:10:22: end of X-cor INFO @ Sun, 02 Jun 2019 19:10:22: #2 finished! INFO @ Sun, 02 Jun 2019 19:10:22: #2 predicted fragment length is 100 bps INFO @ Sun, 02 Jun 2019 19:10:22: #2 alternative fragment length(s) may be 4,39,63,84,100 bps INFO @ Sun, 02 Jun 2019 19:10:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.05_model.r INFO @ Sun, 02 Jun 2019 19:10:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:10:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:10:22: #1 tag size is determined as 35 bps INFO @ Sun, 02 Jun 2019 19:10:22: #1 tag size = 35 INFO @ Sun, 02 Jun 2019 19:10:22: #1 total tags in treatment: 7751991 INFO @ Sun, 02 Jun 2019 19:10:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:10:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:10:23: #1 tags after filtering in treatment: 7751991 INFO @ Sun, 02 Jun 2019 19:10:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:10:23: #1 finished! INFO @ Sun, 02 Jun 2019 19:10:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:10:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:10:23: #2 number of paired peaks: 289 WARNING @ Sun, 02 Jun 2019 19:10:23: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Sun, 02 Jun 2019 19:10:23: start model_add_line... INFO @ Sun, 02 Jun 2019 19:10:23: start X-correlation... INFO @ Sun, 02 Jun 2019 19:10:23: end of X-cor INFO @ Sun, 02 Jun 2019 19:10:23: #2 finished! INFO @ Sun, 02 Jun 2019 19:10:23: #2 predicted fragment length is 100 bps INFO @ Sun, 02 Jun 2019 19:10:23: #2 alternative fragment length(s) may be 4,39,63,84,100 bps INFO @ Sun, 02 Jun 2019 19:10:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.20_model.r INFO @ Sun, 02 Jun 2019 19:10:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:10:23: #2 number of paired peaks: 289 WARNING @ Sun, 02 Jun 2019 19:10:23: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Sun, 02 Jun 2019 19:10:23: start model_add_line... INFO @ Sun, 02 Jun 2019 19:10:23: start X-correlation... INFO @ Sun, 02 Jun 2019 19:10:23: end of X-cor INFO @ Sun, 02 Jun 2019 19:10:23: #2 finished! INFO @ Sun, 02 Jun 2019 19:10:23: #2 predicted fragment length is 100 bps INFO @ Sun, 02 Jun 2019 19:10:23: #2 alternative fragment length(s) may be 4,39,63,84,100 bps INFO @ Sun, 02 Jun 2019 19:10:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.10_model.r INFO @ Sun, 02 Jun 2019 19:10:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:10:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:10:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:10:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:10:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:10:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:10:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.05_summits.bed INFO @ Sun, 02 Jun 2019 19:10:57: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3856 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:10:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:10:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:10:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.20_summits.bed INFO @ Sun, 02 Jun 2019 19:10:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (230 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:10:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:10:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:10:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX463082/SRX463082.10_summits.bed INFO @ Sun, 02 Jun 2019 19:10:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1361 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。