Job ID = 1292036 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,427,841 reads read : 12,427,841 reads written : 12,427,841 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: 00:01:30 12427841 reads; of these: 12427841 (100.00%) were unpaired; of these: 5081719 (40.89%) aligned 0 times 5816247 (46.80%) aligned exactly 1 time 1529875 (12.31%) aligned >1 times 59.11% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 2169682 / 7346122 = 0.2954 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 17:18:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.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 17:18:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:18:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:18:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.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 17:18:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:18:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:18:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.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 17:18:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:18:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:18:35: 1000000 INFO @ Sun, 02 Jun 2019 17:18:36: 1000000 INFO @ Sun, 02 Jun 2019 17:18:36: 1000000 INFO @ Sun, 02 Jun 2019 17:18:42: 2000000 INFO @ Sun, 02 Jun 2019 17:18:42: 2000000 INFO @ Sun, 02 Jun 2019 17:18:43: 2000000 INFO @ Sun, 02 Jun 2019 17:18:48: 3000000 INFO @ Sun, 02 Jun 2019 17:18:49: 3000000 INFO @ Sun, 02 Jun 2019 17:18:50: 3000000 INFO @ Sun, 02 Jun 2019 17:18:54: 4000000 INFO @ Sun, 02 Jun 2019 17:18:56: 4000000 INFO @ Sun, 02 Jun 2019 17:18:57: 4000000 INFO @ Sun, 02 Jun 2019 17:19:00: 5000000 INFO @ Sun, 02 Jun 2019 17:19:02: #1 tag size is determined as 35 bps INFO @ Sun, 02 Jun 2019 17:19:02: #1 tag size = 35 INFO @ Sun, 02 Jun 2019 17:19:02: #1 total tags in treatment: 5176440 INFO @ Sun, 02 Jun 2019 17:19:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:19:02: #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 17:19:02: #1 tags after filtering in treatment: 5176440 INFO @ Sun, 02 Jun 2019 17:19:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:19:02: #1 finished! INFO @ Sun, 02 Jun 2019 17:19:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:19:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:19:02: #2 number of paired peaks: 283 WARNING @ Sun, 02 Jun 2019 17:19:02: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Sun, 02 Jun 2019 17:19:02: start model_add_line... INFO @ Sun, 02 Jun 2019 17:19:02: start X-correlation... INFO @ Sun, 02 Jun 2019 17:19:02: end of X-cor INFO @ Sun, 02 Jun 2019 17:19:02: #2 finished! INFO @ Sun, 02 Jun 2019 17:19:02: #2 predicted fragment length is 169 bps INFO @ Sun, 02 Jun 2019 17:19:02: #2 alternative fragment length(s) may be 169,598 bps INFO @ Sun, 02 Jun 2019 17:19:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.20_model.r INFO @ Sun, 02 Jun 2019 17:19:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:19:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:19:02: 5000000 INFO @ Sun, 02 Jun 2019 17:19:04: #1 tag size is determined as 35 bps INFO @ Sun, 02 Jun 2019 17:19:04: #1 tag size = 35 INFO @ Sun, 02 Jun 2019 17:19:04: #1 total tags in treatment: 5176440 INFO @ Sun, 02 Jun 2019 17:19:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:19:04: #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 17:19:04: #1 tags after filtering in treatment: 5176440 INFO @ Sun, 02 Jun 2019 17:19:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:19:04: #1 finished! INFO @ Sun, 02 Jun 2019 17:19:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:19:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:19:04: #2 number of paired peaks: 283 WARNING @ Sun, 02 Jun 2019 17:19:04: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Sun, 02 Jun 2019 17:19:04: start model_add_line... INFO @ Sun, 02 Jun 2019 17:19:04: start X-correlation... INFO @ Sun, 02 Jun 2019 17:19:04: end of X-cor INFO @ Sun, 02 Jun 2019 17:19:04: #2 finished! INFO @ Sun, 02 Jun 2019 17:19:04: #2 predicted fragment length is 169 bps INFO @ Sun, 02 Jun 2019 17:19:04: #2 alternative fragment length(s) may be 169,598 bps INFO @ Sun, 02 Jun 2019 17:19:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.10_model.r INFO @ Sun, 02 Jun 2019 17:19:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:19:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:19:04: 5000000 INFO @ Sun, 02 Jun 2019 17:19:06: #1 tag size is determined as 35 bps INFO @ Sun, 02 Jun 2019 17:19:06: #1 tag size = 35 INFO @ Sun, 02 Jun 2019 17:19:06: #1 total tags in treatment: 5176440 INFO @ Sun, 02 Jun 2019 17:19:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:19:06: #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 17:19:06: #1 tags after filtering in treatment: 5176440 INFO @ Sun, 02 Jun 2019 17:19:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:19:06: #1 finished! INFO @ Sun, 02 Jun 2019 17:19:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:19:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:19:06: #2 number of paired peaks: 283 WARNING @ Sun, 02 Jun 2019 17:19:06: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Sun, 02 Jun 2019 17:19:06: start model_add_line... INFO @ Sun, 02 Jun 2019 17:19:06: start X-correlation... INFO @ Sun, 02 Jun 2019 17:19:06: end of X-cor INFO @ Sun, 02 Jun 2019 17:19:06: #2 finished! INFO @ Sun, 02 Jun 2019 17:19:06: #2 predicted fragment length is 169 bps INFO @ Sun, 02 Jun 2019 17:19:06: #2 alternative fragment length(s) may be 169,598 bps INFO @ Sun, 02 Jun 2019 17:19:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.05_model.r INFO @ Sun, 02 Jun 2019 17:19:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:19:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:19:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:19:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:19:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:19:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:19:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:19:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.20_summits.bed INFO @ Sun, 02 Jun 2019 17:19:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (203 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:19:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:19:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:19:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.10_summits.bed INFO @ Sun, 02 Jun 2019 17:19:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (508 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:19:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:19:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:19:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX323682/SRX323682.05_summits.bed INFO @ Sun, 02 Jun 2019 17:19:31: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2176 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。