Job ID = 1292030 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,253,546 reads read : 9,253,546 reads written : 9,253,546 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:37 9253546 reads; of these: 9253546 (100.00%) were unpaired; of these: 2801480 (30.27%) aligned 0 times 5412520 (58.49%) aligned exactly 1 time 1039546 (11.23%) aligned >1 times 69.73% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 2024214 / 6452066 = 0.3137 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 17:19:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.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 17:19:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:19:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:19:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.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 17:19:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:19:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:19:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.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 17:19:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:19:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:19:24: 1000000 INFO @ Sun, 02 Jun 2019 17:19:25: 1000000 INFO @ Sun, 02 Jun 2019 17:19:25: 1000000 INFO @ Sun, 02 Jun 2019 17:19:34: 2000000 INFO @ Sun, 02 Jun 2019 17:19:36: 2000000 INFO @ Sun, 02 Jun 2019 17:19:36: 2000000 INFO @ Sun, 02 Jun 2019 17:19:44: 3000000 INFO @ Sun, 02 Jun 2019 17:19:47: 3000000 INFO @ Sun, 02 Jun 2019 17:19:47: 3000000 INFO @ Sun, 02 Jun 2019 17:19:54: 4000000 INFO @ Sun, 02 Jun 2019 17:19:58: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:19:58: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:19:58: #1 total tags in treatment: 4427852 INFO @ Sun, 02 Jun 2019 17:19:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:19:58: #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 17:19:58: 4000000 INFO @ Sun, 02 Jun 2019 17:19:58: 4000000 INFO @ Sun, 02 Jun 2019 17:19:58: #1 tags after filtering in treatment: 4427852 INFO @ Sun, 02 Jun 2019 17:19:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:19:58: #1 finished! INFO @ Sun, 02 Jun 2019 17:19:58: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:19:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:19:58: #2 number of paired peaks: 163 WARNING @ Sun, 02 Jun 2019 17:19:58: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Sun, 02 Jun 2019 17:19:58: start model_add_line... INFO @ Sun, 02 Jun 2019 17:19:58: start X-correlation... INFO @ Sun, 02 Jun 2019 17:19:58: end of X-cor INFO @ Sun, 02 Jun 2019 17:19:58: #2 finished! INFO @ Sun, 02 Jun 2019 17:19:58: #2 predicted fragment length is 131 bps INFO @ Sun, 02 Jun 2019 17:19:58: #2 alternative fragment length(s) may be 4,131,151,598 bps INFO @ Sun, 02 Jun 2019 17:19:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.10_model.r INFO @ Sun, 02 Jun 2019 17:19:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:19:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:20:02: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:20:02: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:20:02: #1 total tags in treatment: 4427852 INFO @ Sun, 02 Jun 2019 17:20:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:20:02: #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 17:20:02: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:20:02: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:20:02: #1 total tags in treatment: 4427852 INFO @ Sun, 02 Jun 2019 17:20:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:20:02: #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 17:20:02: #1 tags after filtering in treatment: 4427852 INFO @ Sun, 02 Jun 2019 17:20:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:20:02: #1 finished! INFO @ Sun, 02 Jun 2019 17:20:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:20:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:20:02: #1 tags after filtering in treatment: 4427852 INFO @ Sun, 02 Jun 2019 17:20:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:20:02: #1 finished! INFO @ Sun, 02 Jun 2019 17:20:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:20:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:20:02: #2 number of paired peaks: 163 WARNING @ Sun, 02 Jun 2019 17:20:02: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Sun, 02 Jun 2019 17:20:02: start model_add_line... INFO @ Sun, 02 Jun 2019 17:20:02: start X-correlation... INFO @ Sun, 02 Jun 2019 17:20:02: #2 number of paired peaks: 163 WARNING @ Sun, 02 Jun 2019 17:20:02: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Sun, 02 Jun 2019 17:20:02: start model_add_line... INFO @ Sun, 02 Jun 2019 17:20:02: end of X-cor INFO @ Sun, 02 Jun 2019 17:20:02: #2 finished! INFO @ Sun, 02 Jun 2019 17:20:02: #2 predicted fragment length is 131 bps INFO @ Sun, 02 Jun 2019 17:20:02: #2 alternative fragment length(s) may be 4,131,151,598 bps INFO @ Sun, 02 Jun 2019 17:20:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.20_model.r INFO @ Sun, 02 Jun 2019 17:20:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:20:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:20:03: start X-correlation... INFO @ Sun, 02 Jun 2019 17:20:03: end of X-cor INFO @ Sun, 02 Jun 2019 17:20:03: #2 finished! INFO @ Sun, 02 Jun 2019 17:20:03: #2 predicted fragment length is 131 bps INFO @ Sun, 02 Jun 2019 17:20:03: #2 alternative fragment length(s) may be 4,131,151,598 bps INFO @ Sun, 02 Jun 2019 17:20:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.05_model.r INFO @ Sun, 02 Jun 2019 17:20:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:20:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:20:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:20:16: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:20:16: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:20:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:20:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:20:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.10_summits.bed INFO @ Sun, 02 Jun 2019 17:20:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (124 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:20:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:20:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:20:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.20_summits.bed INFO @ Sun, 02 Jun 2019 17:20:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:20:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:20:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:20:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX323677/SRX323677.05_summits.bed INFO @ Sun, 02 Jun 2019 17:20:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (292 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。