Job ID = 1291663 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,271,448 reads read : 22,271,448 reads written : 22,271,448 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: 00:05:02 22271448 reads; of these: 22271448 (100.00%) were unpaired; of these: 8706557 (39.09%) aligned 0 times 9226875 (41.43%) aligned exactly 1 time 4338016 (19.48%) aligned >1 times 60.91% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5601794 / 13564891 = 0.4130 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 16:21:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.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 16:21:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:21:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:21:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.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 16:21:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:21:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:21:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.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 16:21:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:21:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:21:59: 1000000 INFO @ Sun, 02 Jun 2019 16:21:59: 1000000 INFO @ Sun, 02 Jun 2019 16:21:59: 1000000 INFO @ Sun, 02 Jun 2019 16:22:07: 2000000 INFO @ Sun, 02 Jun 2019 16:22:07: 2000000 INFO @ Sun, 02 Jun 2019 16:22:07: 2000000 INFO @ Sun, 02 Jun 2019 16:22:14: 3000000 INFO @ Sun, 02 Jun 2019 16:22:14: 3000000 INFO @ Sun, 02 Jun 2019 16:22:14: 3000000 INFO @ Sun, 02 Jun 2019 16:22:21: 4000000 INFO @ Sun, 02 Jun 2019 16:22:22: 4000000 INFO @ Sun, 02 Jun 2019 16:22:22: 4000000 INFO @ Sun, 02 Jun 2019 16:22:28: 5000000 INFO @ Sun, 02 Jun 2019 16:22:29: 5000000 INFO @ Sun, 02 Jun 2019 16:22:29: 5000000 INFO @ Sun, 02 Jun 2019 16:22:35: 6000000 INFO @ Sun, 02 Jun 2019 16:22:36: 6000000 INFO @ Sun, 02 Jun 2019 16:22:36: 6000000 INFO @ Sun, 02 Jun 2019 16:22:42: 7000000 INFO @ Sun, 02 Jun 2019 16:22:44: 7000000 INFO @ Sun, 02 Jun 2019 16:22:44: 7000000 INFO @ Sun, 02 Jun 2019 16:22:49: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 16:22:49: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 16:22:49: #1 total tags in treatment: 7963097 INFO @ Sun, 02 Jun 2019 16:22:49: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:22:49: #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 16:22:49: #1 tags after filtering in treatment: 7963097 INFO @ Sun, 02 Jun 2019 16:22:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:22:49: #1 finished! INFO @ Sun, 02 Jun 2019 16:22:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:22:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:22:50: #2 number of paired peaks: 915 WARNING @ Sun, 02 Jun 2019 16:22:50: Fewer paired peaks (915) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 915 pairs to build model! INFO @ Sun, 02 Jun 2019 16:22:50: start model_add_line... INFO @ Sun, 02 Jun 2019 16:22:50: start X-correlation... INFO @ Sun, 02 Jun 2019 16:22:50: end of X-cor INFO @ Sun, 02 Jun 2019 16:22:50: #2 finished! INFO @ Sun, 02 Jun 2019 16:22:50: #2 predicted fragment length is 217 bps INFO @ Sun, 02 Jun 2019 16:22:50: #2 alternative fragment length(s) may be 217 bps INFO @ Sun, 02 Jun 2019 16:22:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.05_model.r INFO @ Sun, 02 Jun 2019 16:22:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:22:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:22:51: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 16:22:51: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 16:22:51: #1 total tags in treatment: 7963097 INFO @ Sun, 02 Jun 2019 16:22:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:22:51: #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 16:22:51: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 16:22:51: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 16:22:51: #1 total tags in treatment: 7963097 INFO @ Sun, 02 Jun 2019 16:22:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:22:51: #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 16:22:51: #1 tags after filtering in treatment: 7963097 INFO @ Sun, 02 Jun 2019 16:22:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:22:51: #1 finished! INFO @ Sun, 02 Jun 2019 16:22:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:22:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:22:51: #1 tags after filtering in treatment: 7963097 INFO @ Sun, 02 Jun 2019 16:22:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:22:51: #1 finished! INFO @ Sun, 02 Jun 2019 16:22:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:22:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:22:52: #2 number of paired peaks: 915 WARNING @ Sun, 02 Jun 2019 16:22:52: Fewer paired peaks (915) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 915 pairs to build model! INFO @ Sun, 02 Jun 2019 16:22:52: start model_add_line... INFO @ Sun, 02 Jun 2019 16:22:52: #2 number of paired peaks: 915 WARNING @ Sun, 02 Jun 2019 16:22:52: Fewer paired peaks (915) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 915 pairs to build model! INFO @ Sun, 02 Jun 2019 16:22:52: start model_add_line... INFO @ Sun, 02 Jun 2019 16:22:52: start X-correlation... INFO @ Sun, 02 Jun 2019 16:22:52: end of X-cor INFO @ Sun, 02 Jun 2019 16:22:52: #2 finished! INFO @ Sun, 02 Jun 2019 16:22:52: #2 predicted fragment length is 217 bps INFO @ Sun, 02 Jun 2019 16:22:52: #2 alternative fragment length(s) may be 217 bps INFO @ Sun, 02 Jun 2019 16:22:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.10_model.r INFO @ Sun, 02 Jun 2019 16:22:52: start X-correlation... INFO @ Sun, 02 Jun 2019 16:22:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:22:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:22:52: end of X-cor INFO @ Sun, 02 Jun 2019 16:22:52: #2 finished! INFO @ Sun, 02 Jun 2019 16:22:52: #2 predicted fragment length is 217 bps INFO @ Sun, 02 Jun 2019 16:22:52: #2 alternative fragment length(s) may be 217 bps INFO @ Sun, 02 Jun 2019 16:22:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.20_model.r INFO @ Sun, 02 Jun 2019 16:22:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:22:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:23:16: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:23:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:23:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:23:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:23:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:23:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.05_summits.bed INFO @ Sun, 02 Jun 2019 16:23:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1178 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:23:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:23:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:23:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.10_summits.bed INFO @ Sun, 02 Jun 2019 16:23:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (871 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:23:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:23:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:23:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769991/SRX1769991.20_summits.bed INFO @ Sun, 02 Jun 2019 16:23:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (650 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。