Job ID = 1292925 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,587,074 reads read : 8,587,074 reads written : 8,587,074 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: 00:01:59 8587074 reads; of these: 8587074 (100.00%) were unpaired; of these: 481897 (5.61%) aligned 0 times 6762440 (78.75%) aligned exactly 1 time 1342737 (15.64%) aligned >1 times 94.39% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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] 629777 / 8105177 = 0.0777 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 21:09:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.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 21:09:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:09:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:09:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.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 21:09:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:09:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:09:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.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 21:09:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:09:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:09:24: 1000000 INFO @ Sun, 02 Jun 2019 21:09:24: 1000000 INFO @ Sun, 02 Jun 2019 21:09:25: 1000000 INFO @ Sun, 02 Jun 2019 21:09:33: 2000000 INFO @ Sun, 02 Jun 2019 21:09:33: 2000000 INFO @ Sun, 02 Jun 2019 21:09:36: 2000000 INFO @ Sun, 02 Jun 2019 21:09:42: 3000000 INFO @ Sun, 02 Jun 2019 21:09:42: 3000000 INFO @ Sun, 02 Jun 2019 21:09:47: 3000000 INFO @ Sun, 02 Jun 2019 21:09:50: 4000000 INFO @ Sun, 02 Jun 2019 21:09:50: 4000000 INFO @ Sun, 02 Jun 2019 21:09:57: 4000000 INFO @ Sun, 02 Jun 2019 21:09:57: 5000000 INFO @ Sun, 02 Jun 2019 21:09:58: 5000000 INFO @ Sun, 02 Jun 2019 21:10:05: 6000000 INFO @ Sun, 02 Jun 2019 21:10:06: 6000000 INFO @ Sun, 02 Jun 2019 21:10:07: 5000000 INFO @ Sun, 02 Jun 2019 21:10:13: 7000000 INFO @ Sun, 02 Jun 2019 21:10:14: 7000000 INFO @ Sun, 02 Jun 2019 21:10:17: 6000000 INFO @ Sun, 02 Jun 2019 21:10:17: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:10:17: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:10:17: #1 total tags in treatment: 7475400 INFO @ Sun, 02 Jun 2019 21:10:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:10:17: #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 21:10:17: #1 tags after filtering in treatment: 7475400 INFO @ Sun, 02 Jun 2019 21:10:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:10:17: #1 finished! INFO @ Sun, 02 Jun 2019 21:10:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:10:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:10:17: #2 number of paired peaks: 423 WARNING @ Sun, 02 Jun 2019 21:10:17: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Sun, 02 Jun 2019 21:10:17: start model_add_line... INFO @ Sun, 02 Jun 2019 21:10:17: start X-correlation... INFO @ Sun, 02 Jun 2019 21:10:18: end of X-cor INFO @ Sun, 02 Jun 2019 21:10:18: #2 finished! INFO @ Sun, 02 Jun 2019 21:10:18: #2 predicted fragment length is 107 bps INFO @ Sun, 02 Jun 2019 21:10:18: #2 alternative fragment length(s) may be 83,86,107 bps INFO @ Sun, 02 Jun 2019 21:10:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.10_model.r INFO @ Sun, 02 Jun 2019 21:10:18: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:10:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:10:18: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:10:18: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:10:18: #1 total tags in treatment: 7475400 INFO @ Sun, 02 Jun 2019 21:10:18: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:10:18: #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 21:10:18: #1 tags after filtering in treatment: 7475400 INFO @ Sun, 02 Jun 2019 21:10:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:10:18: #1 finished! INFO @ Sun, 02 Jun 2019 21:10:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:10:19: #2 number of paired peaks: 423 WARNING @ Sun, 02 Jun 2019 21:10:19: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Sun, 02 Jun 2019 21:10:19: start model_add_line... INFO @ Sun, 02 Jun 2019 21:10:19: start X-correlation... INFO @ Sun, 02 Jun 2019 21:10:19: end of X-cor INFO @ Sun, 02 Jun 2019 21:10:19: #2 finished! INFO @ Sun, 02 Jun 2019 21:10:19: #2 predicted fragment length is 107 bps INFO @ Sun, 02 Jun 2019 21:10:19: #2 alternative fragment length(s) may be 83,86,107 bps INFO @ Sun, 02 Jun 2019 21:10:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.20_model.r INFO @ Sun, 02 Jun 2019 21:10:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:10:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:10:25: 7000000 INFO @ Sun, 02 Jun 2019 21:10:29: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:10:29: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:10:29: #1 total tags in treatment: 7475400 INFO @ Sun, 02 Jun 2019 21:10:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:10:29: #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 21:10:29: #1 tags after filtering in treatment: 7475400 INFO @ Sun, 02 Jun 2019 21:10:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:10:29: #1 finished! INFO @ Sun, 02 Jun 2019 21:10:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:10:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:10:30: #2 number of paired peaks: 423 WARNING @ Sun, 02 Jun 2019 21:10:30: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Sun, 02 Jun 2019 21:10:30: start model_add_line... INFO @ Sun, 02 Jun 2019 21:10:30: start X-correlation... INFO @ Sun, 02 Jun 2019 21:10:30: end of X-cor INFO @ Sun, 02 Jun 2019 21:10:30: #2 finished! INFO @ Sun, 02 Jun 2019 21:10:30: #2 predicted fragment length is 107 bps INFO @ Sun, 02 Jun 2019 21:10:30: #2 alternative fragment length(s) may be 83,86,107 bps INFO @ Sun, 02 Jun 2019 21:10:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.05_model.r INFO @ Sun, 02 Jun 2019 21:10:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:10:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:10:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:10:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:10:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:10:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:10:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.10_summits.bed INFO @ Sun, 02 Jun 2019 21:10:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (547 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:10:52: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:10:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:10:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:10:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.20_summits.bed INFO @ Sun, 02 Jun 2019 21:10:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (190 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:11:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:11:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:11:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020717/SRX5020717.05_summits.bed INFO @ Sun, 02 Jun 2019 21:11:03: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1798 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。