Job ID = 1292786 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,485,227 reads read : 15,485,227 reads written : 15,485,227 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: 00:04:28 15485227 reads; of these: 15485227 (100.00%) were unpaired; of these: 4039522 (26.09%) aligned 0 times 9414017 (60.79%) aligned exactly 1 time 2031688 (13.12%) aligned >1 times 73.91% overall alignment rate Time searching: 00:04:28 Overall time: 00:04:28 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] 4184941 / 11445705 = 0.3656 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 20:34:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.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 20:34:24: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:34:24: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:34:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.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 20:34:24: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:34:24: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:34:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.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 20:34:24: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:34:24: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:34:39: 1000000 INFO @ Sun, 02 Jun 2019 20:34:39: 1000000 INFO @ Sun, 02 Jun 2019 20:34:40: 1000000 INFO @ Sun, 02 Jun 2019 20:34:53: 2000000 INFO @ Sun, 02 Jun 2019 20:34:55: 2000000 INFO @ Sun, 02 Jun 2019 20:34:55: 2000000 INFO @ Sun, 02 Jun 2019 20:35:07: 3000000 INFO @ Sun, 02 Jun 2019 20:35:10: 3000000 INFO @ Sun, 02 Jun 2019 20:35:10: 3000000 INFO @ Sun, 02 Jun 2019 20:35:21: 4000000 INFO @ Sun, 02 Jun 2019 20:35:26: 4000000 INFO @ Sun, 02 Jun 2019 20:35:26: 4000000 INFO @ Sun, 02 Jun 2019 20:35:35: 5000000 INFO @ Sun, 02 Jun 2019 20:35:41: 5000000 INFO @ Sun, 02 Jun 2019 20:35:41: 5000000 INFO @ Sun, 02 Jun 2019 20:35:48: 6000000 INFO @ Sun, 02 Jun 2019 20:35:57: 6000000 INFO @ Sun, 02 Jun 2019 20:35:57: 6000000 INFO @ Sun, 02 Jun 2019 20:36:03: 7000000 INFO @ Sun, 02 Jun 2019 20:36:06: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:36:06: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:36:06: #1 total tags in treatment: 7260764 INFO @ Sun, 02 Jun 2019 20:36:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:36:06: #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 20:36:07: #1 tags after filtering in treatment: 7260764 INFO @ Sun, 02 Jun 2019 20:36:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:36:07: #1 finished! INFO @ Sun, 02 Jun 2019 20:36:07: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:36:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:36:08: #2 number of paired peaks: 741 WARNING @ Sun, 02 Jun 2019 20:36:08: Fewer paired peaks (741) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 741 pairs to build model! INFO @ Sun, 02 Jun 2019 20:36:08: start model_add_line... INFO @ Sun, 02 Jun 2019 20:36:08: start X-correlation... INFO @ Sun, 02 Jun 2019 20:36:08: end of X-cor INFO @ Sun, 02 Jun 2019 20:36:08: #2 finished! INFO @ Sun, 02 Jun 2019 20:36:08: #2 predicted fragment length is 116 bps INFO @ Sun, 02 Jun 2019 20:36:08: #2 alternative fragment length(s) may be 116 bps INFO @ Sun, 02 Jun 2019 20:36:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.05_model.r INFO @ Sun, 02 Jun 2019 20:36:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:36:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:36:12: 7000000 INFO @ Sun, 02 Jun 2019 20:36:12: 7000000 INFO @ Sun, 02 Jun 2019 20:36:15: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:36:15: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:36:15: #1 total tags in treatment: 7260764 INFO @ Sun, 02 Jun 2019 20:36:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:36:15: #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 20:36:15: #1 tags after filtering in treatment: 7260764 INFO @ Sun, 02 Jun 2019 20:36:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:36:15: #1 finished! INFO @ Sun, 02 Jun 2019 20:36:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:36:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:36:16: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:36:16: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:36:16: #1 total tags in treatment: 7260764 INFO @ Sun, 02 Jun 2019 20:36:16: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:36:16: #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 20:36:16: #1 tags after filtering in treatment: 7260764 INFO @ Sun, 02 Jun 2019 20:36:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:36:16: #1 finished! INFO @ Sun, 02 Jun 2019 20:36:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:36:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:36:16: #2 number of paired peaks: 741 WARNING @ Sun, 02 Jun 2019 20:36:16: Fewer paired peaks (741) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 741 pairs to build model! INFO @ Sun, 02 Jun 2019 20:36:16: start model_add_line... INFO @ Sun, 02 Jun 2019 20:36:16: start X-correlation... INFO @ Sun, 02 Jun 2019 20:36:16: end of X-cor INFO @ Sun, 02 Jun 2019 20:36:16: #2 finished! INFO @ Sun, 02 Jun 2019 20:36:16: #2 predicted fragment length is 116 bps INFO @ Sun, 02 Jun 2019 20:36:16: #2 alternative fragment length(s) may be 116 bps INFO @ Sun, 02 Jun 2019 20:36:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.10_model.r INFO @ Sun, 02 Jun 2019 20:36:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:36:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:36:17: #2 number of paired peaks: 741 WARNING @ Sun, 02 Jun 2019 20:36:17: Fewer paired peaks (741) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 741 pairs to build model! INFO @ Sun, 02 Jun 2019 20:36:17: start model_add_line... INFO @ Sun, 02 Jun 2019 20:36:17: start X-correlation... INFO @ Sun, 02 Jun 2019 20:36:17: end of X-cor INFO @ Sun, 02 Jun 2019 20:36:17: #2 finished! INFO @ Sun, 02 Jun 2019 20:36:17: #2 predicted fragment length is 116 bps INFO @ Sun, 02 Jun 2019 20:36:17: #2 alternative fragment length(s) may be 116 bps INFO @ Sun, 02 Jun 2019 20:36:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.20_model.r INFO @ Sun, 02 Jun 2019 20:36:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:36:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:36:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:36:48: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:36:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:36:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:36:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:36:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.05_summits.bed INFO @ Sun, 02 Jun 2019 20:36:56: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2194 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:37:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:37:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:37:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.10_summits.bed INFO @ Sun, 02 Jun 2019 20:37:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1076 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:37:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:37:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:37:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495035/SRX495035.20_summits.bed INFO @ Sun, 02 Jun 2019 20:37:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (553 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。