Job ID = 1292927 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,528,916 reads read : 8,528,916 reads written : 8,528,916 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: 00:01:57 8528916 reads; of these: 8528916 (100.00%) were unpaired; of these: 1032215 (12.10%) aligned 0 times 6319555 (74.10%) aligned exactly 1 time 1177146 (13.80%) aligned >1 times 87.90% overall alignment rate Time searching: 00:01:57 Overall time: 00:01:57 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] 542608 / 7496701 = 0.0724 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 21:08:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.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 21:08:59: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:08:59: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:08:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.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 21:08:59: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:08:59: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:08:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.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 21:08:59: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:08:59: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:09:09: 1000000 INFO @ Sun, 02 Jun 2019 21:09:09: 1000000 INFO @ Sun, 02 Jun 2019 21:09:11: 1000000 INFO @ Sun, 02 Jun 2019 21:09:17: 2000000 INFO @ Sun, 02 Jun 2019 21:09:20: 2000000 INFO @ Sun, 02 Jun 2019 21:09:22: 2000000 INFO @ Sun, 02 Jun 2019 21:09:26: 3000000 INFO @ Sun, 02 Jun 2019 21:09:30: 3000000 INFO @ Sun, 02 Jun 2019 21:09:32: 3000000 INFO @ Sun, 02 Jun 2019 21:09:35: 4000000 INFO @ Sun, 02 Jun 2019 21:09:41: 4000000 INFO @ Sun, 02 Jun 2019 21:09:42: 4000000 INFO @ Sun, 02 Jun 2019 21:09:44: 5000000 INFO @ Sun, 02 Jun 2019 21:09:51: 5000000 INFO @ Sun, 02 Jun 2019 21:09:52: 5000000 INFO @ Sun, 02 Jun 2019 21:09:53: 6000000 INFO @ Sun, 02 Jun 2019 21:10:02: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:10:02: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:10:02: #1 total tags in treatment: 6954093 INFO @ Sun, 02 Jun 2019 21:10:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:10:02: #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 21:10:02: 6000000 INFO @ Sun, 02 Jun 2019 21:10:02: 6000000 INFO @ Sun, 02 Jun 2019 21:10:02: #1 tags after filtering in treatment: 6954093 INFO @ Sun, 02 Jun 2019 21:10:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:10:02: #1 finished! INFO @ Sun, 02 Jun 2019 21:10:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:10:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:10:02: #2 number of paired peaks: 843 WARNING @ Sun, 02 Jun 2019 21:10:02: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Sun, 02 Jun 2019 21:10:02: start model_add_line... INFO @ Sun, 02 Jun 2019 21:10:03: start X-correlation... INFO @ Sun, 02 Jun 2019 21:10:03: end of X-cor INFO @ Sun, 02 Jun 2019 21:10:03: #2 finished! INFO @ Sun, 02 Jun 2019 21:10:03: #2 predicted fragment length is 194 bps INFO @ Sun, 02 Jun 2019 21:10:03: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 02 Jun 2019 21:10:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.20_model.r INFO @ Sun, 02 Jun 2019 21:10:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:10:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:10:11: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:10:11: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:10:11: #1 total tags in treatment: 6954093 INFO @ Sun, 02 Jun 2019 21:10:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:10:11: #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 21:10:11: #1 tags after filtering in treatment: 6954093 INFO @ Sun, 02 Jun 2019 21:10:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:10:11: #1 finished! INFO @ Sun, 02 Jun 2019 21:10:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:10:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:10:11: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:10:11: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:10:11: #1 total tags in treatment: 6954093 INFO @ Sun, 02 Jun 2019 21:10:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:10:11: #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 21:10:11: #1 tags after filtering in treatment: 6954093 INFO @ Sun, 02 Jun 2019 21:10:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:10:11: #1 finished! INFO @ Sun, 02 Jun 2019 21:10:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:10:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:10:12: #2 number of paired peaks: 843 WARNING @ Sun, 02 Jun 2019 21:10:12: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Sun, 02 Jun 2019 21:10:12: start model_add_line... INFO @ Sun, 02 Jun 2019 21:10:12: start X-correlation... INFO @ Sun, 02 Jun 2019 21:10:12: end of X-cor INFO @ Sun, 02 Jun 2019 21:10:12: #2 finished! INFO @ Sun, 02 Jun 2019 21:10:12: #2 predicted fragment length is 194 bps INFO @ Sun, 02 Jun 2019 21:10:12: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 02 Jun 2019 21:10:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.05_model.r INFO @ Sun, 02 Jun 2019 21:10:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:10:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:10:12: #2 number of paired peaks: 843 WARNING @ Sun, 02 Jun 2019 21:10:12: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Sun, 02 Jun 2019 21:10:12: start model_add_line... INFO @ Sun, 02 Jun 2019 21:10:12: start X-correlation... INFO @ Sun, 02 Jun 2019 21:10:12: end of X-cor INFO @ Sun, 02 Jun 2019 21:10:12: #2 finished! INFO @ Sun, 02 Jun 2019 21:10:12: #2 predicted fragment length is 194 bps INFO @ Sun, 02 Jun 2019 21:10:12: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 02 Jun 2019 21:10:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.10_model.r INFO @ Sun, 02 Jun 2019 21:10:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:10:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:10:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:10:34: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:10:34: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:10:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:10:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:10:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.20_summits.bed INFO @ Sun, 02 Jun 2019 21:10:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (669 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:10:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:10:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:10:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.05_summits.bed INFO @ Sun, 02 Jun 2019 21:10:44: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3168 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:10:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:10:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:10:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020718/SRX5020718.10_summits.bed INFO @ Sun, 02 Jun 2019 21:10:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1659 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。