Job ID = 1292862 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,571,582 reads read : 9,571,582 reads written : 9,571,582 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: 00:02:07 9571582 reads; of these: 9571582 (100.00%) were unpaired; of these: 693893 (7.25%) aligned 0 times 6936459 (72.47%) aligned exactly 1 time 1941230 (20.28%) aligned >1 times 92.75% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 6479439 / 8877689 = 0.7299 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 20:56:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.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 20:56:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:56:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:56:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.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 20:56:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:56:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:56:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.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 20:56:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:56:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:57:03: 1000000 INFO @ Sun, 02 Jun 2019 20:57:03: 1000000 INFO @ Sun, 02 Jun 2019 20:57:04: 1000000 INFO @ Sun, 02 Jun 2019 20:57:09: 2000000 INFO @ Sun, 02 Jun 2019 20:57:10: 2000000 INFO @ Sun, 02 Jun 2019 20:57:11: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:57:11: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:57:11: #1 total tags in treatment: 2398250 INFO @ Sun, 02 Jun 2019 20:57:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:57:11: #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 20:57:11: #1 tags after filtering in treatment: 2398250 INFO @ Sun, 02 Jun 2019 20:57:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:57:11: #1 finished! INFO @ Sun, 02 Jun 2019 20:57:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:57:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:57:12: 2000000 INFO @ Sun, 02 Jun 2019 20:57:12: #2 number of paired peaks: 1563 INFO @ Sun, 02 Jun 2019 20:57:12: start model_add_line... INFO @ Sun, 02 Jun 2019 20:57:12: start X-correlation... INFO @ Sun, 02 Jun 2019 20:57:12: end of X-cor INFO @ Sun, 02 Jun 2019 20:57:12: #2 finished! INFO @ Sun, 02 Jun 2019 20:57:12: #2 predicted fragment length is 173 bps INFO @ Sun, 02 Jun 2019 20:57:12: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 02 Jun 2019 20:57:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.05_model.r INFO @ Sun, 02 Jun 2019 20:57:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:57:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:57:13: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:57:13: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:57:13: #1 total tags in treatment: 2398250 INFO @ Sun, 02 Jun 2019 20:57:13: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:57:13: #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 20:57:13: #1 tags after filtering in treatment: 2398250 INFO @ Sun, 02 Jun 2019 20:57:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:57:13: #1 finished! INFO @ Sun, 02 Jun 2019 20:57:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:57:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:57:13: #2 number of paired peaks: 1563 INFO @ Sun, 02 Jun 2019 20:57:13: start model_add_line... INFO @ Sun, 02 Jun 2019 20:57:13: start X-correlation... INFO @ Sun, 02 Jun 2019 20:57:14: end of X-cor INFO @ Sun, 02 Jun 2019 20:57:14: #2 finished! INFO @ Sun, 02 Jun 2019 20:57:14: #2 predicted fragment length is 173 bps INFO @ Sun, 02 Jun 2019 20:57:14: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 02 Jun 2019 20:57:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.20_model.r INFO @ Sun, 02 Jun 2019 20:57:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:57:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:57:15: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:57:15: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:57:15: #1 total tags in treatment: 2398250 INFO @ Sun, 02 Jun 2019 20:57:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:57:15: #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 20:57:15: #1 tags after filtering in treatment: 2398250 INFO @ Sun, 02 Jun 2019 20:57:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:57:15: #1 finished! INFO @ Sun, 02 Jun 2019 20:57:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:57:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:57:15: #2 number of paired peaks: 1563 INFO @ Sun, 02 Jun 2019 20:57:15: start model_add_line... INFO @ Sun, 02 Jun 2019 20:57:15: start X-correlation... INFO @ Sun, 02 Jun 2019 20:57:15: end of X-cor INFO @ Sun, 02 Jun 2019 20:57:15: #2 finished! INFO @ Sun, 02 Jun 2019 20:57:15: #2 predicted fragment length is 173 bps INFO @ Sun, 02 Jun 2019 20:57:15: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 02 Jun 2019 20:57:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.10_model.r INFO @ Sun, 02 Jun 2019 20:57:15: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:57:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:57:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:57:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:57:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:57:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:57:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:57:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.05_summits.bed INFO @ Sun, 02 Jun 2019 20:57:24: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3230 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:57:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:57:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:57:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.20_summits.bed INFO @ Sun, 02 Jun 2019 20:57:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (576 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:57:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:57:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:57:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495087/SRX495087.10_summits.bed INFO @ Sun, 02 Jun 2019 20:57:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1314 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。