Job ID = 1291807 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,562,205 reads read : 16,562,205 reads written : 16,562,205 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: 00:02:51 16562205 reads; of these: 16562205 (100.00%) were unpaired; of these: 2198170 (13.27%) aligned 0 times 12126717 (73.22%) aligned exactly 1 time 2237318 (13.51%) aligned >1 times 86.73% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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] 9770291 / 14364035 = 0.6802 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 16:38:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.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 16:38:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:38:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:38:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.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 16:38:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:38:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:38:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.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 16:38:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:38:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:38:41: 1000000 INFO @ Sun, 02 Jun 2019 16:38:43: 1000000 INFO @ Sun, 02 Jun 2019 16:38:43: 1000000 INFO @ Sun, 02 Jun 2019 16:38:48: 2000000 INFO @ Sun, 02 Jun 2019 16:38:51: 2000000 INFO @ Sun, 02 Jun 2019 16:38:51: 2000000 INFO @ Sun, 02 Jun 2019 16:38:54: 3000000 INFO @ Sun, 02 Jun 2019 16:38:58: 3000000 INFO @ Sun, 02 Jun 2019 16:39:00: 3000000 INFO @ Sun, 02 Jun 2019 16:39:00: 4000000 INFO @ Sun, 02 Jun 2019 16:39:04: #1 tag size is determined as 35 bps INFO @ Sun, 02 Jun 2019 16:39:04: #1 tag size = 35 INFO @ Sun, 02 Jun 2019 16:39:04: #1 total tags in treatment: 4593744 INFO @ Sun, 02 Jun 2019 16:39:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:39:04: #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 16:39:04: #1 tags after filtering in treatment: 4593744 INFO @ Sun, 02 Jun 2019 16:39:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:39:04: #1 finished! INFO @ Sun, 02 Jun 2019 16:39:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:39:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:39:04: #2 number of paired peaks: 1146 INFO @ Sun, 02 Jun 2019 16:39:04: start model_add_line... INFO @ Sun, 02 Jun 2019 16:39:04: start X-correlation... INFO @ Sun, 02 Jun 2019 16:39:04: end of X-cor INFO @ Sun, 02 Jun 2019 16:39:04: #2 finished! INFO @ Sun, 02 Jun 2019 16:39:04: #2 predicted fragment length is 167 bps INFO @ Sun, 02 Jun 2019 16:39:04: #2 alternative fragment length(s) may be 167 bps INFO @ Sun, 02 Jun 2019 16:39:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.20_model.r INFO @ Sun, 02 Jun 2019 16:39:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:39:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:39:06: 4000000 INFO @ Sun, 02 Jun 2019 16:39:07: 4000000 INFO @ Sun, 02 Jun 2019 16:39:10: #1 tag size is determined as 35 bps INFO @ Sun, 02 Jun 2019 16:39:10: #1 tag size = 35 INFO @ Sun, 02 Jun 2019 16:39:10: #1 total tags in treatment: 4593744 INFO @ Sun, 02 Jun 2019 16:39:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:39:10: #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 16:39:10: #1 tags after filtering in treatment: 4593744 INFO @ Sun, 02 Jun 2019 16:39:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:39:10: #1 finished! INFO @ Sun, 02 Jun 2019 16:39:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:39:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:39:11: #2 number of paired peaks: 1146 INFO @ Sun, 02 Jun 2019 16:39:11: start model_add_line... INFO @ Sun, 02 Jun 2019 16:39:11: start X-correlation... INFO @ Sun, 02 Jun 2019 16:39:11: end of X-cor INFO @ Sun, 02 Jun 2019 16:39:11: #2 finished! INFO @ Sun, 02 Jun 2019 16:39:11: #2 predicted fragment length is 167 bps INFO @ Sun, 02 Jun 2019 16:39:11: #2 alternative fragment length(s) may be 167 bps INFO @ Sun, 02 Jun 2019 16:39:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.05_model.r INFO @ Sun, 02 Jun 2019 16:39:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:39:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:39:12: #1 tag size is determined as 35 bps INFO @ Sun, 02 Jun 2019 16:39:12: #1 tag size = 35 INFO @ Sun, 02 Jun 2019 16:39:12: #1 total tags in treatment: 4593744 INFO @ Sun, 02 Jun 2019 16:39:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:39:12: #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 16:39:13: #1 tags after filtering in treatment: 4593744 INFO @ Sun, 02 Jun 2019 16:39:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:39:13: #1 finished! INFO @ Sun, 02 Jun 2019 16:39:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:39:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:39:13: #2 number of paired peaks: 1146 INFO @ Sun, 02 Jun 2019 16:39:13: start model_add_line... INFO @ Sun, 02 Jun 2019 16:39:13: start X-correlation... INFO @ Sun, 02 Jun 2019 16:39:13: end of X-cor INFO @ Sun, 02 Jun 2019 16:39:13: #2 finished! INFO @ Sun, 02 Jun 2019 16:39:13: #2 predicted fragment length is 167 bps INFO @ Sun, 02 Jun 2019 16:39:13: #2 alternative fragment length(s) may be 167 bps INFO @ Sun, 02 Jun 2019 16:39:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.10_model.r INFO @ Sun, 02 Jun 2019 16:39:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:39:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:39:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:39:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:39:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:39:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:39:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.20_summits.bed INFO @ Sun, 02 Jun 2019 16:39:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (571 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:39:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:39:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:39:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:39:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.05_summits.bed INFO @ Sun, 02 Jun 2019 16:39:33: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1541 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:39:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:39:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:39:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257650/SRX257650.10_summits.bed INFO @ Sun, 02 Jun 2019 16:39:36: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (979 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。