Job ID = 1291530 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,562,954 reads read : 7,562,954 reads written : 7,562,954 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:11 7562954 reads; of these: 7562954 (100.00%) were unpaired; of these: 425290 (5.62%) aligned 0 times 5086738 (67.26%) aligned exactly 1 time 2050926 (27.12%) aligned >1 times 94.38% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 2231296 / 7137664 = 0.3126 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 16:01:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.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 16:01:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:01:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:01:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.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 16:01:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:01:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:01:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.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 16:01:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:01:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:01:14: 1000000 INFO @ Sun, 02 Jun 2019 16:01:14: 1000000 INFO @ Sun, 02 Jun 2019 16:01:16: 1000000 INFO @ Sun, 02 Jun 2019 16:01:22: 2000000 INFO @ Sun, 02 Jun 2019 16:01:22: 2000000 INFO @ Sun, 02 Jun 2019 16:01:25: 2000000 INFO @ Sun, 02 Jun 2019 16:01:29: 3000000 INFO @ Sun, 02 Jun 2019 16:01:30: 3000000 INFO @ Sun, 02 Jun 2019 16:01:34: 3000000 INFO @ Sun, 02 Jun 2019 16:01:37: 4000000 INFO @ Sun, 02 Jun 2019 16:01:38: 4000000 INFO @ Sun, 02 Jun 2019 16:01:43: 4000000 INFO @ Sun, 02 Jun 2019 16:01:44: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:01:44: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:01:44: #1 total tags in treatment: 4906368 INFO @ Sun, 02 Jun 2019 16:01:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:01:44: #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 16:01:44: #1 tags after filtering in treatment: 4906368 INFO @ Sun, 02 Jun 2019 16:01:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:01:44: #1 finished! INFO @ Sun, 02 Jun 2019 16:01:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:01:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:01:44: #2 number of paired peaks: 3446 INFO @ Sun, 02 Jun 2019 16:01:44: start model_add_line... INFO @ Sun, 02 Jun 2019 16:01:44: start X-correlation... INFO @ Sun, 02 Jun 2019 16:01:44: end of X-cor INFO @ Sun, 02 Jun 2019 16:01:44: #2 finished! INFO @ Sun, 02 Jun 2019 16:01:44: #2 predicted fragment length is 163 bps INFO @ Sun, 02 Jun 2019 16:01:44: #2 alternative fragment length(s) may be 1,18,93,123,148,163,180,192,234 bps INFO @ Sun, 02 Jun 2019 16:01:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.05_model.r INFO @ Sun, 02 Jun 2019 16:01:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:01:45: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:01:45: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:01:45: #1 total tags in treatment: 4906368 INFO @ Sun, 02 Jun 2019 16:01:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:01:45: #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 16:01:45: #1 tags after filtering in treatment: 4906368 INFO @ Sun, 02 Jun 2019 16:01:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:01:45: #1 finished! INFO @ Sun, 02 Jun 2019 16:01:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:01:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:01:46: #2 number of paired peaks: 3446 INFO @ Sun, 02 Jun 2019 16:01:46: start model_add_line... INFO @ Sun, 02 Jun 2019 16:01:46: start X-correlation... INFO @ Sun, 02 Jun 2019 16:01:46: end of X-cor INFO @ Sun, 02 Jun 2019 16:01:46: #2 finished! INFO @ Sun, 02 Jun 2019 16:01:46: #2 predicted fragment length is 163 bps INFO @ Sun, 02 Jun 2019 16:01:46: #2 alternative fragment length(s) may be 1,18,93,123,148,163,180,192,234 bps INFO @ Sun, 02 Jun 2019 16:01:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.10_model.r INFO @ Sun, 02 Jun 2019 16:01:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:01:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:01:51: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:01:51: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:01:51: #1 total tags in treatment: 4906368 INFO @ Sun, 02 Jun 2019 16:01:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:01:51: #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 16:01:51: #1 tags after filtering in treatment: 4906368 INFO @ Sun, 02 Jun 2019 16:01:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:01:51: #1 finished! INFO @ Sun, 02 Jun 2019 16:01:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:01:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:01:51: #2 number of paired peaks: 3446 INFO @ Sun, 02 Jun 2019 16:01:51: start model_add_line... INFO @ Sun, 02 Jun 2019 16:01:52: start X-correlation... INFO @ Sun, 02 Jun 2019 16:01:52: end of X-cor INFO @ Sun, 02 Jun 2019 16:01:52: #2 finished! INFO @ Sun, 02 Jun 2019 16:01:52: #2 predicted fragment length is 163 bps INFO @ Sun, 02 Jun 2019 16:01:52: #2 alternative fragment length(s) may be 1,18,93,123,148,163,180,192,234 bps INFO @ Sun, 02 Jun 2019 16:01:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.20_model.r INFO @ Sun, 02 Jun 2019 16:01:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:01:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:02:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:02:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:02:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:02:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:02:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:02:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.05_summits.bed INFO @ Sun, 02 Jun 2019 16:02:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (699 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:02:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:02:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:02:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.10_summits.bed INFO @ Sun, 02 Jun 2019 16:02:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (261 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:02:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:02:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:02:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113619/SRX113619.20_summits.bed INFO @ Sun, 02 Jun 2019 16:02:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (72 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。