Job ID = 2640465 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,408,779 reads read : 8,817,558 reads written : 4,408,779 reads 0-length : 4,408,779 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:03 Multiseed full-index search: 00:03:54 4408779 reads; of these: 4408779 (100.00%) were unpaired; of these: 410732 (9.32%) aligned 0 times 2989018 (67.80%) aligned exactly 1 time 1009029 (22.89%) aligned >1 times 90.68% overall alignment rate Time searching: 00:04:01 Overall time: 00:04:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 129814 / 3998047 = 0.0325 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:07:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:07:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:07:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:07:46: 1000000 INFO @ Sat, 24 Aug 2019 17:07:54: 2000000 INFO @ Sat, 24 Aug 2019 17:08:02: 3000000 INFO @ Sat, 24 Aug 2019 17:08:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:08:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:08:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:08:08: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:08:08: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:08:08: #1 total tags in treatment: 3868233 INFO @ Sat, 24 Aug 2019 17:08:08: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:08:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:08:09: #1 tags after filtering in treatment: 3867928 INFO @ Sat, 24 Aug 2019 17:08:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:08:09: #1 finished! INFO @ Sat, 24 Aug 2019 17:08:09: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:08:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:08:11: #2 number of paired peaks: 25201 INFO @ Sat, 24 Aug 2019 17:08:11: start model_add_line... INFO @ Sat, 24 Aug 2019 17:08:11: start X-correlation... INFO @ Sat, 24 Aug 2019 17:08:11: end of X-cor INFO @ Sat, 24 Aug 2019 17:08:11: #2 finished! INFO @ Sat, 24 Aug 2019 17:08:11: #2 predicted fragment length is 167 bps INFO @ Sat, 24 Aug 2019 17:08:11: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 24 Aug 2019 17:08:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.05_model.r INFO @ Sat, 24 Aug 2019 17:08:11: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:08:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:08:15: 1000000 INFO @ Sat, 24 Aug 2019 17:08:22: 2000000 INFO @ Sat, 24 Aug 2019 17:08:24: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:08:28: 3000000 INFO @ Sat, 24 Aug 2019 17:08:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:08:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:08:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.05_summits.bed INFO @ Sat, 24 Aug 2019 17:08:30: Done! pass1 - making usageList (45 chroms): 3 millis pass2 - checking and writing primary data (3921 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:08:34: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:08:34: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:08:34: #1 total tags in treatment: 3868233 INFO @ Sat, 24 Aug 2019 17:08:34: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:08:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:08:35: #1 tags after filtering in treatment: 3867928 INFO @ Sat, 24 Aug 2019 17:08:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:08:35: #1 finished! INFO @ Sat, 24 Aug 2019 17:08:35: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:08:35: #2 looking for paired plus/minus strand peaks... BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:08:37: #2 number of paired peaks: 25201 INFO @ Sat, 24 Aug 2019 17:08:37: start model_add_line... INFO @ Sat, 24 Aug 2019 17:08:37: start X-correlation... INFO @ Sat, 24 Aug 2019 17:08:37: end of X-cor INFO @ Sat, 24 Aug 2019 17:08:37: #2 finished! INFO @ Sat, 24 Aug 2019 17:08:37: #2 predicted fragment length is 167 bps INFO @ Sat, 24 Aug 2019 17:08:37: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 24 Aug 2019 17:08:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.10_model.r INFO @ Sat, 24 Aug 2019 17:08:37: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:08:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:08:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:08:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:08:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:08:45: 1000000 INFO @ Sat, 24 Aug 2019 17:08:49: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:08:53: 2000000 INFO @ Sat, 24 Aug 2019 17:08:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.10_summits.bed INFO @ Sat, 24 Aug 2019 17:08:56: Done! pass1 - making usageList (26 chroms): 2 millis pass2 - checking and writing primary data (1796 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:09:00: 3000000 INFO @ Sat, 24 Aug 2019 17:09:07: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:09:07: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:09:07: #1 total tags in treatment: 3868233 INFO @ Sat, 24 Aug 2019 17:09:07: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:09:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:09:07: #1 tags after filtering in treatment: 3867928 INFO @ Sat, 24 Aug 2019 17:09:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:09:07: #1 finished! INFO @ Sat, 24 Aug 2019 17:09:07: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:09:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:09:10: #2 number of paired peaks: 25201 INFO @ Sat, 24 Aug 2019 17:09:10: start model_add_line... INFO @ Sat, 24 Aug 2019 17:09:10: start X-correlation... INFO @ Sat, 24 Aug 2019 17:09:10: end of X-cor INFO @ Sat, 24 Aug 2019 17:09:10: #2 finished! INFO @ Sat, 24 Aug 2019 17:09:10: #2 predicted fragment length is 167 bps INFO @ Sat, 24 Aug 2019 17:09:10: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 24 Aug 2019 17:09:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.20_model.r INFO @ Sat, 24 Aug 2019 17:09:10: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:09:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:09:22: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:09:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:09:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:09:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374983/SRX5374983.20_summits.bed INFO @ Sat, 24 Aug 2019 17:09:28: Done! pass1 - making usageList (22 chroms): 2 millis pass2 - checking and writing primary data (620 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。