Job ID = 2590209 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,099,125 reads read : 14,099,125 reads written : 14,099,125 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:54 14099125 reads; of these: 14099125 (100.00%) were unpaired; of these: 4726367 (33.52%) aligned 0 times 6840665 (48.52%) aligned exactly 1 time 2532093 (17.96%) aligned >1 times 66.48% overall alignment rate Time searching: 00:01:54 Overall time: 00:01:54 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] 1263571 / 9372758 = 0.1348 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 @ Mon, 12 Aug 2019 20:10:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.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 @ Mon, 12 Aug 2019 20:10:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:10:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:10:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.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 @ Mon, 12 Aug 2019 20:10:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:10:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:10:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.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 @ Mon, 12 Aug 2019 20:10:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:10:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:11:02: 1000000 INFO @ Mon, 12 Aug 2019 20:11:03: 1000000 INFO @ Mon, 12 Aug 2019 20:11:06: 1000000 INFO @ Mon, 12 Aug 2019 20:11:09: 2000000 INFO @ Mon, 12 Aug 2019 20:11:09: 2000000 INFO @ Mon, 12 Aug 2019 20:11:15: 2000000 INFO @ Mon, 12 Aug 2019 20:11:16: 3000000 INFO @ Mon, 12 Aug 2019 20:11:16: 3000000 INFO @ Mon, 12 Aug 2019 20:11:23: 4000000 INFO @ Mon, 12 Aug 2019 20:11:23: 4000000 INFO @ Mon, 12 Aug 2019 20:11:24: 3000000 INFO @ Mon, 12 Aug 2019 20:11:29: 5000000 INFO @ Mon, 12 Aug 2019 20:11:30: 5000000 INFO @ Mon, 12 Aug 2019 20:11:33: 4000000 INFO @ Mon, 12 Aug 2019 20:11:36: 6000000 INFO @ Mon, 12 Aug 2019 20:11:37: 6000000 INFO @ Mon, 12 Aug 2019 20:11:42: 5000000 INFO @ Mon, 12 Aug 2019 20:11:43: 7000000 INFO @ Mon, 12 Aug 2019 20:11:44: 7000000 INFO @ Mon, 12 Aug 2019 20:11:49: 8000000 INFO @ Mon, 12 Aug 2019 20:11:50: #1 tag size is determined as 28 bps INFO @ Mon, 12 Aug 2019 20:11:50: #1 tag size = 28 INFO @ Mon, 12 Aug 2019 20:11:50: #1 total tags in treatment: 8109187 INFO @ Mon, 12 Aug 2019 20:11:50: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:11:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:11:50: #1 tags after filtering in treatment: 8109187 INFO @ Mon, 12 Aug 2019 20:11:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:11:50: #1 finished! INFO @ Mon, 12 Aug 2019 20:11:50: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:11:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:11:51: 6000000 INFO @ Mon, 12 Aug 2019 20:11:51: #2 number of paired peaks: 1615 INFO @ Mon, 12 Aug 2019 20:11:51: start model_add_line... INFO @ Mon, 12 Aug 2019 20:11:51: start X-correlation... INFO @ Mon, 12 Aug 2019 20:11:51: end of X-cor INFO @ Mon, 12 Aug 2019 20:11:51: #2 finished! INFO @ Mon, 12 Aug 2019 20:11:51: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 20:11:51: #2 alternative fragment length(s) may be 2,128,140 bps INFO @ Mon, 12 Aug 2019 20:11:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.10_model.r INFO @ Mon, 12 Aug 2019 20:11:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:11:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:11:51: 8000000 INFO @ Mon, 12 Aug 2019 20:11:52: #1 tag size is determined as 28 bps INFO @ Mon, 12 Aug 2019 20:11:52: #1 tag size = 28 INFO @ Mon, 12 Aug 2019 20:11:52: #1 total tags in treatment: 8109187 INFO @ Mon, 12 Aug 2019 20:11:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:11:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:11:52: #1 tags after filtering in treatment: 8109187 INFO @ Mon, 12 Aug 2019 20:11:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:11:52: #1 finished! INFO @ Mon, 12 Aug 2019 20:11:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:11:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:11:53: #2 number of paired peaks: 1615 INFO @ Mon, 12 Aug 2019 20:11:53: start model_add_line... INFO @ Mon, 12 Aug 2019 20:11:53: start X-correlation... INFO @ Mon, 12 Aug 2019 20:11:53: end of X-cor INFO @ Mon, 12 Aug 2019 20:11:53: #2 finished! INFO @ Mon, 12 Aug 2019 20:11:53: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 20:11:53: #2 alternative fragment length(s) may be 2,128,140 bps INFO @ Mon, 12 Aug 2019 20:11:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.05_model.r INFO @ Mon, 12 Aug 2019 20:11:53: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:11:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:11:59: 7000000 INFO @ Mon, 12 Aug 2019 20:12:08: 8000000 INFO @ Mon, 12 Aug 2019 20:12:09: #1 tag size is determined as 28 bps INFO @ Mon, 12 Aug 2019 20:12:09: #1 tag size = 28 INFO @ Mon, 12 Aug 2019 20:12:09: #1 total tags in treatment: 8109187 INFO @ Mon, 12 Aug 2019 20:12:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:12:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:12:09: #1 tags after filtering in treatment: 8109187 INFO @ Mon, 12 Aug 2019 20:12:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:12:09: #1 finished! INFO @ Mon, 12 Aug 2019 20:12:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:12:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:12:10: #2 number of paired peaks: 1615 INFO @ Mon, 12 Aug 2019 20:12:10: start model_add_line... INFO @ Mon, 12 Aug 2019 20:12:10: start X-correlation... INFO @ Mon, 12 Aug 2019 20:12:10: end of X-cor INFO @ Mon, 12 Aug 2019 20:12:10: #2 finished! INFO @ Mon, 12 Aug 2019 20:12:10: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 20:12:10: #2 alternative fragment length(s) may be 2,128,140 bps INFO @ Mon, 12 Aug 2019 20:12:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.20_model.r INFO @ Mon, 12 Aug 2019 20:12:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:12:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:12:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:12:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:12:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:12:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:12:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.10_summits.bed INFO @ Mon, 12 Aug 2019 20:12:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (757 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:12:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:12:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:12:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.05_summits.bed INFO @ Mon, 12 Aug 2019 20:12:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2454 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:12:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:12:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:12:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:12:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529216/SRX529216.20_summits.bed INFO @ Mon, 12 Aug 2019 20:12:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (225 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。