Job ID = 1290619 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,677,034 reads read : 8,677,034 reads written : 8,677,034 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: 00:01:32 8677034 reads; of these: 8677034 (100.00%) were unpaired; of these: 1459930 (16.83%) aligned 0 times 5972995 (68.84%) aligned exactly 1 time 1244109 (14.34%) aligned >1 times 83.17% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 1634587 / 7217104 = 0.2265 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 @ Sat, 01 Jun 2019 21:48:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.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 @ Sat, 01 Jun 2019 21:48:18: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:48:18: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:48:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.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 @ Sat, 01 Jun 2019 21:48:19: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:48:19: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:48:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.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 @ Sat, 01 Jun 2019 21:48:19: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:48:19: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:48:26: 1000000 INFO @ Sat, 01 Jun 2019 21:48:27: 1000000 INFO @ Sat, 01 Jun 2019 21:48:27: 1000000 INFO @ Sat, 01 Jun 2019 21:48:33: 2000000 INFO @ Sat, 01 Jun 2019 21:48:35: 2000000 INFO @ Sat, 01 Jun 2019 21:48:35: 2000000 INFO @ Sat, 01 Jun 2019 21:48:41: 3000000 INFO @ Sat, 01 Jun 2019 21:48:42: 3000000 INFO @ Sat, 01 Jun 2019 21:48:43: 3000000 INFO @ Sat, 01 Jun 2019 21:48:48: 4000000 INFO @ Sat, 01 Jun 2019 21:48:50: 4000000 INFO @ Sat, 01 Jun 2019 21:48:51: 4000000 INFO @ Sat, 01 Jun 2019 21:48:55: 5000000 INFO @ Sat, 01 Jun 2019 21:48:57: 5000000 INFO @ Sat, 01 Jun 2019 21:48:59: 5000000 INFO @ Sat, 01 Jun 2019 21:48:59: #1 tag size is determined as 36 bps INFO @ Sat, 01 Jun 2019 21:48:59: #1 tag size = 36 INFO @ Sat, 01 Jun 2019 21:48:59: #1 total tags in treatment: 5582517 INFO @ Sat, 01 Jun 2019 21:48:59: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:48:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:48:59: #1 tags after filtering in treatment: 5582517 INFO @ Sat, 01 Jun 2019 21:48:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:48:59: #1 finished! INFO @ Sat, 01 Jun 2019 21:48:59: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:48:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:49:00: #2 number of paired peaks: 1525 INFO @ Sat, 01 Jun 2019 21:49:00: start model_add_line... INFO @ Sat, 01 Jun 2019 21:49:00: start X-correlation... INFO @ Sat, 01 Jun 2019 21:49:00: end of X-cor INFO @ Sat, 01 Jun 2019 21:49:00: #2 finished! INFO @ Sat, 01 Jun 2019 21:49:00: #2 predicted fragment length is 115 bps INFO @ Sat, 01 Jun 2019 21:49:00: #2 alternative fragment length(s) may be 115 bps INFO @ Sat, 01 Jun 2019 21:49:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.20_model.r INFO @ Sat, 01 Jun 2019 21:49:00: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:49:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:49:01: #1 tag size is determined as 36 bps INFO @ Sat, 01 Jun 2019 21:49:01: #1 tag size = 36 INFO @ Sat, 01 Jun 2019 21:49:01: #1 total tags in treatment: 5582517 INFO @ Sat, 01 Jun 2019 21:49:01: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:49:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:49:01: #1 tags after filtering in treatment: 5582517 INFO @ Sat, 01 Jun 2019 21:49:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:49:01: #1 finished! INFO @ Sat, 01 Jun 2019 21:49:01: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:49:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:49:02: #2 number of paired peaks: 1525 INFO @ Sat, 01 Jun 2019 21:49:02: start model_add_line... INFO @ Sat, 01 Jun 2019 21:49:02: start X-correlation... INFO @ Sat, 01 Jun 2019 21:49:02: end of X-cor INFO @ Sat, 01 Jun 2019 21:49:02: #2 finished! INFO @ Sat, 01 Jun 2019 21:49:02: #2 predicted fragment length is 115 bps INFO @ Sat, 01 Jun 2019 21:49:02: #2 alternative fragment length(s) may be 115 bps INFO @ Sat, 01 Jun 2019 21:49:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.10_model.r INFO @ Sat, 01 Jun 2019 21:49:02: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:49:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:49:03: #1 tag size is determined as 36 bps INFO @ Sat, 01 Jun 2019 21:49:03: #1 tag size = 36 INFO @ Sat, 01 Jun 2019 21:49:03: #1 total tags in treatment: 5582517 INFO @ Sat, 01 Jun 2019 21:49:03: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:49:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:49:03: #1 tags after filtering in treatment: 5582517 INFO @ Sat, 01 Jun 2019 21:49:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:49:03: #1 finished! INFO @ Sat, 01 Jun 2019 21:49:03: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:49:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:49:04: #2 number of paired peaks: 1525 INFO @ Sat, 01 Jun 2019 21:49:04: start model_add_line... INFO @ Sat, 01 Jun 2019 21:49:04: start X-correlation... INFO @ Sat, 01 Jun 2019 21:49:04: end of X-cor INFO @ Sat, 01 Jun 2019 21:49:04: #2 finished! INFO @ Sat, 01 Jun 2019 21:49:04: #2 predicted fragment length is 115 bps INFO @ Sat, 01 Jun 2019 21:49:04: #2 alternative fragment length(s) may be 115 bps INFO @ Sat, 01 Jun 2019 21:49:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.05_model.r INFO @ Sat, 01 Jun 2019 21:49:04: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:49:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:49:18: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:49:20: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:49:22: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:49:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:49:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:49:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.20_summits.bed INFO @ Sat, 01 Jun 2019 21:49:27: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (1633 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:49:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:49:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:49:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.10_summits.bed INFO @ Sat, 01 Jun 2019 21:49:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2628 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:49:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:49:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:49:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2576637/SRX2576637.05_summits.bed INFO @ Sat, 01 Jun 2019 21:49:31: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (4309 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。