Job ID = 1292047 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,074,941 reads read : 7,074,941 reads written : 7,074,941 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: 00:02:58 7074941 reads; of these: 7074941 (100.00%) were unpaired; of these: 495031 (7.00%) aligned 0 times 5018336 (70.93%) aligned exactly 1 time 1561574 (22.07%) aligned >1 times 93.00% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 1822083 / 6579910 = 0.2769 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 17:22:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.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 17:22:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:22:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:22:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.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 17:22:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:22:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:22:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.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 17:22:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:22:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:22:53: 1000000 INFO @ Sun, 02 Jun 2019 17:22:53: 1000000 INFO @ Sun, 02 Jun 2019 17:22:53: 1000000 INFO @ Sun, 02 Jun 2019 17:23:04: 2000000 INFO @ Sun, 02 Jun 2019 17:23:05: 2000000 INFO @ Sun, 02 Jun 2019 17:23:07: 2000000 INFO @ Sun, 02 Jun 2019 17:23:18: 3000000 INFO @ Sun, 02 Jun 2019 17:23:18: 3000000 INFO @ Sun, 02 Jun 2019 17:23:20: 3000000 INFO @ Sun, 02 Jun 2019 17:23:29: 4000000 INFO @ Sun, 02 Jun 2019 17:23:31: 4000000 INFO @ Sun, 02 Jun 2019 17:23:33: 4000000 INFO @ Sun, 02 Jun 2019 17:23:39: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:23:39: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:23:39: #1 total tags in treatment: 4757827 INFO @ Sun, 02 Jun 2019 17:23:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:23:39: #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 17:23:39: #1 tags after filtering in treatment: 4757827 INFO @ Sun, 02 Jun 2019 17:23:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:23:39: #1 finished! INFO @ Sun, 02 Jun 2019 17:23:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:23:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:23:40: #2 number of paired peaks: 1262 INFO @ Sun, 02 Jun 2019 17:23:40: start model_add_line... INFO @ Sun, 02 Jun 2019 17:23:40: start X-correlation... INFO @ Sun, 02 Jun 2019 17:23:40: end of X-cor INFO @ Sun, 02 Jun 2019 17:23:40: #2 finished! INFO @ Sun, 02 Jun 2019 17:23:40: #2 predicted fragment length is 174 bps INFO @ Sun, 02 Jun 2019 17:23:40: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 02 Jun 2019 17:23:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.05_model.r INFO @ Sun, 02 Jun 2019 17:23:40: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:23:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:23:41: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:23:41: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:23:41: #1 total tags in treatment: 4757827 INFO @ Sun, 02 Jun 2019 17:23:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:23:41: #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 17:23:41: #1 tags after filtering in treatment: 4757827 INFO @ Sun, 02 Jun 2019 17:23:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:23:41: #1 finished! INFO @ Sun, 02 Jun 2019 17:23:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:23:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:23:42: #2 number of paired peaks: 1262 INFO @ Sun, 02 Jun 2019 17:23:42: start model_add_line... INFO @ Sun, 02 Jun 2019 17:23:42: start X-correlation... INFO @ Sun, 02 Jun 2019 17:23:42: end of X-cor INFO @ Sun, 02 Jun 2019 17:23:42: #2 finished! INFO @ Sun, 02 Jun 2019 17:23:42: #2 predicted fragment length is 174 bps INFO @ Sun, 02 Jun 2019 17:23:42: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 02 Jun 2019 17:23:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.10_model.r INFO @ Sun, 02 Jun 2019 17:23:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:23:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:23:43: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:23:43: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:23:43: #1 total tags in treatment: 4757827 INFO @ Sun, 02 Jun 2019 17:23:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:23:43: #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 17:23:43: #1 tags after filtering in treatment: 4757827 INFO @ Sun, 02 Jun 2019 17:23:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:23:43: #1 finished! INFO @ Sun, 02 Jun 2019 17:23:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:23:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:23:44: #2 number of paired peaks: 1262 INFO @ Sun, 02 Jun 2019 17:23:44: start model_add_line... INFO @ Sun, 02 Jun 2019 17:23:44: start X-correlation... INFO @ Sun, 02 Jun 2019 17:23:44: end of X-cor INFO @ Sun, 02 Jun 2019 17:23:44: #2 finished! INFO @ Sun, 02 Jun 2019 17:23:44: #2 predicted fragment length is 174 bps INFO @ Sun, 02 Jun 2019 17:23:44: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 02 Jun 2019 17:23:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.20_model.r INFO @ Sun, 02 Jun 2019 17:23:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:23:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:24:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:24:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:24:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:24:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:24:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:24:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.05_summits.bed INFO @ Sun, 02 Jun 2019 17:24:13: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2610 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:24:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:24:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:24:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.10_summits.bed INFO @ Sun, 02 Jun 2019 17:24:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1696 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:24:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:24:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:24:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX330984/SRX330984.20_summits.bed INFO @ Sun, 02 Jun 2019 17:24:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (908 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。