Job ID = 1291528 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,740,995 reads read : 9,740,995 reads written : 9,740,995 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: 00:02:44 9740995 reads; of these: 9740995 (100.00%) were unpaired; of these: 539175 (5.54%) aligned 0 times 6071592 (62.33%) aligned exactly 1 time 3130228 (32.13%) aligned >1 times 94.46% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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] 3674170 / 9201820 = 0.3993 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 16:03:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.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 16:03:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:03:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:03:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.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 16:03:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:03:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:03:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.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 16:03:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:03:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:03:15: 1000000 INFO @ Sun, 02 Jun 2019 16:03:15: 1000000 INFO @ Sun, 02 Jun 2019 16:03:15: 1000000 INFO @ Sun, 02 Jun 2019 16:03:24: 2000000 INFO @ Sun, 02 Jun 2019 16:03:25: 2000000 INFO @ Sun, 02 Jun 2019 16:03:26: 2000000 INFO @ Sun, 02 Jun 2019 16:03:33: 3000000 INFO @ Sun, 02 Jun 2019 16:03:35: 3000000 INFO @ Sun, 02 Jun 2019 16:03:36: 3000000 INFO @ Sun, 02 Jun 2019 16:03:41: 4000000 INFO @ Sun, 02 Jun 2019 16:03:45: 4000000 INFO @ Sun, 02 Jun 2019 16:03:46: 4000000 INFO @ Sun, 02 Jun 2019 16:03:50: 5000000 INFO @ Sun, 02 Jun 2019 16:03:54: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:03:54: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:03:54: #1 total tags in treatment: 5527650 INFO @ Sun, 02 Jun 2019 16:03:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:03:54: #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 16:03:54: #1 tags after filtering in treatment: 5527650 INFO @ Sun, 02 Jun 2019 16:03:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:03:54: #1 finished! INFO @ Sun, 02 Jun 2019 16:03:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:03:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:03:55: 5000000 INFO @ Sun, 02 Jun 2019 16:03:55: #2 number of paired peaks: 5070 INFO @ Sun, 02 Jun 2019 16:03:55: start model_add_line... INFO @ Sun, 02 Jun 2019 16:03:56: start X-correlation... INFO @ Sun, 02 Jun 2019 16:03:56: end of X-cor INFO @ Sun, 02 Jun 2019 16:03:56: #2 finished! INFO @ Sun, 02 Jun 2019 16:03:56: #2 predicted fragment length is 124 bps INFO @ Sun, 02 Jun 2019 16:03:56: #2 alternative fragment length(s) may be 1,124 bps INFO @ Sun, 02 Jun 2019 16:03:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.05_model.r INFO @ Sun, 02 Jun 2019 16:03:56: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:03:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:03:56: 5000000 INFO @ Sun, 02 Jun 2019 16:04:00: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:04:00: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:04:00: #1 total tags in treatment: 5527650 INFO @ Sun, 02 Jun 2019 16:04:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:04:00: #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 16:04:00: #1 tags after filtering in treatment: 5527650 INFO @ Sun, 02 Jun 2019 16:04:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:04:00: #1 finished! INFO @ Sun, 02 Jun 2019 16:04:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:04:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:04:01: #2 number of paired peaks: 5070 INFO @ Sun, 02 Jun 2019 16:04:01: start model_add_line... INFO @ Sun, 02 Jun 2019 16:04:01: start X-correlation... INFO @ Sun, 02 Jun 2019 16:04:01: end of X-cor INFO @ Sun, 02 Jun 2019 16:04:01: #2 finished! INFO @ Sun, 02 Jun 2019 16:04:01: #2 predicted fragment length is 124 bps INFO @ Sun, 02 Jun 2019 16:04:01: #2 alternative fragment length(s) may be 1,124 bps INFO @ Sun, 02 Jun 2019 16:04:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.10_model.r INFO @ Sun, 02 Jun 2019 16:04:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:04:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:04:01: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:04:01: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:04:01: #1 total tags in treatment: 5527650 INFO @ Sun, 02 Jun 2019 16:04:01: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:04:01: #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 16:04:01: #1 tags after filtering in treatment: 5527650 INFO @ Sun, 02 Jun 2019 16:04:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:04:01: #1 finished! INFO @ Sun, 02 Jun 2019 16:04:01: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:04:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:04:02: #2 number of paired peaks: 5070 INFO @ Sun, 02 Jun 2019 16:04:02: start model_add_line... INFO @ Sun, 02 Jun 2019 16:04:02: start X-correlation... INFO @ Sun, 02 Jun 2019 16:04:02: end of X-cor INFO @ Sun, 02 Jun 2019 16:04:02: #2 finished! INFO @ Sun, 02 Jun 2019 16:04:02: #2 predicted fragment length is 124 bps INFO @ Sun, 02 Jun 2019 16:04:02: #2 alternative fragment length(s) may be 1,124 bps INFO @ Sun, 02 Jun 2019 16:04:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.20_model.r INFO @ Sun, 02 Jun 2019 16:04:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:04:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:04:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:04:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:04:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:04:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:04:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:04:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.05_summits.bed INFO @ Sun, 02 Jun 2019 16:04:22: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3169 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:04:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:04:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:04:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.10_summits.bed INFO @ Sun, 02 Jun 2019 16:04:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (816 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:04:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:04:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:04:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113606/SRX113606.20_summits.bed INFO @ Sun, 02 Jun 2019 16:04:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (162 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。