Job ID = 2589403 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,303,031 reads read : 5,303,031 reads written : 5,303,031 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR494581.sra.cache’: 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: 00:00:42 5303031 reads; of these: 5303031 (100.00%) were unpaired; of these: 2257906 (42.58%) aligned 0 times 2664260 (50.24%) aligned exactly 1 time 380865 (7.18%) aligned >1 times 57.42% overall alignment rate Time searching: 00:00:42 Overall time: 00:00:42 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] 1064947 / 3045125 = 0.3497 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 17:36:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.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 17:36:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:36:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:36:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.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 17:36:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:36:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:36:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.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 17:36:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:36:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:36:38: 1000000 INFO @ Mon, 12 Aug 2019 17:36:41: 1000000 INFO @ Mon, 12 Aug 2019 17:36:42: 1000000 INFO @ Mon, 12 Aug 2019 17:36:45: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:36:45: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:36:45: #1 total tags in treatment: 1980178 INFO @ Mon, 12 Aug 2019 17:36:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:36:45: #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 17:36:45: #1 tags after filtering in treatment: 1980178 INFO @ Mon, 12 Aug 2019 17:36:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:36:45: #1 finished! INFO @ Mon, 12 Aug 2019 17:36:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:36:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:36:46: #2 number of paired peaks: 4040 INFO @ Mon, 12 Aug 2019 17:36:46: start model_add_line... INFO @ Mon, 12 Aug 2019 17:36:46: start X-correlation... INFO @ Mon, 12 Aug 2019 17:36:46: end of X-cor INFO @ Mon, 12 Aug 2019 17:36:46: #2 finished! INFO @ Mon, 12 Aug 2019 17:36:46: #2 predicted fragment length is 135 bps INFO @ Mon, 12 Aug 2019 17:36:46: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 12 Aug 2019 17:36:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.05_model.r INFO @ Mon, 12 Aug 2019 17:36:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:36:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:36:51: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:36:51: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:36:51: #1 total tags in treatment: 1980178 INFO @ Mon, 12 Aug 2019 17:36:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:36:51: #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 17:36:51: #1 tags after filtering in treatment: 1980178 INFO @ Mon, 12 Aug 2019 17:36:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:36:51: #1 finished! INFO @ Mon, 12 Aug 2019 17:36:51: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:36:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:36:51: #2 number of paired peaks: 4040 INFO @ Mon, 12 Aug 2019 17:36:51: start model_add_line... INFO @ Mon, 12 Aug 2019 17:36:51: start X-correlation... INFO @ Mon, 12 Aug 2019 17:36:51: end of X-cor INFO @ Mon, 12 Aug 2019 17:36:51: #2 finished! INFO @ Mon, 12 Aug 2019 17:36:51: #2 predicted fragment length is 135 bps INFO @ Mon, 12 Aug 2019 17:36:51: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 12 Aug 2019 17:36:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.10_model.r INFO @ Mon, 12 Aug 2019 17:36:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:36:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:36:51: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:36:51: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:36:51: #1 total tags in treatment: 1980178 INFO @ Mon, 12 Aug 2019 17:36:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:36:51: #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 17:36:51: #1 tags after filtering in treatment: 1980178 INFO @ Mon, 12 Aug 2019 17:36:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:36:51: #1 finished! INFO @ Mon, 12 Aug 2019 17:36:51: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:36:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:36:52: #2 number of paired peaks: 4040 INFO @ Mon, 12 Aug 2019 17:36:52: start model_add_line... INFO @ Mon, 12 Aug 2019 17:36:52: start X-correlation... INFO @ Mon, 12 Aug 2019 17:36:52: end of X-cor INFO @ Mon, 12 Aug 2019 17:36:52: #2 finished! INFO @ Mon, 12 Aug 2019 17:36:52: #2 predicted fragment length is 135 bps INFO @ Mon, 12 Aug 2019 17:36:52: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 12 Aug 2019 17:36:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.20_model.r INFO @ Mon, 12 Aug 2019 17:36:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:36:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:36:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:36:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:36:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:36:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.05_summits.bed INFO @ Mon, 12 Aug 2019 17:36:56: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5758 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:36:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:36:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:37:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:37:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:37:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.10_summits.bed INFO @ Mon, 12 Aug 2019 17:37:02: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4142 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 17:37:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:37:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:37:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX146420/SRX146420.20_summits.bed INFO @ Mon, 12 Aug 2019 17:37:02: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2914 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。