Job ID = 2009670 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,218,287 reads read : 7,218,287 reads written : 7,218,287 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR364334.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: 00:01:03 7218287 reads; of these: 7218287 (100.00%) were unpaired; of these: 1921142 (26.61%) aligned 0 times 4466311 (61.87%) aligned exactly 1 time 830834 (11.51%) aligned >1 times 73.39% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 3261703 / 5297145 = 0.6157 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 @ Fri, 05 Jul 2019 19:27:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 19:27:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:27:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:27:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 19:27:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:27:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:27:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 19:27:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:27:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:27:37: 1000000 INFO @ Fri, 05 Jul 2019 19:27:37: 1000000 INFO @ Fri, 05 Jul 2019 19:27:37: 1000000 INFO @ Fri, 05 Jul 2019 19:27:44: 2000000 INFO @ Fri, 05 Jul 2019 19:27:44: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:27:44: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:27:44: #1 total tags in treatment: 2035442 INFO @ Fri, 05 Jul 2019 19:27:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:27:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:27:44: #1 tags after filtering in treatment: 2035442 INFO @ Fri, 05 Jul 2019 19:27:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:27:44: #1 finished! INFO @ Fri, 05 Jul 2019 19:27:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:27:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:27:44: 2000000 INFO @ Fri, 05 Jul 2019 19:27:44: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:27:44: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:27:44: #1 total tags in treatment: 2035442 INFO @ Fri, 05 Jul 2019 19:27:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:27:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:27:44: #2 number of paired peaks: 1022 INFO @ Fri, 05 Jul 2019 19:27:44: start model_add_line... INFO @ Fri, 05 Jul 2019 19:27:44: #1 tags after filtering in treatment: 2035442 INFO @ Fri, 05 Jul 2019 19:27:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:27:44: #1 finished! INFO @ Fri, 05 Jul 2019 19:27:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:27:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:27:44: start X-correlation... INFO @ Fri, 05 Jul 2019 19:27:45: end of X-cor INFO @ Fri, 05 Jul 2019 19:27:45: #2 finished! INFO @ Fri, 05 Jul 2019 19:27:45: #2 predicted fragment length is 205 bps INFO @ Fri, 05 Jul 2019 19:27:45: #2 alternative fragment length(s) may be 1,174,205,231 bps INFO @ Fri, 05 Jul 2019 19:27:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.20_model.r INFO @ Fri, 05 Jul 2019 19:27:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:27:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:27:45: #2 number of paired peaks: 1022 INFO @ Fri, 05 Jul 2019 19:27:45: start model_add_line... INFO @ Fri, 05 Jul 2019 19:27:45: start X-correlation... INFO @ Fri, 05 Jul 2019 19:27:45: end of X-cor INFO @ Fri, 05 Jul 2019 19:27:45: #2 finished! INFO @ Fri, 05 Jul 2019 19:27:45: #2 predicted fragment length is 205 bps INFO @ Fri, 05 Jul 2019 19:27:45: #2 alternative fragment length(s) may be 1,174,205,231 bps INFO @ Fri, 05 Jul 2019 19:27:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.10_model.r INFO @ Fri, 05 Jul 2019 19:27:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:27:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:27:45: 2000000 INFO @ Fri, 05 Jul 2019 19:27:45: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:27:45: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:27:45: #1 total tags in treatment: 2035442 INFO @ Fri, 05 Jul 2019 19:27:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:27:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:27:45: #1 tags after filtering in treatment: 2035442 INFO @ Fri, 05 Jul 2019 19:27:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:27:45: #1 finished! INFO @ Fri, 05 Jul 2019 19:27:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:27:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:27:46: #2 number of paired peaks: 1022 INFO @ Fri, 05 Jul 2019 19:27:46: start model_add_line... INFO @ Fri, 05 Jul 2019 19:27:46: start X-correlation... INFO @ Fri, 05 Jul 2019 19:27:46: end of X-cor INFO @ Fri, 05 Jul 2019 19:27:46: #2 finished! INFO @ Fri, 05 Jul 2019 19:27:46: #2 predicted fragment length is 205 bps INFO @ Fri, 05 Jul 2019 19:27:46: #2 alternative fragment length(s) may be 1,174,205,231 bps INFO @ Fri, 05 Jul 2019 19:27:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.05_model.r INFO @ Fri, 05 Jul 2019 19:27:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:27:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:27:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:27:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:28:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:28:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:28:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:28:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:28:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.20_summits.bed INFO @ Fri, 05 Jul 2019 19:28:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.10_summits.bed INFO @ Fri, 05 Jul 2019 19:28:22: Done! INFO @ Fri, 05 Jul 2019 19:28:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:28:22: Done! INFO @ Fri, 05 Jul 2019 19:28:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105548/SRX105548.05_summits.bed INFO @ Fri, 05 Jul 2019 19:28:22: Done! pass1 - making usageList (17 chroms): 1 millis pass1 - making usageList (17 chroms): 1 millis pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (265 records, 4 fields): 5 millis pass2 - checking and writing primary data (608 records, 4 fields): 5 millis pass2 - checking and writing primary data (883 records, 4 fields): 6 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。