Job ID = 2011928 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,603,215 reads read : 36,603,215 reads written : 36,603,215 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1284642.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: 00:05:01 36603215 reads; of these: 36603215 (100.00%) were unpaired; of these: 4944602 (13.51%) aligned 0 times 6397323 (17.48%) aligned exactly 1 time 25261290 (69.01%) aligned >1 times 86.49% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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_sort_core] merging from 16 files... [bam_rmdupse_core] 30533476 / 31658613 = 0.9645 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, 06 Jul 2019 03:34:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.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 @ Sat, 06 Jul 2019 03:34:09: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:34:09: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.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 @ Sat, 06 Jul 2019 03:34:10: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:34:10: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:34:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.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 @ Sat, 06 Jul 2019 03:34:11: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:34:11: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:34:18: 1000000 INFO @ Sat, 06 Jul 2019 03:34:19: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:34:19: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:34:19: #1 total tags in treatment: 1125137 INFO @ Sat, 06 Jul 2019 03:34:19: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:34:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:34:19: #1 tags after filtering in treatment: 1125137 INFO @ Sat, 06 Jul 2019 03:34:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 03:34:19: #1 finished! INFO @ Sat, 06 Jul 2019 03:34:19: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:34:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:34:19: 1000000 INFO @ Sat, 06 Jul 2019 03:34:19: #2 number of paired peaks: 1108 INFO @ Sat, 06 Jul 2019 03:34:19: start model_add_line... INFO @ Sat, 06 Jul 2019 03:34:19: start X-correlation... INFO @ Sat, 06 Jul 2019 03:34:19: end of X-cor INFO @ Sat, 06 Jul 2019 03:34:19: #2 finished! INFO @ Sat, 06 Jul 2019 03:34:19: #2 predicted fragment length is 161 bps INFO @ Sat, 06 Jul 2019 03:34:19: #2 alternative fragment length(s) may be 3,161 bps INFO @ Sat, 06 Jul 2019 03:34:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.05_model.r INFO @ Sat, 06 Jul 2019 03:34:19: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:34:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:34:19: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:34:19: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:34:19: #1 total tags in treatment: 1125137 INFO @ Sat, 06 Jul 2019 03:34:19: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:34:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:34:20: #1 tags after filtering in treatment: 1125137 INFO @ Sat, 06 Jul 2019 03:34:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 03:34:20: #1 finished! INFO @ Sat, 06 Jul 2019 03:34:20: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:34:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:34:20: #2 number of paired peaks: 1108 INFO @ Sat, 06 Jul 2019 03:34:20: start model_add_line... INFO @ Sat, 06 Jul 2019 03:34:20: start X-correlation... INFO @ Sat, 06 Jul 2019 03:34:20: end of X-cor INFO @ Sat, 06 Jul 2019 03:34:20: #2 finished! INFO @ Sat, 06 Jul 2019 03:34:20: #2 predicted fragment length is 161 bps INFO @ Sat, 06 Jul 2019 03:34:20: #2 alternative fragment length(s) may be 3,161 bps INFO @ Sat, 06 Jul 2019 03:34:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.10_model.r INFO @ Sat, 06 Jul 2019 03:34:20: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:34:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:34:21: 1000000 INFO @ Sat, 06 Jul 2019 03:34:22: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:34:22: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:34:22: #1 total tags in treatment: 1125137 INFO @ Sat, 06 Jul 2019 03:34:22: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:34:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:34:22: #1 tags after filtering in treatment: 1125137 INFO @ Sat, 06 Jul 2019 03:34:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 03:34:22: #1 finished! INFO @ Sat, 06 Jul 2019 03:34:22: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:34:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:34:22: #2 number of paired peaks: 1108 INFO @ Sat, 06 Jul 2019 03:34:22: start model_add_line... INFO @ Sat, 06 Jul 2019 03:34:22: start X-correlation... INFO @ Sat, 06 Jul 2019 03:34:22: end of X-cor INFO @ Sat, 06 Jul 2019 03:34:22: #2 finished! INFO @ Sat, 06 Jul 2019 03:34:22: #2 predicted fragment length is 161 bps INFO @ Sat, 06 Jul 2019 03:34:22: #2 alternative fragment length(s) may be 3,161 bps INFO @ Sat, 06 Jul 2019 03:34:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.20_model.r INFO @ Sat, 06 Jul 2019 03:34:22: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:34:22: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:34:27: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:34:28: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:34:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:34:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:34:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.05_summits.bed INFO @ Sat, 06 Jul 2019 03:34:28: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (556 records, 4 fields): 4 millis INFO @ Sat, 06 Jul 2019 03:34:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:34:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:34:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.10_summits.bed INFO @ Sat, 06 Jul 2019 03:34:29: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (441 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:34:30: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:34:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.20_peaks.xls CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:34:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:34:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX541155/SRX541155.20_summits.bed INFO @ Sat, 06 Jul 2019 03:34:53: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 7 millis CompletedMACS2peakCalling