Job ID = 2011929 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,135,622 reads read : 32,135,622 reads written : 32,135,622 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1284643.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: 00:05:21 32135622 reads; of these: 32135622 (100.00%) were unpaired; of these: 12274709 (38.20%) aligned 0 times 15376725 (47.85%) aligned exactly 1 time 4484188 (13.95%) aligned >1 times 61.80% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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 12 files... [bam_rmdupse_core] 17596764 / 19860913 = 0.8860 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 03:32:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.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 03:32:45: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:32:45: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:32:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.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 03:32:46: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:32:46: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:32:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.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 03:32:47: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:32:47: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:32:55: 1000000 INFO @ Sat, 06 Jul 2019 03:32:56: 1000000 INFO @ Sat, 06 Jul 2019 03:32:58: 1000000 INFO @ Sat, 06 Jul 2019 03:33:05: 2000000 INFO @ Sat, 06 Jul 2019 03:33:06: 2000000 INFO @ Sat, 06 Jul 2019 03:33:07: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:33:07: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:33:07: #1 total tags in treatment: 2264149 INFO @ Sat, 06 Jul 2019 03:33:07: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:33:07: #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 03:33:07: #1 tags after filtering in treatment: 2264149 INFO @ Sat, 06 Jul 2019 03:33:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 03:33:07: #1 finished! INFO @ Sat, 06 Jul 2019 03:33:07: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:33:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:33:07: #2 number of paired peaks: 1597 INFO @ Sat, 06 Jul 2019 03:33:07: start model_add_line... INFO @ Sat, 06 Jul 2019 03:33:07: start X-correlation... INFO @ Sat, 06 Jul 2019 03:33:07: end of X-cor INFO @ Sat, 06 Jul 2019 03:33:07: #2 finished! INFO @ Sat, 06 Jul 2019 03:33:07: #2 predicted fragment length is 165 bps INFO @ Sat, 06 Jul 2019 03:33:07: #2 alternative fragment length(s) may be 1,145,165 bps INFO @ Sat, 06 Jul 2019 03:33:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.10_model.r INFO @ Sat, 06 Jul 2019 03:33:07: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:33:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:33:09: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:33:09: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:33:09: #1 total tags in treatment: 2264149 INFO @ Sat, 06 Jul 2019 03:33:09: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:33:09: #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 03:33:09: #1 tags after filtering in treatment: 2264149 INFO @ Sat, 06 Jul 2019 03:33:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 03:33:09: #1 finished! INFO @ Sat, 06 Jul 2019 03:33:09: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:33:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:33:09: 2000000 INFO @ Sat, 06 Jul 2019 03:33:09: #2 number of paired peaks: 1597 INFO @ Sat, 06 Jul 2019 03:33:09: start model_add_line... INFO @ Sat, 06 Jul 2019 03:33:09: start X-correlation... INFO @ Sat, 06 Jul 2019 03:33:09: end of X-cor INFO @ Sat, 06 Jul 2019 03:33:09: #2 finished! INFO @ Sat, 06 Jul 2019 03:33:09: #2 predicted fragment length is 165 bps INFO @ Sat, 06 Jul 2019 03:33:09: #2 alternative fragment length(s) may be 1,145,165 bps INFO @ Sat, 06 Jul 2019 03:33:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.05_model.r INFO @ Sat, 06 Jul 2019 03:33:09: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:33:09: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:33:11: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:33:11: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:33:11: #1 total tags in treatment: 2264149 INFO @ Sat, 06 Jul 2019 03:33:11: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:33:11: #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 03:33:11: #1 tags after filtering in treatment: 2264149 INFO @ Sat, 06 Jul 2019 03:33:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 03:33:11: #1 finished! INFO @ Sat, 06 Jul 2019 03:33:11: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:33:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:33:12: #2 number of paired peaks: 1597 INFO @ Sat, 06 Jul 2019 03:33:12: start model_add_line... INFO @ Sat, 06 Jul 2019 03:33:12: start X-correlation... INFO @ Sat, 06 Jul 2019 03:33:12: end of X-cor INFO @ Sat, 06 Jul 2019 03:33:12: #2 finished! INFO @ Sat, 06 Jul 2019 03:33:12: #2 predicted fragment length is 165 bps INFO @ Sat, 06 Jul 2019 03:33:12: #2 alternative fragment length(s) may be 1,145,165 bps INFO @ Sat, 06 Jul 2019 03:33:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.20_model.r INFO @ Sat, 06 Jul 2019 03:33:12: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:33:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:33:22: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:33:24: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:33:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:33:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:33:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.10_summits.bed INFO @ Sat, 06 Jul 2019 03:33:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (692 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:33:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:33:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:33:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.05_summits.bed INFO @ Sat, 06 Jul 2019 03:33:26: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (756 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:33:27: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:33:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:33:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:33:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX541156/SRX541156.20_summits.bed INFO @ Sat, 06 Jul 2019 03:33:29: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (575 records, 4 fields): 4 millis CompletedMACS2peakCalling