Job ID = 2011932 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,728,038 reads read : 2,728,038 reads written : 2,728,038 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1284646.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: 00:00:29 2728038 reads; of these: 2728038 (100.00%) were unpaired; of these: 193029 (7.08%) aligned 0 times 961243 (35.24%) aligned exactly 1 time 1573766 (57.69%) aligned >1 times 92.92% overall alignment rate Time searching: 00:00:29 Overall time: 00:00:29 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] 1968616 / 2535009 = 0.7766 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 03:23:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.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 03:23:20: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:23:20: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:23:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.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 03:23:20: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:23:20: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:23:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.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 03:23:21: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:23:21: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:23:25: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:23:25: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:23:25: #1 total tags in treatment: 566393 INFO @ Sat, 06 Jul 2019 03:23:25: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:23:25: #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 03:23:25: #1 tags after filtering in treatment: 566393 INFO @ Sat, 06 Jul 2019 03:23:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 03:23:25: #1 finished! INFO @ Sat, 06 Jul 2019 03:23:25: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:23:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:23:25: #2 number of paired peaks: 801 WARNING @ Sat, 06 Jul 2019 03:23:25: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! INFO @ Sat, 06 Jul 2019 03:23:25: start model_add_line... INFO @ Sat, 06 Jul 2019 03:23:25: start X-correlation... INFO @ Sat, 06 Jul 2019 03:23:25: end of X-cor INFO @ Sat, 06 Jul 2019 03:23:25: #2 finished! INFO @ Sat, 06 Jul 2019 03:23:25: #2 predicted fragment length is 232 bps INFO @ Sat, 06 Jul 2019 03:23:25: #2 alternative fragment length(s) may be 2,232 bps INFO @ Sat, 06 Jul 2019 03:23:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.05_model.r INFO @ Sat, 06 Jul 2019 03:23:26: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:23:26: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:23:26: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:23:26: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:23:26: #1 total tags in treatment: 566393 INFO @ Sat, 06 Jul 2019 03:23:26: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:23:26: #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 03:23:26: #1 tags after filtering in treatment: 566393 INFO @ Sat, 06 Jul 2019 03:23:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 03:23:26: #1 finished! INFO @ Sat, 06 Jul 2019 03:23:26: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:23:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:23:26: #2 number of paired peaks: 801 WARNING @ Sat, 06 Jul 2019 03:23:26: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! INFO @ Sat, 06 Jul 2019 03:23:26: start model_add_line... INFO @ Sat, 06 Jul 2019 03:23:26: start X-correlation... INFO @ Sat, 06 Jul 2019 03:23:26: end of X-cor INFO @ Sat, 06 Jul 2019 03:23:26: #2 finished! INFO @ Sat, 06 Jul 2019 03:23:26: #2 predicted fragment length is 232 bps INFO @ Sat, 06 Jul 2019 03:23:26: #2 alternative fragment length(s) may be 2,232 bps INFO @ Sat, 06 Jul 2019 03:23:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.10_model.r INFO @ Sat, 06 Jul 2019 03:23:26: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:23:27: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:23:27: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:23:27: #1 total tags in treatment: 566393 INFO @ Sat, 06 Jul 2019 03:23:27: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:23:27: #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 03:23:27: #1 tags after filtering in treatment: 566393 INFO @ Sat, 06 Jul 2019 03:23:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 03:23:27: #1 finished! INFO @ Sat, 06 Jul 2019 03:23:27: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:23:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:23:27: #2 number of paired peaks: 801 WARNING @ Sat, 06 Jul 2019 03:23:27: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! INFO @ Sat, 06 Jul 2019 03:23:27: start model_add_line... INFO @ Sat, 06 Jul 2019 03:23:27: start X-correlation... INFO @ Sat, 06 Jul 2019 03:23:27: end of X-cor INFO @ Sat, 06 Jul 2019 03:23:27: #2 finished! INFO @ Sat, 06 Jul 2019 03:23:27: #2 predicted fragment length is 232 bps INFO @ Sat, 06 Jul 2019 03:23:27: #2 alternative fragment length(s) may be 2,232 bps INFO @ Sat, 06 Jul 2019 03:23:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.20_model.r INFO @ Sat, 06 Jul 2019 03:23:27: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:23:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:23:30: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:23:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:23:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:23:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.05_summits.bed INFO @ Sat, 06 Jul 2019 03:23:31: Done! INFO @ Sat, 06 Jul 2019 03:23:31: #3 Call peaks for each chromosome... pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (333 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:23:32: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:23:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:23:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:23:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.10_summits.bed INFO @ Sat, 06 Jul 2019 03:23:32: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (280 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:23:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:23:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:23:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX541159/SRX541159.20_summits.bed INFO @ Sat, 06 Jul 2019 03:23:32: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (188 records, 4 fields): 3 millis CompletedMACS2peakCalling