Job ID = 2006006 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,141,867 reads read : 1,141,867 reads written : 1,141,867 spots read : 1,090,129 reads read : 1,090,129 reads written : 1,090,129 spots read : 1,115,407 reads read : 1,115,407 reads written : 1,115,407 spots read : 1,101,402 reads read : 1,101,402 reads written : 1,101,402 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529274.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529275.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529276.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529277.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: 00:01:38 4448805 reads; of these: 4448805 (100.00%) were unpaired; of these: 114310 (2.57%) aligned 0 times 3689273 (82.93%) aligned exactly 1 time 645222 (14.50%) aligned >1 times 97.43% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 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] 3995062 / 4334495 = 0.9217 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 14:51:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.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 14:51:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:51:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:51:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.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 14:51:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:51:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:51:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.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 14:51:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:51:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:51:41: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:51:41: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:51:41: #1 total tags in treatment: 339433 INFO @ Fri, 05 Jul 2019 14:51:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:51:41: #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 14:51:41: #1 tags after filtering in treatment: 339433 INFO @ Fri, 05 Jul 2019 14:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:51:41: #1 finished! INFO @ Fri, 05 Jul 2019 14:51:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:51:41: #2 number of paired peaks: 323 WARNING @ Fri, 05 Jul 2019 14:51:41: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Fri, 05 Jul 2019 14:51:41: start model_add_line... INFO @ Fri, 05 Jul 2019 14:51:41: start X-correlation... INFO @ Fri, 05 Jul 2019 14:51:41: end of X-cor INFO @ Fri, 05 Jul 2019 14:51:41: #2 finished! INFO @ Fri, 05 Jul 2019 14:51:41: #2 predicted fragment length is 173 bps INFO @ Fri, 05 Jul 2019 14:51:41: #2 alternative fragment length(s) may be 173 bps INFO @ Fri, 05 Jul 2019 14:51:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.05_model.r INFO @ Fri, 05 Jul 2019 14:51:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:51:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:51:41: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:51:41: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:51:41: #1 total tags in treatment: 339433 INFO @ Fri, 05 Jul 2019 14:51:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:51:41: #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 14:51:41: #1 tags after filtering in treatment: 339433 INFO @ Fri, 05 Jul 2019 14:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:51:41: #1 finished! INFO @ Fri, 05 Jul 2019 14:51:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:51:41: #2 number of paired peaks: 323 WARNING @ Fri, 05 Jul 2019 14:51:41: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Fri, 05 Jul 2019 14:51:41: start model_add_line... INFO @ Fri, 05 Jul 2019 14:51:41: start X-correlation... INFO @ Fri, 05 Jul 2019 14:51:41: end of X-cor INFO @ Fri, 05 Jul 2019 14:51:41: #2 finished! INFO @ Fri, 05 Jul 2019 14:51:41: #2 predicted fragment length is 173 bps INFO @ Fri, 05 Jul 2019 14:51:41: #2 alternative fragment length(s) may be 173 bps INFO @ Fri, 05 Jul 2019 14:51:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.10_model.r INFO @ Fri, 05 Jul 2019 14:51:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:51:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:51:42: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:51:42: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:51:42: #1 total tags in treatment: 339433 INFO @ Fri, 05 Jul 2019 14:51:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:51:42: #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 14:51:42: #1 tags after filtering in treatment: 339433 INFO @ Fri, 05 Jul 2019 14:51:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:51:42: #1 finished! INFO @ Fri, 05 Jul 2019 14:51:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:51:42: #2 number of paired peaks: 323 WARNING @ Fri, 05 Jul 2019 14:51:42: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Fri, 05 Jul 2019 14:51:42: start model_add_line... INFO @ Fri, 05 Jul 2019 14:51:42: start X-correlation... INFO @ Fri, 05 Jul 2019 14:51:42: end of X-cor INFO @ Fri, 05 Jul 2019 14:51:42: #2 finished! INFO @ Fri, 05 Jul 2019 14:51:42: #2 predicted fragment length is 173 bps INFO @ Fri, 05 Jul 2019 14:51:42: #2 alternative fragment length(s) may be 173 bps INFO @ Fri, 05 Jul 2019 14:51:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.20_model.r INFO @ Fri, 05 Jul 2019 14:51:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:51:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:51:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:51:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:51:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:51:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:51:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.05_summits.bed INFO @ Fri, 05 Jul 2019 14:51:43: Done! INFO @ Fri, 05 Jul 2019 14:51:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:51:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:51:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.10_summits.bed INFO @ Fri, 05 Jul 2019 14:51:43: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (397 records, 4 fields): 5 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (248 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 14:51:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:51:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:51:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:51:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548090/ERX2548090.20_summits.bed INFO @ Fri, 05 Jul 2019 14:51:44: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (128 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。