Job ID = 2006615 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,372,694 reads read : 3,372,694 reads written : 3,372,694 spots read : 3,196,830 reads read : 3,196,830 reads written : 3,196,830 spots read : 3,217,142 reads read : 3,217,142 reads written : 3,217,142 spots read : 3,077,421 reads read : 3,077,421 reads written : 3,077,421 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529514.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529515.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529516.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529517.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: 00:00:01 Multiseed full-index search: 00:03:24 12864087 reads; of these: 12864087 (100.00%) were unpaired; of these: 410267 (3.19%) aligned 0 times 10660108 (82.87%) aligned exactly 1 time 1793712 (13.94%) aligned >1 times 96.81% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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 8 files... [bam_rmdupse_core] 12100796 / 12453820 = 0.9717 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 15:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.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 15:46:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:46:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:46:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.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 15:46:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:46:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:46:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.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 15:46:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:46:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:46:32: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:46:32: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:46:32: #1 total tags in treatment: 353024 INFO @ Fri, 05 Jul 2019 15:46:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:46:32: #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 15:46:32: #1 tags after filtering in treatment: 353024 INFO @ Fri, 05 Jul 2019 15:46:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:46:32: #1 finished! INFO @ Fri, 05 Jul 2019 15:46:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:46:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:46:32: #2 number of paired peaks: 444 WARNING @ Fri, 05 Jul 2019 15:46:32: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Fri, 05 Jul 2019 15:46:32: start model_add_line... INFO @ Fri, 05 Jul 2019 15:46:32: start X-correlation... INFO @ Fri, 05 Jul 2019 15:46:32: end of X-cor INFO @ Fri, 05 Jul 2019 15:46:32: #2 finished! INFO @ Fri, 05 Jul 2019 15:46:32: #2 predicted fragment length is 177 bps INFO @ Fri, 05 Jul 2019 15:46:32: #2 alternative fragment length(s) may be 155,177,194,201 bps INFO @ Fri, 05 Jul 2019 15:46:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.05_model.r INFO @ Fri, 05 Jul 2019 15:46:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:46:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:46:33: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:46:33: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:46:33: #1 total tags in treatment: 353024 INFO @ Fri, 05 Jul 2019 15:46:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:46:33: #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 15:46:33: #1 tags after filtering in treatment: 353024 INFO @ Fri, 05 Jul 2019 15:46:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:46:33: #1 finished! INFO @ Fri, 05 Jul 2019 15:46:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:46:33: #2 number of paired peaks: 444 WARNING @ Fri, 05 Jul 2019 15:46:33: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Fri, 05 Jul 2019 15:46:33: start model_add_line... INFO @ Fri, 05 Jul 2019 15:46:33: start X-correlation... INFO @ Fri, 05 Jul 2019 15:46:33: end of X-cor INFO @ Fri, 05 Jul 2019 15:46:33: #2 finished! INFO @ Fri, 05 Jul 2019 15:46:33: #2 predicted fragment length is 177 bps INFO @ Fri, 05 Jul 2019 15:46:33: #2 alternative fragment length(s) may be 155,177,194,201 bps INFO @ Fri, 05 Jul 2019 15:46:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.10_model.r INFO @ Fri, 05 Jul 2019 15:46:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:46:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:46:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:46:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:46:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:46:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.05_summits.bed INFO @ Fri, 05 Jul 2019 15:46:34: Done! INFO @ Fri, 05 Jul 2019 15:46:34: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:46:34: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:46:34: #1 total tags in treatment: 353024 INFO @ Fri, 05 Jul 2019 15:46:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:46:34: #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 15:46:34: #1 tags after filtering in treatment: 353024 INFO @ Fri, 05 Jul 2019 15:46:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:46:34: #1 finished! INFO @ Fri, 05 Jul 2019 15:46:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:46:34: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (16 chroms): 1 millis INFO @ Fri, 05 Jul 2019 15:46:34: #2 number of paired peaks: 444 WARNING @ Fri, 05 Jul 2019 15:46:34: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Fri, 05 Jul 2019 15:46:34: start model_add_line... INFO @ Fri, 05 Jul 2019 15:46:34: start X-correlation... INFO @ Fri, 05 Jul 2019 15:46:34: end of X-cor INFO @ Fri, 05 Jul 2019 15:46:34: #2 finished! INFO @ Fri, 05 Jul 2019 15:46:34: #2 predicted fragment length is 177 bps INFO @ Fri, 05 Jul 2019 15:46:34: #2 alternative fragment length(s) may be 155,177,194,201 bps INFO @ Fri, 05 Jul 2019 15:46:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.20_model.r INFO @ Fri, 05 Jul 2019 15:46:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:46:34: #3 Pre-compute pvalue-qvalue table... pass2 - checking and writing primary data (330 records, 4 fields): 135 millis INFO @ Fri, 05 Jul 2019 15:46:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:46:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:46:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:46:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.10_summits.bed INFO @ Fri, 05 Jul 2019 15:46:35: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (170 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:46:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:46:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:46:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:46:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548162/ERX2548162.20_summits.bed INFO @ Fri, 05 Jul 2019 15:46:36: Done! pass1 - making usageList (16 chroms): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... pass2 - checking and writing primary data (72 records, 4 fields): 43 millis CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling