Job ID = 2007234 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,839,915 reads read : 1,839,915 reads written : 1,839,915 spots read : 1,744,095 reads read : 1,744,095 reads written : 1,744,095 spots read : 1,735,775 reads read : 1,735,775 reads written : 1,735,775 spots read : 1,667,353 reads read : 1,667,353 reads written : 1,667,353 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529658.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529659.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529660.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529661.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: 00:04:19 6987138 reads; of these: 6987138 (100.00%) were unpaired; of these: 374342 (5.36%) aligned 0 times 5869338 (84.00%) aligned exactly 1 time 743458 (10.64%) aligned >1 times 94.64% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 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] 6418407 / 6612796 = 0.9706 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 16:03:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.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 16:03:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:03:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:03:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.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 16:03:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:03:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:03:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.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 16:03:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:03:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:03:05: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:03:05: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:03:05: #1 total tags in treatment: 194389 INFO @ Fri, 05 Jul 2019 16:03:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:03:05: #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 16:03:05: #1 tags after filtering in treatment: 194389 INFO @ Fri, 05 Jul 2019 16:03:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:03:05: #1 finished! INFO @ Fri, 05 Jul 2019 16:03:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:03:05: #2 number of paired peaks: 403 WARNING @ Fri, 05 Jul 2019 16:03:05: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Fri, 05 Jul 2019 16:03:05: start model_add_line... INFO @ Fri, 05 Jul 2019 16:03:05: start X-correlation... INFO @ Fri, 05 Jul 2019 16:03:05: end of X-cor INFO @ Fri, 05 Jul 2019 16:03:05: #2 finished! INFO @ Fri, 05 Jul 2019 16:03:05: #2 predicted fragment length is 198 bps INFO @ Fri, 05 Jul 2019 16:03:05: #2 alternative fragment length(s) may be 175,198,569 bps INFO @ Fri, 05 Jul 2019 16:03:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.05_model.r INFO @ Fri, 05 Jul 2019 16:03:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:03:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:03:06: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:03:06: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:03:06: #1 total tags in treatment: 194389 INFO @ Fri, 05 Jul 2019 16:03:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:03:06: #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 16:03:06: #1 tags after filtering in treatment: 194389 INFO @ Fri, 05 Jul 2019 16:03:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:03:06: #1 finished! INFO @ Fri, 05 Jul 2019 16:03:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:03:06: #2 number of paired peaks: 403 WARNING @ Fri, 05 Jul 2019 16:03:06: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Fri, 05 Jul 2019 16:03:06: start model_add_line... INFO @ Fri, 05 Jul 2019 16:03:06: start X-correlation... INFO @ Fri, 05 Jul 2019 16:03:06: end of X-cor INFO @ Fri, 05 Jul 2019 16:03:06: #2 finished! INFO @ Fri, 05 Jul 2019 16:03:06: #2 predicted fragment length is 198 bps INFO @ Fri, 05 Jul 2019 16:03:06: #2 alternative fragment length(s) may be 175,198,569 bps INFO @ Fri, 05 Jul 2019 16:03:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.10_model.r INFO @ Fri, 05 Jul 2019 16:03:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:03:06: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:03:06: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:03:06: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:03:06: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:03:06: #1 total tags in treatment: 194389 INFO @ Fri, 05 Jul 2019 16:03:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:03:06: #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 16:03:06: #1 tags after filtering in treatment: 194389 INFO @ Fri, 05 Jul 2019 16:03:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:03:06: #1 finished! INFO @ Fri, 05 Jul 2019 16:03:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:03:06: #2 number of paired peaks: 403 WARNING @ Fri, 05 Jul 2019 16:03:06: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Fri, 05 Jul 2019 16:03:06: start model_add_line... INFO @ Fri, 05 Jul 2019 16:03:06: start X-correlation... INFO @ Fri, 05 Jul 2019 16:03:06: end of X-cor INFO @ Fri, 05 Jul 2019 16:03:06: #2 finished! INFO @ Fri, 05 Jul 2019 16:03:06: #2 predicted fragment length is 198 bps INFO @ Fri, 05 Jul 2019 16:03:06: #2 alternative fragment length(s) may be 175,198,569 bps INFO @ Fri, 05 Jul 2019 16:03:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.20_model.r INFO @ Fri, 05 Jul 2019 16:03:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:03:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:03:06: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:03:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:03:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:03:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.05_summits.bed INFO @ Fri, 05 Jul 2019 16:03:07: Done! BigWig に変換しました。 pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (173 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 16:03:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:03:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:03:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.10_summits.bed INFO @ Fri, 05 Jul 2019 16:03:07: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (68 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:03:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:03:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:03:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:03:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548204/ERX2548204.20_summits.bed INFO @ Fri, 05 Jul 2019 16:03:08: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (24 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling