Job ID = 2007649 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,120,936 reads read : 3,120,936 reads written : 3,120,936 spots read : 2,961,605 reads read : 2,961,605 reads written : 2,961,605 spots read : 2,944,484 reads read : 2,944,484 reads written : 2,944,484 spots read : 2,810,845 reads read : 2,810,845 reads written : 2,810,845 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529802.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529803.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529804.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529805.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: 00:03:00 11837870 reads; of these: 11837870 (100.00%) were unpaired; of these: 663004 (5.60%) aligned 0 times 9468462 (79.98%) aligned exactly 1 time 1706404 (14.41%) aligned >1 times 94.40% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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] 10884958 / 11174866 = 0.9741 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 16:20:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.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 16:20:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:20:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:20:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.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 16:20:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:20:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:20:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.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 16:20:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:20:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:20:37: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:20:37: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:20:37: #1 total tags in treatment: 289908 INFO @ Fri, 05 Jul 2019 16:20:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:20:37: #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 16:20:37: #1 tags after filtering in treatment: 289908 INFO @ Fri, 05 Jul 2019 16:20:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:20:37: #1 finished! INFO @ Fri, 05 Jul 2019 16:20:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:20:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:20:37: #2 number of paired peaks: 441 WARNING @ Fri, 05 Jul 2019 16:20:37: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Fri, 05 Jul 2019 16:20:37: start model_add_line... INFO @ Fri, 05 Jul 2019 16:20:37: start X-correlation... INFO @ Fri, 05 Jul 2019 16:20:37: end of X-cor INFO @ Fri, 05 Jul 2019 16:20:37: #2 finished! INFO @ Fri, 05 Jul 2019 16:20:37: #2 predicted fragment length is 190 bps INFO @ Fri, 05 Jul 2019 16:20:37: #2 alternative fragment length(s) may be 190 bps INFO @ Fri, 05 Jul 2019 16:20:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.05_model.r INFO @ Fri, 05 Jul 2019 16:20:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:20:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:20:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:20:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:20:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:20:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.05_summits.bed INFO @ Fri, 05 Jul 2019 16:20:39: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 16:20:39: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:20:39: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:20:39: #1 total tags in treatment: 289908 INFO @ Fri, 05 Jul 2019 16:20:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:20:39: #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 16:20:39: #1 tags after filtering in treatment: 289908 INFO @ Fri, 05 Jul 2019 16:20:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:20:39: #1 finished! INFO @ Fri, 05 Jul 2019 16:20:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:20:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:20:39: #2 number of paired peaks: 441 WARNING @ Fri, 05 Jul 2019 16:20:39: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Fri, 05 Jul 2019 16:20:39: start model_add_line... INFO @ Fri, 05 Jul 2019 16:20:39: start X-correlation... INFO @ Fri, 05 Jul 2019 16:20:39: end of X-cor INFO @ Fri, 05 Jul 2019 16:20:39: #2 finished! INFO @ Fri, 05 Jul 2019 16:20:39: #2 predicted fragment length is 190 bps INFO @ Fri, 05 Jul 2019 16:20:39: #2 alternative fragment length(s) may be 190 bps INFO @ Fri, 05 Jul 2019 16:20:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.10_model.r INFO @ Fri, 05 Jul 2019 16:20:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:20:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:20:39: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:20:39: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:20:39: #1 total tags in treatment: 289908 INFO @ Fri, 05 Jul 2019 16:20:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:20:39: #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 16:20:39: #1 tags after filtering in treatment: 289908 INFO @ Fri, 05 Jul 2019 16:20:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:20:39: #1 finished! INFO @ Fri, 05 Jul 2019 16:20:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:20:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:20:39: #2 number of paired peaks: 441 WARNING @ Fri, 05 Jul 2019 16:20:39: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Fri, 05 Jul 2019 16:20:39: start model_add_line... INFO @ Fri, 05 Jul 2019 16:20:39: start X-correlation... INFO @ Fri, 05 Jul 2019 16:20:39: end of X-cor INFO @ Fri, 05 Jul 2019 16:20:39: #2 finished! INFO @ Fri, 05 Jul 2019 16:20:39: #2 predicted fragment length is 190 bps INFO @ Fri, 05 Jul 2019 16:20:39: #2 alternative fragment length(s) may be 190 bps INFO @ Fri, 05 Jul 2019 16:20:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.20_model.r INFO @ Fri, 05 Jul 2019 16:20:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:20:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:20:40: #3 Call peaks for each chromosome... BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 16:20:41: #3 Call peaks for each chromosome... BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:20:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:20:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:20:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.10_summits.bed INFO @ Fri, 05 Jul 2019 16:20:41: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:20:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:20:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:20:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548246/ERX2548246.20_summits.bed INFO @ Fri, 05 Jul 2019 16:20:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (103 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling