Job ID = 2007227 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,053,269 reads read : 1,053,269 reads written : 1,053,269 spots read : 1,013,587 reads read : 1,013,587 reads written : 1,013,587 spots read : 1,036,632 reads read : 1,036,632 reads written : 1,036,632 spots read : 998,899 reads read : 998,899 reads written : 998,899 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529630.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529631.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529632.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529633.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: 00:01:06 4102387 reads; of these: 4102387 (100.00%) were unpaired; of these: 174522 (4.25%) aligned 0 times 3313545 (80.77%) aligned exactly 1 time 614320 (14.97%) aligned >1 times 95.75% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 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] 3720276 / 3927865 = 0.9471 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 15:54:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.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 15:54:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:54:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:54:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.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 15:54:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:54:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:54:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.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 15:54:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:54:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:54:12: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:54:12: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:54:12: #1 total tags in treatment: 207589 INFO @ Fri, 05 Jul 2019 15:54:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:54:12: #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 15:54:12: #1 tags after filtering in treatment: 207589 INFO @ Fri, 05 Jul 2019 15:54:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:54:12: #1 finished! INFO @ Fri, 05 Jul 2019 15:54:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:54:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:54:12: #2 number of paired peaks: 385 WARNING @ Fri, 05 Jul 2019 15:54:12: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Fri, 05 Jul 2019 15:54:12: start model_add_line... INFO @ Fri, 05 Jul 2019 15:54:12: start X-correlation... INFO @ Fri, 05 Jul 2019 15:54:12: end of X-cor INFO @ Fri, 05 Jul 2019 15:54:12: #2 finished! INFO @ Fri, 05 Jul 2019 15:54:12: #2 predicted fragment length is 277 bps INFO @ Fri, 05 Jul 2019 15:54:12: #2 alternative fragment length(s) may be 4,14,59,113,139,199,225,259,261,277,301,323,357,384,412,447,469,506,565 bps INFO @ Fri, 05 Jul 2019 15:54:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.05_model.r INFO @ Fri, 05 Jul 2019 15:54:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:54:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:54:12: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:54:12: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:54:12: #1 total tags in treatment: 207589 INFO @ Fri, 05 Jul 2019 15:54:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:54:12: #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 15:54:12: #1 tags after filtering in treatment: 207589 INFO @ Fri, 05 Jul 2019 15:54:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:54:12: #1 finished! INFO @ Fri, 05 Jul 2019 15:54:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:54:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:54:12: #2 number of paired peaks: 385 WARNING @ Fri, 05 Jul 2019 15:54:12: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Fri, 05 Jul 2019 15:54:12: start model_add_line... INFO @ Fri, 05 Jul 2019 15:54:12: start X-correlation... INFO @ Fri, 05 Jul 2019 15:54:12: end of X-cor INFO @ Fri, 05 Jul 2019 15:54:12: #2 finished! INFO @ Fri, 05 Jul 2019 15:54:12: #2 predicted fragment length is 277 bps INFO @ Fri, 05 Jul 2019 15:54:12: #2 alternative fragment length(s) may be 4,14,59,113,139,199,225,259,261,277,301,323,357,384,412,447,469,506,565 bps INFO @ Fri, 05 Jul 2019 15:54:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.10_model.r INFO @ Fri, 05 Jul 2019 15:54:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:54:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:54:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:54:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:54:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:54:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.05_summits.bed INFO @ Fri, 05 Jul 2019 15:54:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (62 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:54:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:54:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:54:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:54:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.10_summits.bed INFO @ Fri, 05 Jul 2019 15:54:14: Done! INFO @ Fri, 05 Jul 2019 15:54:14: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:54:14: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:54:14: #1 total tags in treatment: 207589 INFO @ Fri, 05 Jul 2019 15:54:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:54:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (6 chroms): 1 millis INFO @ Fri, 05 Jul 2019 15:54:14: #1 tags after filtering in treatment: 207589 INFO @ Fri, 05 Jul 2019 15:54:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:54:14: #1 finished! INFO @ Fri, 05 Jul 2019 15:54:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:54:14: #2 looking for paired plus/minus strand peaks... pass2 - checking and writing primary data (13 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:54:14: #2 number of paired peaks: 385 WARNING @ Fri, 05 Jul 2019 15:54:14: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Fri, 05 Jul 2019 15:54:14: start model_add_line... INFO @ Fri, 05 Jul 2019 15:54:14: start X-correlation... INFO @ Fri, 05 Jul 2019 15:54:14: end of X-cor INFO @ Fri, 05 Jul 2019 15:54:14: #2 finished! INFO @ Fri, 05 Jul 2019 15:54:14: #2 predicted fragment length is 277 bps INFO @ Fri, 05 Jul 2019 15:54:14: #2 alternative fragment length(s) may be 4,14,59,113,139,199,225,259,261,277,301,323,357,384,412,447,469,506,565 bps INFO @ Fri, 05 Jul 2019 15:54:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.20_model.r INFO @ Fri, 05 Jul 2019 15:54:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:54:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:54:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:54:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:54:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:54:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548197/ERX2548197.20_summits.bed INFO @ Fri, 05 Jul 2019 15:54:15: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling