Job ID = 2007230 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,836,312 reads read : 1,836,312 reads written : 1,836,312 spots read : 1,765,377 reads read : 1,765,377 reads written : 1,765,377 spots read : 1,805,538 reads read : 1,805,538 reads written : 1,805,538 spots read : 1,735,821 reads read : 1,735,821 reads written : 1,735,821 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529642.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529643.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529644.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529645.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: 00:01:50 7143048 reads; of these: 7143048 (100.00%) were unpaired; of these: 470637 (6.59%) aligned 0 times 5659248 (79.23%) aligned exactly 1 time 1013163 (14.18%) aligned >1 times 93.41% overall alignment rate Time searching: 00:01:50 Overall time: 00:01:50 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] 6556429 / 6672411 = 0.9826 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 16:03:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.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 16:03:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:03:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:03:41: #1 tag size is determined as 74 bps INFO @ Fri, 05 Jul 2019 16:03:41: #1 tag size = 74 INFO @ Fri, 05 Jul 2019 16:03:41: #1 total tags in treatment: 115982 INFO @ Fri, 05 Jul 2019 16:03:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:03:41: #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 16:03:41: #1 tags after filtering in treatment: 115982 INFO @ Fri, 05 Jul 2019 16:03:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:03:41: #1 finished! INFO @ Fri, 05 Jul 2019 16:03:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:03:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:03:41: #2 number of paired peaks: 454 WARNING @ Fri, 05 Jul 2019 16:03:41: Fewer paired peaks (454) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 454 pairs to build model! INFO @ Fri, 05 Jul 2019 16:03:41: start model_add_line... INFO @ Fri, 05 Jul 2019 16:03:41: start X-correlation... INFO @ Fri, 05 Jul 2019 16:03:41: end of X-cor INFO @ Fri, 05 Jul 2019 16:03:41: #2 finished! INFO @ Fri, 05 Jul 2019 16:03:41: #2 predicted fragment length is 223 bps INFO @ Fri, 05 Jul 2019 16:03:41: #2 alternative fragment length(s) may be 12,60,103,128,154,175,223,246,267,289,305,364,389,462,512,533,562 bps INFO @ Fri, 05 Jul 2019 16:03:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.05_model.r INFO @ Fri, 05 Jul 2019 16:03:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:03:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:03:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.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 16:03:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:03:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:03:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:03:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:03:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:03:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.05_summits.bed INFO @ Fri, 05 Jul 2019 16:03:42: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:03:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.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 16:03:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:03:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:03:42: #1 tag size is determined as 74 bps INFO @ Fri, 05 Jul 2019 16:03:42: #1 tag size = 74 INFO @ Fri, 05 Jul 2019 16:03:42: #1 total tags in treatment: 115982 INFO @ Fri, 05 Jul 2019 16:03:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:03:42: #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 16:03:42: #1 tags after filtering in treatment: 115982 INFO @ Fri, 05 Jul 2019 16:03:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:03:42: #1 finished! INFO @ Fri, 05 Jul 2019 16:03:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:03:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:03:42: #2 number of paired peaks: 454 WARNING @ Fri, 05 Jul 2019 16:03:42: Fewer paired peaks (454) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 454 pairs to build model! INFO @ Fri, 05 Jul 2019 16:03:42: start model_add_line... INFO @ Fri, 05 Jul 2019 16:03:42: start X-correlation... INFO @ Fri, 05 Jul 2019 16:03:42: end of X-cor INFO @ Fri, 05 Jul 2019 16:03:42: #2 finished! INFO @ Fri, 05 Jul 2019 16:03:42: #2 predicted fragment length is 223 bps INFO @ Fri, 05 Jul 2019 16:03:42: #2 alternative fragment length(s) may be 12,60,103,128,154,175,223,246,267,289,305,364,389,462,512,533,562 bps INFO @ Fri, 05 Jul 2019 16:03:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.10_model.r INFO @ Fri, 05 Jul 2019 16:03:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:03:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:03:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:03:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:03:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:03:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.10_summits.bed INFO @ Fri, 05 Jul 2019 16:03:43: Done! INFO @ Fri, 05 Jul 2019 16:03:43: #1 tag size is determined as 74 bps INFO @ Fri, 05 Jul 2019 16:03:43: #1 tag size = 74 INFO @ Fri, 05 Jul 2019 16:03:43: #1 total tags in treatment: 115982 INFO @ Fri, 05 Jul 2019 16:03:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:03:43: #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 16:03:43: #1 tags after filtering in treatment: 115982 INFO @ Fri, 05 Jul 2019 16:03:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:03:43: #1 finished! INFO @ Fri, 05 Jul 2019 16:03:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:03:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:03:43: #2 number of paired peaks: 454 WARNING @ Fri, 05 Jul 2019 16:03:43: Fewer paired peaks (454) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 454 pairs to build model! INFO @ Fri, 05 Jul 2019 16:03:43: start model_add_line... INFO @ Fri, 05 Jul 2019 16:03:43: start X-correlation... INFO @ Fri, 05 Jul 2019 16:03:43: end of X-cor INFO @ Fri, 05 Jul 2019 16:03:43: #2 finished! INFO @ Fri, 05 Jul 2019 16:03:43: #2 predicted fragment length is 223 bps INFO @ Fri, 05 Jul 2019 16:03:43: #2 alternative fragment length(s) may be 12,60,103,128,154,175,223,246,267,289,305,364,389,462,512,533,562 bps INFO @ Fri, 05 Jul 2019 16:03:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.20_model.r INFO @ Fri, 05 Jul 2019 16:03:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:03:43: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:03:43: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:03:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:03:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:03:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548200/ERX2548200.20_summits.bed INFO @ Fri, 05 Jul 2019 16:03:44: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling