Job ID = 2005923 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,370,409 reads read : 1,370,409 reads written : 1,370,409 spots read : 1,359,451 reads read : 1,359,451 reads written : 1,359,451 spots read : 1,346,542 reads read : 1,346,542 reads written : 1,346,542 spots read : 1,318,754 reads read : 1,318,754 reads written : 1,318,754 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529255.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529256.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529257.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: 00:02:27 5395156 reads; of these: 5395156 (100.00%) were unpaired; of these: 221235 (4.10%) aligned 0 times 4653259 (86.25%) aligned exactly 1 time 520662 (9.65%) aligned >1 times 95.90% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 4880832 / 5173921 = 0.9434 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 14:50:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.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 14:50:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:50:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:50:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.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 14:50:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:50:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.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 14:50:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:50:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:50:22: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:50:22: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:50:22: #1 total tags in treatment: 293089 INFO @ Fri, 05 Jul 2019 14:50:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:50:22: #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 14:50:22: #1 tags after filtering in treatment: 293089 INFO @ Fri, 05 Jul 2019 14:50:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:50:22: #1 finished! INFO @ Fri, 05 Jul 2019 14:50:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:50:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:50:22: #2 number of paired peaks: 511 WARNING @ Fri, 05 Jul 2019 14:50:22: Fewer paired peaks (511) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 511 pairs to build model! INFO @ Fri, 05 Jul 2019 14:50:22: start model_add_line... INFO @ Fri, 05 Jul 2019 14:50:22: start X-correlation... INFO @ Fri, 05 Jul 2019 14:50:22: end of X-cor INFO @ Fri, 05 Jul 2019 14:50:22: #2 finished! INFO @ Fri, 05 Jul 2019 14:50:22: #2 predicted fragment length is 200 bps INFO @ Fri, 05 Jul 2019 14:50:22: #2 alternative fragment length(s) may be 200 bps INFO @ Fri, 05 Jul 2019 14:50:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.05_model.r INFO @ Fri, 05 Jul 2019 14:50:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:50:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:50:23: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:50:23: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:50:23: #1 total tags in treatment: 293089 INFO @ Fri, 05 Jul 2019 14:50:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:50:23: #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 14:50:24: #1 tags after filtering in treatment: 293089 INFO @ Fri, 05 Jul 2019 14:50:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:50:24: #1 finished! INFO @ Fri, 05 Jul 2019 14:50:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:50:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:50:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:50:24: #2 number of paired peaks: 511 WARNING @ Fri, 05 Jul 2019 14:50:24: Fewer paired peaks (511) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 511 pairs to build model! INFO @ Fri, 05 Jul 2019 14:50:24: start model_add_line... INFO @ Fri, 05 Jul 2019 14:50:24: start X-correlation... INFO @ Fri, 05 Jul 2019 14:50:24: end of X-cor INFO @ Fri, 05 Jul 2019 14:50:24: #2 finished! INFO @ Fri, 05 Jul 2019 14:50:24: #2 predicted fragment length is 200 bps INFO @ Fri, 05 Jul 2019 14:50:24: #2 alternative fragment length(s) may be 200 bps INFO @ Fri, 05 Jul 2019 14:50:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.10_model.r INFO @ Fri, 05 Jul 2019 14:50:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:50:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:50:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:50:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:50:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.05_summits.bed INFO @ Fri, 05 Jul 2019 14:50:24: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (479 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 14:50:24: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:50:24: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:50:24: #1 total tags in treatment: 293089 INFO @ Fri, 05 Jul 2019 14:50:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:50:24: #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 14:50:24: #1 tags after filtering in treatment: 293089 INFO @ Fri, 05 Jul 2019 14:50:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:50:24: #1 finished! INFO @ Fri, 05 Jul 2019 14:50:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:50:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:50:24: #2 number of paired peaks: 511 WARNING @ Fri, 05 Jul 2019 14:50:24: Fewer paired peaks (511) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 511 pairs to build model! INFO @ Fri, 05 Jul 2019 14:50:24: start model_add_line... INFO @ Fri, 05 Jul 2019 14:50:24: start X-correlation... INFO @ Fri, 05 Jul 2019 14:50:24: end of X-cor INFO @ Fri, 05 Jul 2019 14:50:24: #2 finished! INFO @ Fri, 05 Jul 2019 14:50:24: #2 predicted fragment length is 200 bps INFO @ Fri, 05 Jul 2019 14:50:24: #2 alternative fragment length(s) may be 200 bps INFO @ Fri, 05 Jul 2019 14:50:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.20_model.r INFO @ Fri, 05 Jul 2019 14:50:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:50:24: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 14:50:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:50:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:50:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:50:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.10_summits.bed INFO @ Fri, 05 Jul 2019 14:50:26: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 14:50:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:50:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:50:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:50:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548085/ERX2548085.20_summits.bed INFO @ Fri, 05 Jul 2019 14:50:26: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (286 records, 4 fields): 4 millis BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling