Job ID = 2005988 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,334,083 reads read : 1,334,083 reads written : 1,334,083 spots read : 1,320,015 reads read : 1,320,015 reads written : 1,320,015 spots read : 1,314,569 reads read : 1,314,569 reads written : 1,314,569 spots read : 1,281,204 reads read : 1,281,204 reads written : 1,281,204 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529258.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529259.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529260.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529261.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: 00:01:20 5249871 reads; of these: 5249871 (100.00%) were unpaired; of these: 216079 (4.12%) aligned 0 times 4495006 (85.62%) aligned exactly 1 time 538786 (10.26%) aligned >1 times 95.88% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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] 4745830 / 5033792 = 0.9428 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 14:49:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.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 14:49:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:49:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:49:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.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 14:49:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:49:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:49:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.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 14:49:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:49:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:49:29: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:49:29: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:49:29: #1 total tags in treatment: 287962 INFO @ Fri, 05 Jul 2019 14:49:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:49:29: #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 14:49:29: #1 tags after filtering in treatment: 287962 INFO @ Fri, 05 Jul 2019 14:49:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:49:29: #1 finished! INFO @ Fri, 05 Jul 2019 14:49:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:49:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:49:29: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:49:29: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:49:29: #1 total tags in treatment: 287962 INFO @ Fri, 05 Jul 2019 14:49:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:49:29: #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 14:49:29: #2 number of paired peaks: 495 WARNING @ Fri, 05 Jul 2019 14:49:29: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Fri, 05 Jul 2019 14:49:29: start model_add_line... INFO @ Fri, 05 Jul 2019 14:49:29: #1 tags after filtering in treatment: 287962 INFO @ Fri, 05 Jul 2019 14:49:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:49:29: #1 finished! INFO @ Fri, 05 Jul 2019 14:49:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:49:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:49:29: start X-correlation... INFO @ Fri, 05 Jul 2019 14:49:29: end of X-cor INFO @ Fri, 05 Jul 2019 14:49:29: #2 finished! INFO @ Fri, 05 Jul 2019 14:49:29: #2 predicted fragment length is 200 bps INFO @ Fri, 05 Jul 2019 14:49:29: #2 alternative fragment length(s) may be 200 bps INFO @ Fri, 05 Jul 2019 14:49:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.05_model.r INFO @ Fri, 05 Jul 2019 14:49:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:49:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:49:29: #2 number of paired peaks: 495 WARNING @ Fri, 05 Jul 2019 14:49:29: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Fri, 05 Jul 2019 14:49:29: start model_add_line... INFO @ Fri, 05 Jul 2019 14:49:29: start X-correlation... INFO @ Fri, 05 Jul 2019 14:49:29: end of X-cor INFO @ Fri, 05 Jul 2019 14:49:29: #2 finished! INFO @ Fri, 05 Jul 2019 14:49:29: #2 predicted fragment length is 200 bps INFO @ Fri, 05 Jul 2019 14:49:29: #2 alternative fragment length(s) may be 200 bps INFO @ Fri, 05 Jul 2019 14:49:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.10_model.r INFO @ Fri, 05 Jul 2019 14:49:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:49:29: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 14:49:30: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:49:30: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:49:30: #1 total tags in treatment: 287962 INFO @ Fri, 05 Jul 2019 14:49:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:49:30: #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 14:49:30: #1 tags after filtering in treatment: 287962 INFO @ Fri, 05 Jul 2019 14:49:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:49:30: #1 finished! INFO @ Fri, 05 Jul 2019 14:49:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:49:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:49:30: #2 number of paired peaks: 495 WARNING @ Fri, 05 Jul 2019 14:49:30: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Fri, 05 Jul 2019 14:49:30: start model_add_line... INFO @ Fri, 05 Jul 2019 14:49:30: start X-correlation... INFO @ Fri, 05 Jul 2019 14:49:30: end of X-cor INFO @ Fri, 05 Jul 2019 14:49:30: #2 finished! INFO @ Fri, 05 Jul 2019 14:49:30: #2 predicted fragment length is 200 bps INFO @ Fri, 05 Jul 2019 14:49:30: #2 alternative fragment length(s) may be 200 bps INFO @ Fri, 05 Jul 2019 14:49:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.20_model.r INFO @ Fri, 05 Jul 2019 14:49:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:49:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:49:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:49:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 14:49:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:49:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:49:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.10_summits.bed INFO @ Fri, 05 Jul 2019 14:49:31: Done! INFO @ Fri, 05 Jul 2019 14:49:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:49:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:49:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.05_summits.bed INFO @ Fri, 05 Jul 2019 14:49:31: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (347 records, 4 fields): 3 millis pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (459 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 14:49:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:49:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:49:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:49:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548086/ERX2548086.20_summits.bed INFO @ Fri, 05 Jul 2019 14:49:32: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (263 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling