Job ID = 2006048 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,077,933 reads read : 1,077,933 reads written : 1,077,933 spots read : 1,052,741 reads read : 1,052,741 reads written : 1,052,741 spots read : 1,089,152 reads read : 1,089,152 reads written : 1,089,152 spots read : 1,014,823 reads read : 1,014,823 reads written : 1,014,823 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529296.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529297.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529298.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529299.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: 00:04:03 4234649 reads; of these: 4234649 (100.00%) were unpaired; of these: 214309 (5.06%) aligned 0 times 3334390 (78.74%) aligned exactly 1 time 685950 (16.20%) aligned >1 times 94.94% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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] 3937808 / 4020340 = 0.9795 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 14:59:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.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 14:59:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:59:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:59:49: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:59:49: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:59:49: #1 total tags in treatment: 82532 INFO @ Fri, 05 Jul 2019 14:59:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:59:49: #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 14:59:49: #1 tags after filtering in treatment: 82532 INFO @ Fri, 05 Jul 2019 14:59:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:59:49: #1 finished! INFO @ Fri, 05 Jul 2019 14:59:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:59:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:59:49: #2 number of paired peaks: 458 WARNING @ Fri, 05 Jul 2019 14:59:49: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Fri, 05 Jul 2019 14:59:49: start model_add_line... INFO @ Fri, 05 Jul 2019 14:59:49: start X-correlation... INFO @ Fri, 05 Jul 2019 14:59:49: end of X-cor INFO @ Fri, 05 Jul 2019 14:59:49: #2 finished! INFO @ Fri, 05 Jul 2019 14:59:49: #2 predicted fragment length is 232 bps INFO @ Fri, 05 Jul 2019 14:59:49: #2 alternative fragment length(s) may be 12,53,79,103,114,139,170,200,232,294,321,388,459,487,496,520,553,583 bps INFO @ Fri, 05 Jul 2019 14:59:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.05_model.r INFO @ Fri, 05 Jul 2019 14:59:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:59:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:59:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:59:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.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 14:59:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:59:49: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 14:59:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:59:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:59:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.05_summits.bed INFO @ Fri, 05 Jul 2019 14:59:49: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 14:59:50: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:59:50: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:59:50: #1 total tags in treatment: 82532 INFO @ Fri, 05 Jul 2019 14:59:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:59:50: #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 14:59:50: #1 tags after filtering in treatment: 82532 INFO @ Fri, 05 Jul 2019 14:59:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:59:50: #1 finished! INFO @ Fri, 05 Jul 2019 14:59:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:59:50: #2 number of paired peaks: 458 WARNING @ Fri, 05 Jul 2019 14:59:50: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Fri, 05 Jul 2019 14:59:50: start model_add_line... INFO @ Fri, 05 Jul 2019 14:59:50: start X-correlation... INFO @ Fri, 05 Jul 2019 14:59:50: end of X-cor INFO @ Fri, 05 Jul 2019 14:59:50: #2 finished! INFO @ Fri, 05 Jul 2019 14:59:50: #2 predicted fragment length is 232 bps INFO @ Fri, 05 Jul 2019 14:59:50: #2 alternative fragment length(s) may be 12,53,79,103,114,139,170,200,232,294,321,388,459,487,496,520,553,583 bps INFO @ Fri, 05 Jul 2019 14:59:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.10_model.r INFO @ Fri, 05 Jul 2019 14:59:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:59:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:59:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.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 14:59:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:59:50: #1 read treatment tags... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 14:59:51: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:59:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:59:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:59:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.10_summits.bed INFO @ Fri, 05 Jul 2019 14:59:51: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 14:59:51: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:59:51: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:59:51: #1 total tags in treatment: 82532 INFO @ Fri, 05 Jul 2019 14:59:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:59:51: #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 14:59:51: #1 tags after filtering in treatment: 82532 INFO @ Fri, 05 Jul 2019 14:59:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:59:51: #1 finished! INFO @ Fri, 05 Jul 2019 14:59:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:59:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:59:51: #2 number of paired peaks: 458 WARNING @ Fri, 05 Jul 2019 14:59:51: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Fri, 05 Jul 2019 14:59:51: start model_add_line... INFO @ Fri, 05 Jul 2019 14:59:51: start X-correlation... INFO @ Fri, 05 Jul 2019 14:59:51: end of X-cor INFO @ Fri, 05 Jul 2019 14:59:51: #2 finished! INFO @ Fri, 05 Jul 2019 14:59:51: #2 predicted fragment length is 232 bps INFO @ Fri, 05 Jul 2019 14:59:51: #2 alternative fragment length(s) may be 12,53,79,103,114,139,170,200,232,294,321,388,459,487,496,520,553,583 bps INFO @ Fri, 05 Jul 2019 14:59:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.20_model.r INFO @ Fri, 05 Jul 2019 14:59:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:59:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:59:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:59:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:59:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548097/ERX2548097.20_summits.bed INFO @ Fri, 05 Jul 2019 14:59:52: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling