Job ID = 2007641 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,941,022 reads read : 1,941,022 reads written : 1,941,022 spots read : 1,866,144 reads read : 1,866,144 reads written : 1,866,144 spots read : 1,905,653 reads read : 1,905,653 reads written : 1,905,653 spots read : 1,833,148 reads read : 1,833,148 reads written : 1,833,148 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529780.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529781.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: 00:01:39 7545967 reads; of these: 7545967 (100.00%) were unpaired; of these: 1212345 (16.07%) aligned 0 times 5263068 (69.75%) aligned exactly 1 time 1070554 (14.19%) aligned >1 times 83.93% overall alignment rate Time searching: 00:01:39 Overall time: 00:01:39 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] 6012526 / 6333622 = 0.9493 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 16:15:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.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 16:15:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:15:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:15:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.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 16:15:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:15:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:15:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.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 16:15:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:15:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:15:39: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:15:39: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:15:39: #1 total tags in treatment: 321096 INFO @ Fri, 05 Jul 2019 16:15:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:15:39: #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 16:15:39: #1 tags after filtering in treatment: 321096 INFO @ Fri, 05 Jul 2019 16:15:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:15:39: #1 finished! INFO @ Fri, 05 Jul 2019 16:15:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:15:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:15:39: #2 number of paired peaks: 434 WARNING @ Fri, 05 Jul 2019 16:15:39: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Fri, 05 Jul 2019 16:15:39: start model_add_line... INFO @ Fri, 05 Jul 2019 16:15:39: start X-correlation... INFO @ Fri, 05 Jul 2019 16:15:39: end of X-cor INFO @ Fri, 05 Jul 2019 16:15:39: #2 finished! INFO @ Fri, 05 Jul 2019 16:15:39: #2 predicted fragment length is 180 bps INFO @ Fri, 05 Jul 2019 16:15:39: #2 alternative fragment length(s) may be 106,130,157,180 bps INFO @ Fri, 05 Jul 2019 16:15:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.05_model.r INFO @ Fri, 05 Jul 2019 16:15:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:15:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:15:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:15:40: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:15:40: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:15:40: #1 total tags in treatment: 321096 INFO @ Fri, 05 Jul 2019 16:15:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:15:40: #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 16:15:40: #1 tags after filtering in treatment: 321096 INFO @ Fri, 05 Jul 2019 16:15:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:15:41: #1 finished! INFO @ Fri, 05 Jul 2019 16:15:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:15:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:15:41: #2 number of paired peaks: 434 WARNING @ Fri, 05 Jul 2019 16:15:41: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Fri, 05 Jul 2019 16:15:41: start model_add_line... INFO @ Fri, 05 Jul 2019 16:15:41: start X-correlation... INFO @ Fri, 05 Jul 2019 16:15:41: end of X-cor INFO @ Fri, 05 Jul 2019 16:15:41: #2 finished! INFO @ Fri, 05 Jul 2019 16:15:41: #2 predicted fragment length is 180 bps INFO @ Fri, 05 Jul 2019 16:15:41: #2 alternative fragment length(s) may be 106,130,157,180 bps INFO @ Fri, 05 Jul 2019 16:15:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.10_model.r INFO @ Fri, 05 Jul 2019 16:15:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:15:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:15:41: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:15:41: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:15:41: #1 total tags in treatment: 321096 INFO @ Fri, 05 Jul 2019 16:15:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:15:41: #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 16:15:41: #1 tags after filtering in treatment: 321096 INFO @ Fri, 05 Jul 2019 16:15:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:15:41: #1 finished! INFO @ Fri, 05 Jul 2019 16:15:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:15:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:15:41: #2 number of paired peaks: 434 WARNING @ Fri, 05 Jul 2019 16:15:41: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Fri, 05 Jul 2019 16:15:41: start model_add_line... INFO @ Fri, 05 Jul 2019 16:15:41: start X-correlation... INFO @ Fri, 05 Jul 2019 16:15:41: end of X-cor INFO @ Fri, 05 Jul 2019 16:15:41: #2 finished! INFO @ Fri, 05 Jul 2019 16:15:41: #2 predicted fragment length is 180 bps INFO @ Fri, 05 Jul 2019 16:15:41: #2 alternative fragment length(s) may be 106,130,157,180 bps INFO @ Fri, 05 Jul 2019 16:15:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.20_model.r INFO @ Fri, 05 Jul 2019 16:15:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:15:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:15:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:15:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:15:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.05_summits.bed INFO @ Fri, 05 Jul 2019 16:15:41: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (170 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:15:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:15:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:15:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:15:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:15:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.10_summits.bed INFO @ Fri, 05 Jul 2019 16:15:43: Done! INFO @ Fri, 05 Jul 2019 16:15:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:15:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:15:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548240/ERX2548240.20_summits.bed INFO @ Fri, 05 Jul 2019 16:15:43: Done! pass1 - making usageList (14 chroms): 1 millis pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (58 records, 4 fields): 2 millis pass2 - checking and writing primary data (21 records, 4 fields): 81 millis BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling