Job ID = 2008387 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,504,017 reads read : 8,504,017 reads written : 8,504,017 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637589.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: 00:00:52 8504017 reads; of these: 8504017 (100.00%) were unpaired; of these: 3539099 (41.62%) aligned 0 times 4117270 (48.42%) aligned exactly 1 time 847648 (9.97%) aligned >1 times 58.38% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 2421522 / 4964918 = 0.4877 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 05 Jul 2019 18:56:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.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 18:56:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:32: #1 read treatment tags... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 18:56:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.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 18:56:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:56:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.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 18:56:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:56:37: 1000000 INFO @ Fri, 05 Jul 2019 18:56:38: 1000000 INFO @ Fri, 05 Jul 2019 18:56:39: 1000000 INFO @ Fri, 05 Jul 2019 18:56:42: 2000000 INFO @ Fri, 05 Jul 2019 18:56:43: 2000000 INFO @ Fri, 05 Jul 2019 18:56:44: 2000000 INFO @ Fri, 05 Jul 2019 18:56:45: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 18:56:45: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 18:56:45: #1 total tags in treatment: 2543396 INFO @ Fri, 05 Jul 2019 18:56:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:56:45: #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 18:56:45: #1 tags after filtering in treatment: 2543396 INFO @ Fri, 05 Jul 2019 18:56:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:56:45: #1 finished! INFO @ Fri, 05 Jul 2019 18:56:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:56:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:56:45: #2 number of paired peaks: 308 WARNING @ Fri, 05 Jul 2019 18:56:45: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Fri, 05 Jul 2019 18:56:45: start model_add_line... INFO @ Fri, 05 Jul 2019 18:56:45: start X-correlation... INFO @ Fri, 05 Jul 2019 18:56:45: end of X-cor INFO @ Fri, 05 Jul 2019 18:56:45: #2 finished! INFO @ Fri, 05 Jul 2019 18:56:45: #2 predicted fragment length is 148 bps INFO @ Fri, 05 Jul 2019 18:56:45: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 05 Jul 2019 18:56:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.05_model.r INFO @ Fri, 05 Jul 2019 18:56:46: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 18:56:46: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 18:56:46: #1 total tags in treatment: 2543396 INFO @ Fri, 05 Jul 2019 18:56:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:56:46: #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 18:56:46: #1 tags after filtering in treatment: 2543396 INFO @ Fri, 05 Jul 2019 18:56:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:56:46: #1 finished! INFO @ Fri, 05 Jul 2019 18:56:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:56:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:56:46: #2 number of paired peaks: 308 WARNING @ Fri, 05 Jul 2019 18:56:46: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Fri, 05 Jul 2019 18:56:46: start model_add_line... INFO @ Fri, 05 Jul 2019 18:56:46: start X-correlation... INFO @ Fri, 05 Jul 2019 18:56:46: end of X-cor INFO @ Fri, 05 Jul 2019 18:56:46: #2 finished! INFO @ Fri, 05 Jul 2019 18:56:46: #2 predicted fragment length is 148 bps INFO @ Fri, 05 Jul 2019 18:56:46: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 05 Jul 2019 18:56:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.10_model.r INFO @ Fri, 05 Jul 2019 18:56:47: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 18:56:47: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 18:56:47: #1 total tags in treatment: 2543396 INFO @ Fri, 05 Jul 2019 18:56:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:56:47: #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 18:56:47: #1 tags after filtering in treatment: 2543396 INFO @ Fri, 05 Jul 2019 18:56:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:56:47: #1 finished! INFO @ Fri, 05 Jul 2019 18:56:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:56:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:56:47: #2 number of paired peaks: 308 WARNING @ Fri, 05 Jul 2019 18:56:47: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Fri, 05 Jul 2019 18:56:47: start model_add_line... INFO @ Fri, 05 Jul 2019 18:56:47: start X-correlation... INFO @ Fri, 05 Jul 2019 18:56:47: end of X-cor INFO @ Fri, 05 Jul 2019 18:56:47: #2 finished! INFO @ Fri, 05 Jul 2019 18:56:47: #2 predicted fragment length is 148 bps INFO @ Fri, 05 Jul 2019 18:56:47: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 05 Jul 2019 18:56:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.20_model.r INFO @ Fri, 05 Jul 2019 18:56:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:56:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:56:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:56:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:56:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:56:59: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:57:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:57:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:57:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 18:57:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:57:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:57:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.10_summits.bed INFO @ Fri, 05 Jul 2019 18:57:07: Done! INFO @ Fri, 05 Jul 2019 18:57:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:57:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:57:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.05_summits.bed INFO @ Fri, 05 Jul 2019 18:57:07: Done! INFO @ Fri, 05 Jul 2019 18:57:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:57:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:57:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594000/ERX594000.20_summits.bed pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (3120 records, 4 fields): 6 millis INFO @ Fri, 05 Jul 2019 18:57:07: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (3735 records, 4 fields): 5 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (2300 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling