Job ID = 2008358 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,048,191 reads read : 11,048,191 reads written : 11,048,191 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637600.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: 00:02:12 11048191 reads; of these: 11048191 (100.00%) were unpaired; of these: 3882374 (35.14%) aligned 0 times 4008880 (36.29%) aligned exactly 1 time 3156937 (28.57%) aligned >1 times 64.86% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 5428236 / 7165817 = 0.7575 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 18:56:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.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 18:56:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:56:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.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 18:56:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:56:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.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 18:56:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:56:39: 1000000 INFO @ Fri, 05 Jul 2019 18:56:40: 1000000 INFO @ Fri, 05 Jul 2019 18:56:44: 1000000 INFO @ Fri, 05 Jul 2019 18:56:46: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 18:56:46: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 18:56:46: #1 total tags in treatment: 1737581 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: 1737581 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: 468 WARNING @ Fri, 05 Jul 2019 18:56:46: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 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 159 bps INFO @ Fri, 05 Jul 2019 18:56:46: #2 alternative fragment length(s) may be 159 bps INFO @ Fri, 05 Jul 2019 18:56:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.10_model.r INFO @ Fri, 05 Jul 2019 18:56:46: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 18:56:46: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 18:56:46: #1 total tags in treatment: 1737581 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 18:56:47: #1 tags after filtering in treatment: 1737581 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: 468 WARNING @ Fri, 05 Jul 2019 18:56:47: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 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 159 bps INFO @ Fri, 05 Jul 2019 18:56:47: #2 alternative fragment length(s) may be 159 bps INFO @ Fri, 05 Jul 2019 18:56:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.05_model.r INFO @ Fri, 05 Jul 2019 18:56:52: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 18:56:52: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 18:56:52: #1 total tags in treatment: 1737581 INFO @ Fri, 05 Jul 2019 18:56:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:56:52: #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 18:56:52: #1 tags after filtering in treatment: 1737581 INFO @ Fri, 05 Jul 2019 18:56:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:56:52: #1 finished! INFO @ Fri, 05 Jul 2019 18:56:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:56:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:56:52: #2 number of paired peaks: 468 WARNING @ Fri, 05 Jul 2019 18:56:52: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Fri, 05 Jul 2019 18:56:52: start model_add_line... INFO @ Fri, 05 Jul 2019 18:56:52: start X-correlation... INFO @ Fri, 05 Jul 2019 18:56:52: end of X-cor INFO @ Fri, 05 Jul 2019 18:56:52: #2 finished! INFO @ Fri, 05 Jul 2019 18:56:52: #2 predicted fragment length is 159 bps INFO @ Fri, 05 Jul 2019 18:56:52: #2 alternative fragment length(s) may be 159 bps INFO @ Fri, 05 Jul 2019 18:56:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.20_model.r 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 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 Call peaks... 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... INFO @ Fri, 05 Jul 2019 18:57:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:57:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:57:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:57:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.10_summits.bed INFO @ Fri, 05 Jul 2019 18:57:08: Done! INFO @ Fri, 05 Jul 2019 18:57:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:57:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.05_summits.bed INFO @ Fri, 05 Jul 2019 18:57:08: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (1401 records, 4 fields): 5 millis pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1898 records, 4 fields): 6 millis INFO @ Fri, 05 Jul 2019 18:57:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:57:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:57:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX593986/ERX593986.20_summits.bed INFO @ Fri, 05 Jul 2019 18:57:08: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (924 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling