Job ID = 2008244 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 20,826,848 reads read : 41,653,696 reads written : 41,653,696 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629075.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:27 20826848 reads; of these: 20826848 (100.00%) were paired; of these: 2074836 (9.96%) aligned concordantly 0 times 16826199 (80.79%) aligned concordantly exactly 1 time 1925813 (9.25%) aligned concordantly >1 times ---- 2074836 pairs aligned concordantly 0 times; of these: 225423 (10.86%) aligned discordantly 1 time ---- 1849413 pairs aligned 0 times concordantly or discordantly; of these: 3698826 mates make up the pairs; of these: 3485808 (94.24%) aligned 0 times 114426 (3.09%) aligned exactly 1 time 98592 (2.67%) aligned >1 times 91.63% overall alignment rate Time searching: 00:15:28 Overall time: 00:15:28 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_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 18175837 / 18869293 = 0.9632 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 18:29:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.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 18:29:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:29:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:29:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.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 18:29:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:29:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:29:26: 1000000 INFO @ Fri, 05 Jul 2019 18:29:27: 1000000 INFO @ Fri, 05 Jul 2019 18:29:32: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:29:32: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:29:32: #1 total tags in treatment: 677987 INFO @ Fri, 05 Jul 2019 18:29:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:29:32: #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 18:29:32: #1 tags after filtering in treatment: 527133 INFO @ Fri, 05 Jul 2019 18:29:32: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 05 Jul 2019 18:29:32: #1 finished! INFO @ Fri, 05 Jul 2019 18:29:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:29:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:29:32: #2 number of paired peaks: 341 WARNING @ Fri, 05 Jul 2019 18:29:32: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Fri, 05 Jul 2019 18:29:32: start model_add_line... INFO @ Fri, 05 Jul 2019 18:29:32: start X-correlation... INFO @ Fri, 05 Jul 2019 18:29:32: end of X-cor INFO @ Fri, 05 Jul 2019 18:29:32: #2 finished! INFO @ Fri, 05 Jul 2019 18:29:32: #2 predicted fragment length is 153 bps INFO @ Fri, 05 Jul 2019 18:29:32: #2 alternative fragment length(s) may be 70,103,116,153,182,208,259,307,360,378,478,482,531,572 bps INFO @ Fri, 05 Jul 2019 18:29:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.05_model.r INFO @ Fri, 05 Jul 2019 18:29:33: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:29:33: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:29:33: #1 total tags in treatment: 677987 INFO @ Fri, 05 Jul 2019 18:29:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:29:33: #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 18:29:33: #1 tags after filtering in treatment: 527133 INFO @ Fri, 05 Jul 2019 18:29:33: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 05 Jul 2019 18:29:33: #1 finished! INFO @ Fri, 05 Jul 2019 18:29:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:29:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:29:33: #2 number of paired peaks: 341 WARNING @ Fri, 05 Jul 2019 18:29:33: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Fri, 05 Jul 2019 18:29:33: start model_add_line... INFO @ Fri, 05 Jul 2019 18:29:33: start X-correlation... INFO @ Fri, 05 Jul 2019 18:29:33: end of X-cor INFO @ Fri, 05 Jul 2019 18:29:33: #2 finished! INFO @ Fri, 05 Jul 2019 18:29:33: #2 predicted fragment length is 153 bps INFO @ Fri, 05 Jul 2019 18:29:33: #2 alternative fragment length(s) may be 70,103,116,153,182,208,259,307,360,378,478,482,531,572 bps INFO @ Fri, 05 Jul 2019 18:29:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.10_model.r INFO @ Fri, 05 Jul 2019 18:29:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:29:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:29:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:29:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:30:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:30:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:30:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.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 18:30:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:30:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:30:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:30:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:30:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:30:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:30:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.05_summits.bed INFO @ Fri, 05 Jul 2019 18:30:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.10_summits.bed INFO @ Fri, 05 Jul 2019 18:30:02: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (34 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 18:30:02: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (141 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:30:08: 1000000 INFO @ Fri, 05 Jul 2019 18:30:14: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:30:14: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:30:14: #1 total tags in treatment: 677987 INFO @ Fri, 05 Jul 2019 18:30:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:30:14: #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 18:30:14: #1 tags after filtering in treatment: 527133 INFO @ Fri, 05 Jul 2019 18:30:14: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 05 Jul 2019 18:30:14: #1 finished! INFO @ Fri, 05 Jul 2019 18:30:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:30:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:30:14: #2 number of paired peaks: 341 WARNING @ Fri, 05 Jul 2019 18:30:14: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Fri, 05 Jul 2019 18:30:14: start model_add_line... INFO @ Fri, 05 Jul 2019 18:30:14: start X-correlation... INFO @ Fri, 05 Jul 2019 18:30:14: end of X-cor INFO @ Fri, 05 Jul 2019 18:30:14: #2 finished! INFO @ Fri, 05 Jul 2019 18:30:14: #2 predicted fragment length is 153 bps INFO @ Fri, 05 Jul 2019 18:30:14: #2 alternative fragment length(s) may be 70,103,116,153,182,208,259,307,360,378,478,482,531,572 bps INFO @ Fri, 05 Jul 2019 18:30:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.20_model.r INFO @ Fri, 05 Jul 2019 18:30:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:30:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:30:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:30:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:30:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:30:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585768/ERX585768.20_summits.bed INFO @ Fri, 05 Jul 2019 18:30:17: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。