Job ID = 2008332 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,537,874 reads read : 27,075,748 reads written : 27,075,748 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629020.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: 00:12:55 13537874 reads; of these: 13537874 (100.00%) were paired; of these: 1129259 (8.34%) aligned concordantly 0 times 11408994 (84.27%) aligned concordantly exactly 1 time 999621 (7.38%) aligned concordantly >1 times ---- 1129259 pairs aligned concordantly 0 times; of these: 150479 (13.33%) aligned discordantly 1 time ---- 978780 pairs aligned 0 times concordantly or discordantly; of these: 1957560 mates make up the pairs; of these: 1879002 (95.99%) aligned 0 times 42672 (2.18%) aligned exactly 1 time 35886 (1.83%) aligned >1 times 93.06% overall alignment rate Time searching: 00:12:55 Overall time: 00:12:55 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 8 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] 11913471 / 12551999 = 0.9491 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 19:04:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.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 19:04:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:04:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:04:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.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 19:04:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:04:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:04:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.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 19:04:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:04:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:04:18: 1000000 INFO @ Fri, 05 Jul 2019 19:04:18: 1000000 INFO @ Fri, 05 Jul 2019 19:04:21: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 19:04:21: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 19:04:21: #1 total tags in treatment: 579506 INFO @ Fri, 05 Jul 2019 19:04:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:04:21: #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 19:04:21: #1 tags after filtering in treatment: 464546 INFO @ Fri, 05 Jul 2019 19:04:21: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 05 Jul 2019 19:04:21: #1 finished! INFO @ Fri, 05 Jul 2019 19:04:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:04:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:04:21: #2 number of paired peaks: 288 WARNING @ Fri, 05 Jul 2019 19:04:21: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Fri, 05 Jul 2019 19:04:21: start model_add_line... INFO @ Fri, 05 Jul 2019 19:04:21: start X-correlation... INFO @ Fri, 05 Jul 2019 19:04:21: end of X-cor INFO @ Fri, 05 Jul 2019 19:04:21: #2 finished! INFO @ Fri, 05 Jul 2019 19:04:21: #2 predicted fragment length is 281 bps INFO @ Fri, 05 Jul 2019 19:04:21: #2 alternative fragment length(s) may be 30,60,93,126,161,185,223,263,281,347,379,409,441,466,528,537,561,592 bps INFO @ Fri, 05 Jul 2019 19:04:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.05_model.r INFO @ Fri, 05 Jul 2019 19:04:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:04:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:04:21: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 19:04:21: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 19:04:21: #1 total tags in treatment: 579506 INFO @ Fri, 05 Jul 2019 19:04:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:04:21: #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 19:04:21: #1 tags after filtering in treatment: 464546 INFO @ Fri, 05 Jul 2019 19:04:21: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 05 Jul 2019 19:04:21: #1 finished! INFO @ Fri, 05 Jul 2019 19:04:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:04:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:04:21: #2 number of paired peaks: 288 WARNING @ Fri, 05 Jul 2019 19:04:21: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Fri, 05 Jul 2019 19:04:21: start model_add_line... INFO @ Fri, 05 Jul 2019 19:04:21: start X-correlation... INFO @ Fri, 05 Jul 2019 19:04:21: end of X-cor INFO @ Fri, 05 Jul 2019 19:04:21: #2 finished! INFO @ Fri, 05 Jul 2019 19:04:21: #2 predicted fragment length is 281 bps INFO @ Fri, 05 Jul 2019 19:04:21: #2 alternative fragment length(s) may be 30,60,93,126,161,185,223,263,281,347,379,409,441,466,528,537,561,592 bps INFO @ Fri, 05 Jul 2019 19:04:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.10_model.r INFO @ Fri, 05 Jul 2019 19:04:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:04:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:04:22: 1000000 INFO @ Fri, 05 Jul 2019 19:04:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:04:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:04:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:04:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:04:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.05_summits.bed INFO @ Fri, 05 Jul 2019 19:04:23: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (123 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 19:04:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:04:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:04:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.10_summits.bed INFO @ Fri, 05 Jul 2019 19:04:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (79 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 19:04:25: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 19:04:25: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 19:04:25: #1 total tags in treatment: 579506 INFO @ Fri, 05 Jul 2019 19:04:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:04:25: #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 19:04:25: #1 tags after filtering in treatment: 464546 INFO @ Fri, 05 Jul 2019 19:04:25: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 05 Jul 2019 19:04:25: #1 finished! INFO @ Fri, 05 Jul 2019 19:04:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:04:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:04:25: #2 number of paired peaks: 288 WARNING @ Fri, 05 Jul 2019 19:04:25: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Fri, 05 Jul 2019 19:04:25: start model_add_line... INFO @ Fri, 05 Jul 2019 19:04:25: start X-correlation... INFO @ Fri, 05 Jul 2019 19:04:25: end of X-cor INFO @ Fri, 05 Jul 2019 19:04:25: #2 finished! INFO @ Fri, 05 Jul 2019 19:04:25: #2 predicted fragment length is 281 bps INFO @ Fri, 05 Jul 2019 19:04:25: #2 alternative fragment length(s) may be 30,60,93,126,161,185,223,263,281,347,379,409,441,466,528,537,561,592 bps INFO @ Fri, 05 Jul 2019 19:04:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.20_model.r INFO @ Fri, 05 Jul 2019 19:04:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:04:25: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:04:27: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:04:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.20_peaks.xls BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 19:04:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.20_peaks.narrowPeak BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:04:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585840/ERX585840.20_summits.bed INFO @ Fri, 05 Jul 2019 19:04:34: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis BigWig に変換しました。 CompletedMACS2peakCalling