Job ID = 2007961 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,709,716 reads read : 3,419,432 reads written : 3,419,432 rm: cannot remove ‘[DSE]RR*’: 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: 00:01:58 1709716 reads; of these: 1709716 (100.00%) were paired; of these: 147406 (8.62%) aligned concordantly 0 times 1439618 (84.20%) aligned concordantly exactly 1 time 122692 (7.18%) aligned concordantly >1 times ---- 147406 pairs aligned concordantly 0 times; of these: 34202 (23.20%) aligned discordantly 1 time ---- 113204 pairs aligned 0 times concordantly or discordantly; of these: 226408 mates make up the pairs; of these: 199807 (88.25%) aligned 0 times 17141 (7.57%) aligned exactly 1 time 9460 (4.18%) aligned >1 times 94.16% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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_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] 112079 / 1588115 = 0.0706 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 17:00:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.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 17:00:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:00:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:00:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.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 17:00:51: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:00:51: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:00:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.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 17:00:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:00:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:01:01: 1000000 INFO @ Fri, 05 Jul 2019 17:01:01: 1000000 INFO @ Fri, 05 Jul 2019 17:01:03: 1000000 INFO @ Fri, 05 Jul 2019 17:01:10: 2000000 INFO @ Fri, 05 Jul 2019 17:01:14: 2000000 INFO @ Fri, 05 Jul 2019 17:01:16: 2000000 INFO @ Fri, 05 Jul 2019 17:01:18: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:01:18: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:01:18: #1 total tags in treatment: 1451175 INFO @ Fri, 05 Jul 2019 17:01:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:01:18: #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 17:01:18: #1 tags after filtering in treatment: 1355417 INFO @ Fri, 05 Jul 2019 17:01:18: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:01:18: #1 finished! INFO @ Fri, 05 Jul 2019 17:01:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:01:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:01:18: #2 number of paired peaks: 183 WARNING @ Fri, 05 Jul 2019 17:01:18: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Fri, 05 Jul 2019 17:01:18: start model_add_line... INFO @ Fri, 05 Jul 2019 17:01:18: start X-correlation... INFO @ Fri, 05 Jul 2019 17:01:18: end of X-cor INFO @ Fri, 05 Jul 2019 17:01:18: #2 finished! INFO @ Fri, 05 Jul 2019 17:01:18: #2 predicted fragment length is 232 bps INFO @ Fri, 05 Jul 2019 17:01:18: #2 alternative fragment length(s) may be 1,168,189,232,285,493,542,590 bps INFO @ Fri, 05 Jul 2019 17:01:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.20_model.r INFO @ Fri, 05 Jul 2019 17:01:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:01:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:01:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:01:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:01:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:01:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.20_summits.bed INFO @ Fri, 05 Jul 2019 17:01:25: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:01:27: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:01:27: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:01:27: #1 total tags in treatment: 1451175 INFO @ Fri, 05 Jul 2019 17:01:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:01:27: #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 17:01:27: #1 tags after filtering in treatment: 1355417 INFO @ Fri, 05 Jul 2019 17:01:27: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:01:27: #1 finished! INFO @ Fri, 05 Jul 2019 17:01:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:01:27: #2 looking for paired plus/minus strand peaks... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:01:27: #2 number of paired peaks: 183 WARNING @ Fri, 05 Jul 2019 17:01:27: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Fri, 05 Jul 2019 17:01:27: start model_add_line... INFO @ Fri, 05 Jul 2019 17:01:27: start X-correlation... INFO @ Fri, 05 Jul 2019 17:01:27: end of X-cor INFO @ Fri, 05 Jul 2019 17:01:27: #2 finished! INFO @ Fri, 05 Jul 2019 17:01:27: #2 predicted fragment length is 232 bps INFO @ Fri, 05 Jul 2019 17:01:27: #2 alternative fragment length(s) may be 1,168,189,232,285,493,542,590 bps INFO @ Fri, 05 Jul 2019 17:01:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.05_model.r INFO @ Fri, 05 Jul 2019 17:01:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:01:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:01:28: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:01:28: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:01:28: #1 total tags in treatment: 1451175 INFO @ Fri, 05 Jul 2019 17:01:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:01:28: #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 17:01:28: #1 tags after filtering in treatment: 1355417 INFO @ Fri, 05 Jul 2019 17:01:28: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:01:28: #1 finished! INFO @ Fri, 05 Jul 2019 17:01:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:01:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:01:28: #2 number of paired peaks: 183 WARNING @ Fri, 05 Jul 2019 17:01:28: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Fri, 05 Jul 2019 17:01:28: start model_add_line... INFO @ Fri, 05 Jul 2019 17:01:28: start X-correlation... INFO @ Fri, 05 Jul 2019 17:01:28: end of X-cor INFO @ Fri, 05 Jul 2019 17:01:28: #2 finished! INFO @ Fri, 05 Jul 2019 17:01:28: #2 predicted fragment length is 232 bps INFO @ Fri, 05 Jul 2019 17:01:28: #2 alternative fragment length(s) may be 1,168,189,232,285,493,542,590 bps INFO @ Fri, 05 Jul 2019 17:01:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.10_model.r INFO @ Fri, 05 Jul 2019 17:01:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:01:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:01:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:01:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:01:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:01:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:01:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.05_summits.bed INFO @ Fri, 05 Jul 2019 17:01:33: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (106 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 17:01:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:01:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:01:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471752/ERX471752.10_summits.bed INFO @ Fri, 05 Jul 2019 17:01:35: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。