Job ID = 2007900 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 180,763 reads read : 361,526 reads written : 361,526 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: 00:00:07 180763 reads; of these: 180763 (100.00%) were paired; of these: 21688 (12.00%) aligned concordantly 0 times 146198 (80.88%) aligned concordantly exactly 1 time 12877 (7.12%) aligned concordantly >1 times ---- 21688 pairs aligned concordantly 0 times; of these: 12842 (59.21%) aligned discordantly 1 time ---- 8846 pairs aligned 0 times concordantly or discordantly; of these: 17692 mates make up the pairs; of these: 12650 (71.50%) aligned 0 times 2343 (13.24%) aligned exactly 1 time 2699 (15.26%) aligned >1 times 96.50% overall alignment rate Time searching: 00:00:07 Overall time: 00:00:07 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] 605 / 171111 = 0.0035 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 16:39:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.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 16:39:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:39:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:39:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.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 16:39:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:39:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:39:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.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 16:39:51: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:39:51: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:39:51: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:39:51: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:39:51: #1 total tags in treatment: 158521 INFO @ Fri, 05 Jul 2019 16:39:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:39:51: #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 16:39:51: #1 tags after filtering in treatment: 157307 INFO @ Fri, 05 Jul 2019 16:39:51: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:39:51: #1 finished! INFO @ Fri, 05 Jul 2019 16:39:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:39:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:39:51: #2 number of paired peaks: 267 WARNING @ Fri, 05 Jul 2019 16:39:51: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Fri, 05 Jul 2019 16:39:51: start model_add_line... INFO @ Fri, 05 Jul 2019 16:39:51: start X-correlation... INFO @ Fri, 05 Jul 2019 16:39:51: end of X-cor INFO @ Fri, 05 Jul 2019 16:39:51: #2 finished! INFO @ Fri, 05 Jul 2019 16:39:51: #2 predicted fragment length is 227 bps INFO @ Fri, 05 Jul 2019 16:39:51: #2 alternative fragment length(s) may be 172,191,227,260,282,526 bps INFO @ Fri, 05 Jul 2019 16:39:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.05_model.r INFO @ Fri, 05 Jul 2019 16:39:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:39:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:39:51: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:39:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:39:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:39:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.05_summits.bed INFO @ Fri, 05 Jul 2019 16:39:52: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 16:39:52: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:39:52: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:39:52: #1 total tags in treatment: 158521 INFO @ Fri, 05 Jul 2019 16:39:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:39:52: #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 16:39:52: #1 tags after filtering in treatment: 157307 INFO @ Fri, 05 Jul 2019 16:39:52: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:39:52: #1 finished! INFO @ Fri, 05 Jul 2019 16:39:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:39:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:39:52: #2 number of paired peaks: 267 WARNING @ Fri, 05 Jul 2019 16:39:52: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Fri, 05 Jul 2019 16:39:52: start model_add_line... INFO @ Fri, 05 Jul 2019 16:39:52: start X-correlation... INFO @ Fri, 05 Jul 2019 16:39:52: end of X-cor INFO @ Fri, 05 Jul 2019 16:39:52: #2 finished! INFO @ Fri, 05 Jul 2019 16:39:52: #2 predicted fragment length is 227 bps INFO @ Fri, 05 Jul 2019 16:39:52: #2 alternative fragment length(s) may be 172,191,227,260,282,526 bps INFO @ Fri, 05 Jul 2019 16:39:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.10_model.r INFO @ Fri, 05 Jul 2019 16:39:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:39:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:39:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:39:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:39:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:39:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.10_summits.bed INFO @ Fri, 05 Jul 2019 16:39:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:39:53: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:39:53: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:39:53: #1 total tags in treatment: 158521 INFO @ Fri, 05 Jul 2019 16:39:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:39:53: #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 16:39:53: #1 tags after filtering in treatment: 157307 INFO @ Fri, 05 Jul 2019 16:39:53: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:39:53: #1 finished! INFO @ Fri, 05 Jul 2019 16:39:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:39:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:39:53: #2 number of paired peaks: 267 WARNING @ Fri, 05 Jul 2019 16:39:53: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Fri, 05 Jul 2019 16:39:53: start model_add_line... INFO @ Fri, 05 Jul 2019 16:39:53: start X-correlation... INFO @ Fri, 05 Jul 2019 16:39:53: end of X-cor INFO @ Fri, 05 Jul 2019 16:39:53: #2 finished! INFO @ Fri, 05 Jul 2019 16:39:53: #2 predicted fragment length is 227 bps INFO @ Fri, 05 Jul 2019 16:39:53: #2 alternative fragment length(s) may be 172,191,227,260,282,526 bps INFO @ Fri, 05 Jul 2019 16:39:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.20_model.r INFO @ Fri, 05 Jul 2019 16:39:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:39:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:39:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:39:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:39:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:39:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462433/ERX462433.20_summits.bed INFO @ Fri, 05 Jul 2019 16:39:54: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling