Job ID = 11245022 sra ファイルのダウンロード中... Completed: 168563K bytes transferred in 5 seconds (263935K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 5618267 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554734/SRR7696406.sra Written 5618267 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554734/SRR7696406.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:01:50 5618267 reads; of these: 5618267 (100.00%) were paired; of these: 4580365 (81.53%) aligned concordantly 0 times 879484 (15.65%) aligned concordantly exactly 1 time 158418 (2.82%) aligned concordantly >1 times ---- 4580365 pairs aligned concordantly 0 times; of these: 985 (0.02%) aligned discordantly 1 time ---- 4579380 pairs aligned 0 times concordantly or discordantly; of these: 9158760 mates make up the pairs; of these: 8001943 (87.37%) aligned 0 times 994194 (10.86%) aligned exactly 1 time 162623 (1.78%) aligned >1 times 28.79% overall alignment rate Time searching: 00:01:50 Overall time: 00:01:50 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] 208402 / 1038659 = 0.2006 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 @ Tue, 09 Oct 2018 23:12:10: # Command line: callpeak -t SRX4554734.bam -f BAM -g 12100000 -n SRX4554734.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554734.10 # format = BAM # ChIP-seq file = ['SRX4554734.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 @ Tue, 09 Oct 2018 23:12:10: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:12:10: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:12:10: # Command line: callpeak -t SRX4554734.bam -f BAM -g 12100000 -n SRX4554734.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554734.20 # format = BAM # ChIP-seq file = ['SRX4554734.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 @ Tue, 09 Oct 2018 23:12:10: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:12:10: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:12:10: # Command line: callpeak -t SRX4554734.bam -f BAM -g 12100000 -n SRX4554734.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554734.05 # format = BAM # ChIP-seq file = ['SRX4554734.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 @ Tue, 09 Oct 2018 23:12:10: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:12:10: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:12:15: 1000000 INFO @ Tue, 09 Oct 2018 23:12:15: 1000000 INFO @ Tue, 09 Oct 2018 23:12:15: 1000000 INFO @ Tue, 09 Oct 2018 23:12:20: 2000000 INFO @ Tue, 09 Oct 2018 23:12:20: 2000000 INFO @ Tue, 09 Oct 2018 23:12:20: 2000000 INFO @ Tue, 09 Oct 2018 23:12:24: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:12:24: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:12:24: #1 total tags in treatment: 829563 INFO @ Tue, 09 Oct 2018 23:12:24: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:12:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:12:24: #1 tags after filtering in treatment: 479807 INFO @ Tue, 09 Oct 2018 23:12:24: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 09 Oct 2018 23:12:24: #1 finished! INFO @ Tue, 09 Oct 2018 23:12:24: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:12:24: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:12:24: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:12:24: #1 total tags in treatment: 829563 INFO @ Tue, 09 Oct 2018 23:12:24: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:12:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:12:24: #1 tags after filtering in treatment: 479807 INFO @ Tue, 09 Oct 2018 23:12:24: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 09 Oct 2018 23:12:24: #1 finished! INFO @ Tue, 09 Oct 2018 23:12:24: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:12:24: #2 number of paired peaks: 840 WARNING @ Tue, 09 Oct 2018 23:12:24: Fewer paired peaks (840) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 840 pairs to build model! INFO @ Tue, 09 Oct 2018 23:12:24: start model_add_line... INFO @ Tue, 09 Oct 2018 23:12:24: start X-correlation... INFO @ Tue, 09 Oct 2018 23:12:24: end of X-cor INFO @ Tue, 09 Oct 2018 23:12:24: #2 finished! INFO @ Tue, 09 Oct 2018 23:12:24: #2 predicted fragment length is 222 bps INFO @ Tue, 09 Oct 2018 23:12:24: #2 alternative fragment length(s) may be 4,222,574 bps INFO @ Tue, 09 Oct 2018 23:12:24: #2.2 Generate R script for model : SRX4554734.20_model.r INFO @ Tue, 09 Oct 2018 23:12:24: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:12:24: #2 number of paired peaks: 840 WARNING @ Tue, 09 Oct 2018 23:12:24: Fewer paired peaks (840) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 840 pairs to build model! INFO @ Tue, 09 Oct 2018 23:12:24: start model_add_line... INFO @ Tue, 09 Oct 2018 23:12:24: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:12:24: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:12:24: #1 total tags in treatment: 829563 INFO @ Tue, 09 Oct 2018 23:12:24: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:12:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:12:24: start X-correlation... INFO @ Tue, 09 Oct 2018 23:12:24: end of X-cor INFO @ Tue, 09 Oct 2018 23:12:24: #2 finished! INFO @ Tue, 09 Oct 2018 23:12:24: #2 predicted fragment length is 222 bps INFO @ Tue, 09 Oct 2018 23:12:24: #2 alternative fragment length(s) may be 4,222,574 bps INFO @ Tue, 09 Oct 2018 23:12:24: #2.2 Generate R script for model : SRX4554734.10_model.r INFO @ Tue, 09 Oct 2018 23:12:24: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:12:24: #1 tags after filtering in treatment: 479807 INFO @ Tue, 09 Oct 2018 23:12:24: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 09 Oct 2018 23:12:24: #1 finished! INFO @ Tue, 09 Oct 2018 23:12:24: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:12:24: #2 number of paired peaks: 840 WARNING @ Tue, 09 Oct 2018 23:12:24: Fewer paired peaks (840) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 840 pairs to build model! INFO @ Tue, 09 Oct 2018 23:12:24: start model_add_line... INFO @ Tue, 09 Oct 2018 23:12:24: start X-correlation... INFO @ Tue, 09 Oct 2018 23:12:24: end of X-cor INFO @ Tue, 09 Oct 2018 23:12:24: #2 finished! INFO @ Tue, 09 Oct 2018 23:12:24: #2 predicted fragment length is 222 bps INFO @ Tue, 09 Oct 2018 23:12:24: #2 alternative fragment length(s) may be 4,222,574 bps INFO @ Tue, 09 Oct 2018 23:12:24: #2.2 Generate R script for model : SRX4554734.05_model.r INFO @ Tue, 09 Oct 2018 23:12:24: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:12:27: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:12:27: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:12:27: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:12:27: #4 Write output xls file... SRX4554734.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:12:27: #4 Write peak in narrowPeak format file... SRX4554734.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:12:27: #4 Write summits bed file... SRX4554734.20_summits.bed INFO @ Tue, 09 Oct 2018 23:12:27: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (252 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:12:28: #4 Write output xls file... SRX4554734.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:12:28: #4 Write peak in narrowPeak format file... SRX4554734.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:12:28: #4 Write summits bed file... SRX4554734.10_summits.bed INFO @ Tue, 09 Oct 2018 23:12:28: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (464 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:12:28: #4 Write output xls file... SRX4554734.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:12:28: #4 Write peak in narrowPeak format file... SRX4554734.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:12:28: #4 Write summits bed file... SRX4554734.05_summits.bed INFO @ Tue, 09 Oct 2018 23:12:28: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (588 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。