Job ID = 11245041 sra ファイルのダウンロード中... Completed: 93410K bytes transferred in 5 seconds (148732K 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 1859195 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554752/SRR7696425.sra Written 1859195 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554752/SRR7696425.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: 00:00:32 1859195 reads; of these: 1859195 (100.00%) were paired; of these: 1446619 (77.81%) aligned concordantly 0 times 356364 (19.17%) aligned concordantly exactly 1 time 56212 (3.02%) aligned concordantly >1 times ---- 1446619 pairs aligned concordantly 0 times; of these: 1523 (0.11%) aligned discordantly 1 time ---- 1445096 pairs aligned 0 times concordantly or discordantly; of these: 2890192 mates make up the pairs; of these: 2879769 (99.64%) aligned 0 times 8530 (0.30%) aligned exactly 1 time 1893 (0.07%) aligned >1 times 22.55% overall alignment rate Time searching: 00:00:32 Overall time: 00:00:32 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] 51483 / 413667 = 0.1245 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 23:12:54: # Command line: callpeak -t SRX4554752.bam -f BAM -g 12100000 -n SRX4554752.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554752.10 # format = BAM # ChIP-seq file = ['SRX4554752.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 23:12:54: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:12:54: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:12:54: # Command line: callpeak -t SRX4554752.bam -f BAM -g 12100000 -n SRX4554752.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554752.05 # format = BAM # ChIP-seq file = ['SRX4554752.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 23:12:54: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:12:54: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:12:54: # Command line: callpeak -t SRX4554752.bam -f BAM -g 12100000 -n SRX4554752.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554752.20 # format = BAM # ChIP-seq file = ['SRX4554752.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 23:12:54: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:12:54: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:12:58: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:12:58: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:12:58: #1 total tags in treatment: 361133 INFO @ Tue, 09 Oct 2018 23:12:58: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:12:58: #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 23:12:58: #1 tags after filtering in treatment: 291719 INFO @ Tue, 09 Oct 2018 23:12:58: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 09 Oct 2018 23:12:58: #1 finished! INFO @ Tue, 09 Oct 2018 23:12:58: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:12:58: #2 number of paired peaks: 798 WARNING @ Tue, 09 Oct 2018 23:12:58: Fewer paired peaks (798) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 798 pairs to build model! INFO @ Tue, 09 Oct 2018 23:12:58: start model_add_line... INFO @ Tue, 09 Oct 2018 23:12:58: start X-correlation... INFO @ Tue, 09 Oct 2018 23:12:58: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:12:58: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:12:58: #1 total tags in treatment: 361133 INFO @ Tue, 09 Oct 2018 23:12:58: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:12:58: #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 23:12:58: end of X-cor INFO @ Tue, 09 Oct 2018 23:12:58: #2 finished! INFO @ Tue, 09 Oct 2018 23:12:58: #2 predicted fragment length is 294 bps INFO @ Tue, 09 Oct 2018 23:12:58: #2 alternative fragment length(s) may be 2,126,141,209,236,294,441,459,582 bps INFO @ Tue, 09 Oct 2018 23:12:58: #2.2 Generate R script for model : SRX4554752.10_model.r INFO @ Tue, 09 Oct 2018 23:12:58: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:12:58: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:12:58: #1 total tags in treatment: 361133 INFO @ Tue, 09 Oct 2018 23:12:58: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:12:58: #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 23:12:58: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:12:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:12:58: #1 tags after filtering in treatment: 291719 INFO @ Tue, 09 Oct 2018 23:12:58: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 09 Oct 2018 23:12:58: #1 finished! INFO @ Tue, 09 Oct 2018 23:12:58: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:12:58: #1 tags after filtering in treatment: 291719 INFO @ Tue, 09 Oct 2018 23:12:58: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 09 Oct 2018 23:12:58: #1 finished! INFO @ Tue, 09 Oct 2018 23:12:58: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:12:59: #2 number of paired peaks: 798 WARNING @ Tue, 09 Oct 2018 23:12:59: Fewer paired peaks (798) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 798 pairs to build model! INFO @ Tue, 09 Oct 2018 23:12:59: start model_add_line... INFO @ Tue, 09 Oct 2018 23:12:59: #2 number of paired peaks: 798 WARNING @ Tue, 09 Oct 2018 23:12:59: Fewer paired peaks (798) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 798 pairs to build model! INFO @ Tue, 09 Oct 2018 23:12:59: start model_add_line... INFO @ Tue, 09 Oct 2018 23:12:59: start X-correlation... INFO @ Tue, 09 Oct 2018 23:12:59: end of X-cor INFO @ Tue, 09 Oct 2018 23:12:59: #2 finished! INFO @ Tue, 09 Oct 2018 23:12:59: #2 predicted fragment length is 294 bps INFO @ Tue, 09 Oct 2018 23:12:59: #2 alternative fragment length(s) may be 2,126,141,209,236,294,441,459,582 bps INFO @ Tue, 09 Oct 2018 23:12:59: #2.2 Generate R script for model : SRX4554752.20_model.r INFO @ Tue, 09 Oct 2018 23:12:59: start X-correlation... INFO @ Tue, 09 Oct 2018 23:12:59: end of X-cor INFO @ Tue, 09 Oct 2018 23:12:59: #2 finished! INFO @ Tue, 09 Oct 2018 23:12:59: #2 predicted fragment length is 294 bps INFO @ Tue, 09 Oct 2018 23:12:59: #2 alternative fragment length(s) may be 2,126,141,209,236,294,441,459,582 bps INFO @ Tue, 09 Oct 2018 23:12:59: #2.2 Generate R script for model : SRX4554752.05_model.r INFO @ Tue, 09 Oct 2018 23:12:59: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:12:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:12:59: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:12:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:13:00: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:13:00: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:13:00: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:13:00: #4 Write output xls file... SRX4554752.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:13:00: #4 Write peak in narrowPeak format file... SRX4554752.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:13:00: #4 Write summits bed file... SRX4554752.10_summits.bed INFO @ Tue, 09 Oct 2018 23:13:00: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (202 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:13:01: #4 Write output xls file... SRX4554752.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:13:01: #4 Write peak in narrowPeak format file... SRX4554752.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:13:01: #4 Write summits bed file... SRX4554752.20_summits.bed INFO @ Tue, 09 Oct 2018 23:13:01: Done! INFO @ Tue, 09 Oct 2018 23:13:01: #4 Write output xls file... SRX4554752.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:13:01: #4 Write peak in narrowPeak format file... SRX4554752.05_peaks.narrowPeak pass1 - making usageList (16 chroms): 1 millis INFO @ Tue, 09 Oct 2018 23:13:01: #4 Write summits bed file... SRX4554752.05_summits.bed pass2 - checking and writing primary data (127 records, 4 fields): 2 millis INFO @ Tue, 09 Oct 2018 23:13:01: Done! CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (257 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。