Job ID = 11192922 sra ファイルのダウンロード中... Completed: 183592K bytes transferred in 5 seconds (300488K 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 4801762 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242037/SRR6129625.sra Written 4801762 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242037/SRR6129625.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: 00:01:00 4801762 reads; of these: 4801762 (100.00%) were paired; of these: 4654758 (96.94%) aligned concordantly 0 times 121407 (2.53%) aligned concordantly exactly 1 time 25597 (0.53%) aligned concordantly >1 times ---- 4654758 pairs aligned concordantly 0 times; of these: 65278 (1.40%) aligned discordantly 1 time ---- 4589480 pairs aligned 0 times concordantly or discordantly; of these: 9178960 mates make up the pairs; of these: 8626742 (93.98%) aligned 0 times 454407 (4.95%) aligned exactly 1 time 97811 (1.07%) aligned >1 times 10.17% overall alignment rate Time searching: 00:01:00 Overall time: 00:01:00 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] 50832 / 210973 = 0.2409 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 @ Sat, 15 Sep 2018 10:31:42: # Command line: callpeak -t SRX3242037.bam -f BAM -g 12100000 -n SRX3242037.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3242037.10 # format = BAM # ChIP-seq file = ['SRX3242037.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 @ Sat, 15 Sep 2018 10:31:42: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:31:42: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:31:42: # Command line: callpeak -t SRX3242037.bam -f BAM -g 12100000 -n SRX3242037.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3242037.05 # format = BAM # ChIP-seq file = ['SRX3242037.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 @ Sat, 15 Sep 2018 10:31:42: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:31:42: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:31:42: # Command line: callpeak -t SRX3242037.bam -f BAM -g 12100000 -n SRX3242037.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3242037.20 # format = BAM # ChIP-seq file = ['SRX3242037.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 @ Sat, 15 Sep 2018 10:31:42: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:31:42: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:31:47: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:31:47: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:31:47: #1 total tags in treatment: 125609 INFO @ Sat, 15 Sep 2018 10:31:47: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:31:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:31:47: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:31:47: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:31:47: #1 total tags in treatment: 125609 INFO @ Sat, 15 Sep 2018 10:31:47: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:31:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:31:47: #1 tags after filtering in treatment: 119535 INFO @ Sat, 15 Sep 2018 10:31:47: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 15 Sep 2018 10:31:47: #1 finished! INFO @ Sat, 15 Sep 2018 10:31:47: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:31:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:31:47: #1 tags after filtering in treatment: 119535 INFO @ Sat, 15 Sep 2018 10:31:47: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 15 Sep 2018 10:31:47: #1 finished! INFO @ Sat, 15 Sep 2018 10:31:47: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:31:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:31:47: #2 number of paired peaks: 172 WARNING @ Sat, 15 Sep 2018 10:31:47: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Sep 2018 10:31:47: #2 number of paired peaks: 172 INFO @ Sat, 15 Sep 2018 10:31:47: start model_add_line... WARNING @ Sat, 15 Sep 2018 10:31:47: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Sep 2018 10:31:47: start model_add_line... INFO @ Sat, 15 Sep 2018 10:31:47: start X-correlation... INFO @ Sat, 15 Sep 2018 10:31:47: start X-correlation... INFO @ Sat, 15 Sep 2018 10:31:47: end of X-cor INFO @ Sat, 15 Sep 2018 10:31:47: end of X-cor INFO @ Sat, 15 Sep 2018 10:31:47: #2 finished! INFO @ Sat, 15 Sep 2018 10:31:47: #2 finished! INFO @ Sat, 15 Sep 2018 10:31:47: #2 predicted fragment length is 161 bps INFO @ Sat, 15 Sep 2018 10:31:47: #2 predicted fragment length is 161 bps INFO @ Sat, 15 Sep 2018 10:31:47: #2 alternative fragment length(s) may be 147,161,185,589 bps INFO @ Sat, 15 Sep 2018 10:31:47: #2 alternative fragment length(s) may be 147,161,185,589 bps INFO @ Sat, 15 Sep 2018 10:31:47: #2.2 Generate R script for model : SRX3242037.05_model.r INFO @ Sat, 15 Sep 2018 10:31:47: #2.2 Generate R script for model : SRX3242037.10_model.r INFO @ Sat, 15 Sep 2018 10:31:47: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:31:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:31:47: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:31:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:31:47: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:31:47: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:31:48: #4 Write output xls file... SRX3242037.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:31:48: #4 Write peak in narrowPeak format file... SRX3242037.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:31:48: #4 Write summits bed file... SRX3242037.10_summits.bed INFO @ Sat, 15 Sep 2018 10:31:48: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:31:48: #4 Write output xls file... SRX3242037.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:31:48: #4 Write peak in narrowPeak format file... SRX3242037.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:31:48: #4 Write summits bed file... SRX3242037.05_summits.bed INFO @ Sat, 15 Sep 2018 10:31:48: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (130 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:31:48: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:31:48: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:31:48: #1 total tags in treatment: 125609 INFO @ Sat, 15 Sep 2018 10:31:48: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:31:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:31:48: #1 tags after filtering in treatment: 119535 INFO @ Sat, 15 Sep 2018 10:31:48: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 15 Sep 2018 10:31:48: #1 finished! INFO @ Sat, 15 Sep 2018 10:31:48: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:31:48: #2 number of paired peaks: 172 WARNING @ Sat, 15 Sep 2018 10:31:48: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Sep 2018 10:31:48: start model_add_line... INFO @ Sat, 15 Sep 2018 10:31:48: start X-correlation... INFO @ Sat, 15 Sep 2018 10:31:48: end of X-cor INFO @ Sat, 15 Sep 2018 10:31:48: #2 finished! INFO @ Sat, 15 Sep 2018 10:31:48: #2 predicted fragment length is 161 bps INFO @ Sat, 15 Sep 2018 10:31:48: #2 alternative fragment length(s) may be 147,161,185,589 bps INFO @ Sat, 15 Sep 2018 10:31:48: #2.2 Generate R script for model : SRX3242037.20_model.r INFO @ Sat, 15 Sep 2018 10:31:48: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:31:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:31:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:31:49: #4 Write output xls file... SRX3242037.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:31:49: #4 Write peak in narrowPeak format file... SRX3242037.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:31:49: #4 Write summits bed file... SRX3242037.20_summits.bed INFO @ Sat, 15 Sep 2018 10:31:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (24 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。