Job ID = 11193231 sra ファイルのダウンロード中... Completed: 31277K bytes transferred in 3 seconds (79951K 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 790213 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977517/SRR1951363.sra Written 790213 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977517/SRR1951363.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: 00:00:21 790213 reads; of these: 790213 (100.00%) were paired; of these: 319420 (40.42%) aligned concordantly 0 times 407902 (51.62%) aligned concordantly exactly 1 time 62891 (7.96%) aligned concordantly >1 times ---- 319420 pairs aligned concordantly 0 times; of these: 11252 (3.52%) aligned discordantly 1 time ---- 308168 pairs aligned 0 times concordantly or discordantly; of these: 616336 mates make up the pairs; of these: 583565 (94.68%) aligned 0 times 23757 (3.85%) aligned exactly 1 time 9014 (1.46%) aligned >1 times 63.08% overall alignment rate Time searching: 00:00:21 Overall time: 00:00:21 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] 471580 / 478843 = 0.9848 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 11:14:52: # Command line: callpeak -t SRX977517.bam -f BAM -g 12100000 -n SRX977517.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977517.05 # format = BAM # ChIP-seq file = ['SRX977517.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 11:14:52: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:14:52: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:14:52: # Command line: callpeak -t SRX977517.bam -f BAM -g 12100000 -n SRX977517.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977517.10 # format = BAM # ChIP-seq file = ['SRX977517.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 11:14:52: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:14:52: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:14:52: # Command line: callpeak -t SRX977517.bam -f BAM -g 12100000 -n SRX977517.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977517.20 # format = BAM # ChIP-seq file = ['SRX977517.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 11:14:52: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:14:52: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:14:53: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:14:53: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:14:53: #1 total tags in treatment: 9654 INFO @ Sat, 15 Sep 2018 11:14:53: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:14:53: #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 11:14:53: #1 tags after filtering in treatment: 6632 INFO @ Sat, 15 Sep 2018 11:14:53: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Sep 2018 11:14:53: #1 finished! INFO @ Sat, 15 Sep 2018 11:14:53: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:14:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:14:53: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:14:53: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:14:53: #1 total tags in treatment: 9654 INFO @ Sat, 15 Sep 2018 11:14:53: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:14:53: #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 11:14:53: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:14:53: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:14:53: #1 total tags in treatment: 9654 INFO @ Sat, 15 Sep 2018 11:14:53: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:14:53: #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 11:14:53: #1 tags after filtering in treatment: 6632 INFO @ Sat, 15 Sep 2018 11:14:53: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Sep 2018 11:14:53: #1 finished! INFO @ Sat, 15 Sep 2018 11:14:53: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:14:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:14:53: #1 tags after filtering in treatment: 6632 INFO @ Sat, 15 Sep 2018 11:14:53: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Sep 2018 11:14:53: #1 finished! INFO @ Sat, 15 Sep 2018 11:14:53: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:14:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:14:53: #2 number of paired peaks: 230 WARNING @ Sat, 15 Sep 2018 11:14:53: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Sat, 15 Sep 2018 11:14:53: start model_add_line... INFO @ Sat, 15 Sep 2018 11:14:53: start X-correlation... INFO @ Sat, 15 Sep 2018 11:14:53: end of X-cor INFO @ Sat, 15 Sep 2018 11:14:53: #2 number of paired peaks: 230 INFO @ Sat, 15 Sep 2018 11:14:53: #2 finished! WARNING @ Sat, 15 Sep 2018 11:14:53: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Sat, 15 Sep 2018 11:14:53: #2 predicted fragment length is 56 bps INFO @ Sat, 15 Sep 2018 11:14:53: #2 alternative fragment length(s) may be 56,174,252,366,421,458,482,502 bps INFO @ Sat, 15 Sep 2018 11:14:53: start model_add_line... INFO @ Sat, 15 Sep 2018 11:14:53: #2.2 Generate R script for model : SRX977517.10_model.r INFO @ Sat, 15 Sep 2018 11:14:53: start X-correlation... INFO @ Sat, 15 Sep 2018 11:14:53: #2 number of paired peaks: 230 WARNING @ Sat, 15 Sep 2018 11:14:53: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Sat, 15 Sep 2018 11:14:53: start model_add_line... INFO @ Sat, 15 Sep 2018 11:14:53: start X-correlation... INFO @ Sat, 15 Sep 2018 11:14:53: end of X-cor INFO @ Sat, 15 Sep 2018 11:14:53: #2 finished! INFO @ Sat, 15 Sep 2018 11:14:53: #2 predicted fragment length is 56 bps INFO @ Sat, 15 Sep 2018 11:14:53: #2 alternative fragment length(s) may be 56,174,252,366,421,458,482,502 bps INFO @ Sat, 15 Sep 2018 11:14:53: #2.2 Generate R script for model : SRX977517.05_model.r INFO @ Sat, 15 Sep 2018 11:14:53: end of X-cor WARNING @ Sat, 15 Sep 2018 11:14:53: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! INFO @ Sat, 15 Sep 2018 11:14:53: #2 finished! WARNING @ Sat, 15 Sep 2018 11:14:53: #2 You may need to consider one of the other alternative d(s): 56,174,252,366,421,458,482,502 INFO @ Sat, 15 Sep 2018 11:14:53: #2 predicted fragment length is 56 bps WARNING @ Sat, 15 Sep 2018 11:14:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 11:14:53: #2 alternative fragment length(s) may be 56,174,252,366,421,458,482,502 bps INFO @ Sat, 15 Sep 2018 11:14:53: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:14:53: #2.2 Generate R script for model : SRX977517.20_model.r INFO @ Sat, 15 Sep 2018 11:14:53: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 15 Sep 2018 11:14:53: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:14:53: #2 You may need to consider one of the other alternative d(s): 56,174,252,366,421,458,482,502 WARNING @ Sat, 15 Sep 2018 11:14:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 11:14:53: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:14:53: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 15 Sep 2018 11:14:53: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:14:53: #2 You may need to consider one of the other alternative d(s): 56,174,252,366,421,458,482,502 WARNING @ Sat, 15 Sep 2018 11:14:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 11:14:53: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:14:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:14:53: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:14:53: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:14:53: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:14:53: #4 Write output xls file... SRX977517.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:14:53: #4 Write peak in narrowPeak format file... SRX977517.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:14:53: #4 Write summits bed file... SRX977517.10_summits.bed INFO @ Sat, 15 Sep 2018 11:14:53: Done! INFO @ Sat, 15 Sep 2018 11:14:53: #4 Write output xls file... SRX977517.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:14:53: #4 Write peak in narrowPeak format file... SRX977517.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:14:53: #4 Write output xls file... SRX977517.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:14:53: #4 Write summits bed file... SRX977517.05_summits.bed INFO @ Sat, 15 Sep 2018 11:14:53: #4 Write peak in narrowPeak format file... SRX977517.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:14:53: Done! INFO @ Sat, 15 Sep 2018 11:14:53: #4 Write summits bed file... SRX977517.20_summits.bed INFO @ Sat, 15 Sep 2018 11:14:53: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (2 records, 4 fields): 2 millis pass1 - making usageList (8 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (9 records, 4 fields): 3 millis pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。