Job ID = 11192845 sra ファイルのダウンロード中... Completed: 716746K bytes transferred in 10 seconds (570219K 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 10478800 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2252369/SRR4432860.sra Written 10478800 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2252369/SRR4432860.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: 00:10:24 10478800 reads; of these: 10478800 (100.00%) were paired; of these: 1035230 (9.88%) aligned concordantly 0 times 7603744 (72.56%) aligned concordantly exactly 1 time 1839826 (17.56%) aligned concordantly >1 times ---- 1035230 pairs aligned concordantly 0 times; of these: 68679 (6.63%) aligned discordantly 1 time ---- 966551 pairs aligned 0 times concordantly or discordantly; of these: 1933102 mates make up the pairs; of these: 1447879 (74.90%) aligned 0 times 350443 (18.13%) aligned exactly 1 time 134780 (6.97%) aligned >1 times 93.09% overall alignment rate Time searching: 00:10:24 Overall time: 00:10:24 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_sort_core] merging from 8 files... [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] 9180152 / 9510493 = 0.9653 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 10:14:38: # Command line: callpeak -t SRX2252369.bam -f BAM -g 12100000 -n SRX2252369.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2252369.20 # format = BAM # ChIP-seq file = ['SRX2252369.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 10:14:38: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:14:38: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:14:38: # Command line: callpeak -t SRX2252369.bam -f BAM -g 12100000 -n SRX2252369.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2252369.05 # format = BAM # ChIP-seq file = ['SRX2252369.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 10:14:38: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:14:38: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:14:38: # Command line: callpeak -t SRX2252369.bam -f BAM -g 12100000 -n SRX2252369.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2252369.10 # format = BAM # ChIP-seq file = ['SRX2252369.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 10:14:38: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:14:38: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:14:44: 1000000 INFO @ Sat, 15 Sep 2018 10:14:44: 1000000 INFO @ Sat, 15 Sep 2018 10:14:44: 1000000 INFO @ Sat, 15 Sep 2018 10:14:45: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:14:45: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:14:45: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:14:45: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:14:45: #1 total tags in treatment: 322464 INFO @ Sat, 15 Sep 2018 10:14:45: #1 total tags in treatment: 322464 INFO @ Sat, 15 Sep 2018 10:14:45: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:14:45: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:14:45: #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 10:14:45: #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 10:14:45: #1 tags after filtering in treatment: 252176 INFO @ Sat, 15 Sep 2018 10:14:45: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Sep 2018 10:14:45: #1 tags after filtering in treatment: 252176 INFO @ Sat, 15 Sep 2018 10:14:45: #1 finished! INFO @ Sat, 15 Sep 2018 10:14:45: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Sep 2018 10:14:45: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:14:45: #1 finished! INFO @ Sat, 15 Sep 2018 10:14:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:14:45: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:14:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:14:45: #2 number of paired peaks: 474 WARNING @ Sat, 15 Sep 2018 10:14:45: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Sat, 15 Sep 2018 10:14:45: start model_add_line... INFO @ Sat, 15 Sep 2018 10:14:45: #2 number of paired peaks: 474 WARNING @ Sat, 15 Sep 2018 10:14:45: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Sat, 15 Sep 2018 10:14:45: start model_add_line... INFO @ Sat, 15 Sep 2018 10:14:45: start X-correlation... INFO @ Sat, 15 Sep 2018 10:14:45: start X-correlation... INFO @ Sat, 15 Sep 2018 10:14:45: end of X-cor INFO @ Sat, 15 Sep 2018 10:14:45: #2 finished! INFO @ Sat, 15 Sep 2018 10:14:45: #2 predicted fragment length is 148 bps INFO @ Sat, 15 Sep 2018 10:14:45: #2 alternative fragment length(s) may be 148 bps INFO @ Sat, 15 Sep 2018 10:14:45: #2.2 Generate R script for model : SRX2252369.10_model.r INFO @ Sat, 15 Sep 2018 10:14:45: end of X-cor INFO @ Sat, 15 Sep 2018 10:14:45: #2 finished! INFO @ Sat, 15 Sep 2018 10:14:45: #2 predicted fragment length is 148 bps INFO @ Sat, 15 Sep 2018 10:14:45: #2 alternative fragment length(s) may be 148 bps INFO @ Sat, 15 Sep 2018 10:14:45: #2.2 Generate R script for model : SRX2252369.20_model.r INFO @ Sat, 15 Sep 2018 10:14:45: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:14:45: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:14:45: #1 total tags in treatment: 322464 INFO @ Sat, 15 Sep 2018 10:14:45: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:14:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) WARNING @ Sat, 15 Sep 2018 10:14:45: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 10:14:45: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 10:14:45: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sat, 15 Sep 2018 10:14:45: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sat, 15 Sep 2018 10:14:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Sat, 15 Sep 2018 10:14:45: #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 10:14:45: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:14:45: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:14:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:14:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:14:45: #1 tags after filtering in treatment: 252176 INFO @ Sat, 15 Sep 2018 10:14:45: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Sep 2018 10:14:45: #1 finished! INFO @ Sat, 15 Sep 2018 10:14:45: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:14:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:14:45: #2 number of paired peaks: 474 WARNING @ Sat, 15 Sep 2018 10:14:45: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Sat, 15 Sep 2018 10:14:45: start model_add_line... INFO @ Sat, 15 Sep 2018 10:14:45: start X-correlation... INFO @ Sat, 15 Sep 2018 10:14:45: end of X-cor INFO @ Sat, 15 Sep 2018 10:14:45: #2 finished! INFO @ Sat, 15 Sep 2018 10:14:45: #2 predicted fragment length is 148 bps INFO @ Sat, 15 Sep 2018 10:14:45: #2 alternative fragment length(s) may be 148 bps INFO @ Sat, 15 Sep 2018 10:14:45: #2.2 Generate R script for model : SRX2252369.05_model.r WARNING @ Sat, 15 Sep 2018 10:14:45: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 10:14:45: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sat, 15 Sep 2018 10:14:45: #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 10:14:45: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:14:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:14:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:14:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:14:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:14:47: #4 Write output xls file... SRX2252369.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:14:47: #4 Write peak in narrowPeak format file... SRX2252369.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:14:47: #4 Write summits bed file... SRX2252369.20_summits.bed INFO @ Sat, 15 Sep 2018 10:14:47: Done! INFO @ Sat, 15 Sep 2018 10:14:47: #4 Write output xls file... SRX2252369.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:14:47: #4 Write peak in narrowPeak format file... SRX2252369.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:14:47: #4 Write summits bed file... SRX2252369.10_summits.bed INFO @ Sat, 15 Sep 2018 10:14:47: Done! INFO @ Sat, 15 Sep 2018 10:14:47: #4 Write output xls file... SRX2252369.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:14:47: #4 Write peak in narrowPeak format file... SRX2252369.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:14:47: #4 Write summits bed file... SRX2252369.05_summits.bed INFO @ Sat, 15 Sep 2018 10:14:47: Done! pass1 - making usageList (16 chroms)pass1 - making usageList (16 chroms)pass1 - making usageList (15 chroms): 4 millis : 4 millis : 5 millis pass2 - checking and writing primary data (146 records, 4 fields): 64 millis pass2 - checking and writing primary data (296 records, 4 fields): 66 millis pass2 - checking and writing primary data (499 records, 4 fields): 66 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。