Job ID = 11192876 sra ファイルのダウンロード中... Completed: 1477705K bytes transferred in 54 seconds (223762K 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 12095710 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2767196/SRR5483852.sra Written 12095710 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2767196/SRR5483852.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: 00:19:33 12095710 reads; of these: 12095710 (100.00%) were paired; of these: 845874 (6.99%) aligned concordantly 0 times 9416694 (77.85%) aligned concordantly exactly 1 time 1833142 (15.16%) aligned concordantly >1 times ---- 845874 pairs aligned concordantly 0 times; of these: 66395 (7.85%) aligned discordantly 1 time ---- 779479 pairs aligned 0 times concordantly or discordantly; of these: 1558958 mates make up the pairs; of these: 1076212 (69.03%) aligned 0 times 365231 (23.43%) aligned exactly 1 time 117515 (7.54%) aligned >1 times 95.55% overall alignment rate Time searching: 00:19:33 Overall time: 00:19:33 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 20 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] 10459601 / 10577841 = 0.9888 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 10:40:27: # Command line: callpeak -t SRX2767196.bam -f BAM -g 12100000 -n SRX2767196.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2767196.10 # format = BAM # ChIP-seq file = ['SRX2767196.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 10:40:27: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:40:27: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:40:27: # Command line: callpeak -t SRX2767196.bam -f BAM -g 12100000 -n SRX2767196.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2767196.20 # format = BAM # ChIP-seq file = ['SRX2767196.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 10:40:27: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:40:27: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:40:27: # Command line: callpeak -t SRX2767196.bam -f BAM -g 12100000 -n SRX2767196.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2767196.05 # format = BAM # ChIP-seq file = ['SRX2767196.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 10:40:27: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:40:27: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:40:35: 1000000 INFO @ Sat, 15 Sep 2018 10:40:35: 1000000 INFO @ Sat, 15 Sep 2018 10:40:35: 1000000 INFO @ Sat, 15 Sep 2018 10:40:42: 2000000 INFO @ Sat, 15 Sep 2018 10:40:43: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Sep 2018 10:40:44: 2000000 INFO @ Sat, 15 Sep 2018 10:40:44: #1 tag size is determined as 150 bps INFO @ Sat, 15 Sep 2018 10:40:44: #1 tag size = 150 INFO @ Sat, 15 Sep 2018 10:40:44: #1 total tags in treatment: 837140 INFO @ Sat, 15 Sep 2018 10:40:44: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:40:44: #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 10:40:44: #1 tags after filtering in treatment: 136144 INFO @ Sat, 15 Sep 2018 10:40:44: #1 Redundant rate of treatment: 0.84 INFO @ Sat, 15 Sep 2018 10:40:44: #1 finished! INFO @ Sat, 15 Sep 2018 10:40:44: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:40:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:40:44: #2 number of paired peaks: 260 WARNING @ Sat, 15 Sep 2018 10:40:44: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Sat, 15 Sep 2018 10:40:44: start model_add_line... INFO @ Sat, 15 Sep 2018 10:40:44: start X-correlation... INFO @ Sat, 15 Sep 2018 10:40:44: end of X-cor INFO @ Sat, 15 Sep 2018 10:40:44: #2 finished! INFO @ Sat, 15 Sep 2018 10:40:44: #2 predicted fragment length is 165 bps INFO @ Sat, 15 Sep 2018 10:40:44: #2 alternative fragment length(s) may be 57,165,188,211,231,247,273,292,353,398,421,444,486,509,530,552,594 bps INFO @ Sat, 15 Sep 2018 10:40:44: #2.2 Generate R script for model : SRX2767196.20_model.r WARNING @ Sat, 15 Sep 2018 10:40:44: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 10:40:44: #2 You may need to consider one of the other alternative d(s): 57,165,188,211,231,247,273,292,353,398,421,444,486,509,530,552,594 WARNING @ Sat, 15 Sep 2018 10:40:44: #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 10:40:44: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:40:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Sep 2018 10:40:44: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:40:45: #4 Write output xls file... SRX2767196.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:40:45: #4 Write peak in narrowPeak format file... SRX2767196.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:40:45: #4 Write summits bed file... SRX2767196.20_summits.bed INFO @ Sat, 15 Sep 2018 10:40:45: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:40:45: #1 tag size is determined as 150 bps INFO @ Sat, 15 Sep 2018 10:40:45: #1 tag size = 150 INFO @ Sat, 15 Sep 2018 10:40:45: #1 total tags in treatment: 837140 INFO @ Sat, 15 Sep 2018 10:40:45: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:40:45: #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 10:40:45: #1 tags after filtering in treatment: 136144 INFO @ Sat, 15 Sep 2018 10:40:45: #1 Redundant rate of treatment: 0.84 INFO @ Sat, 15 Sep 2018 10:40:45: #1 finished! INFO @ Sat, 15 Sep 2018 10:40:45: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:40:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:40:45: #2 number of paired peaks: 260 WARNING @ Sat, 15 Sep 2018 10:40:45: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Sat, 15 Sep 2018 10:40:45: start model_add_line... INFO @ Sat, 15 Sep 2018 10:40:45: start X-correlation... INFO @ Sat, 15 Sep 2018 10:40:45: end of X-cor INFO @ Sat, 15 Sep 2018 10:40:45: #2 finished! INFO @ Sat, 15 Sep 2018 10:40:45: #2 predicted fragment length is 165 bps INFO @ Sat, 15 Sep 2018 10:40:45: #2 alternative fragment length(s) may be 57,165,188,211,231,247,273,292,353,398,421,444,486,509,530,552,594 bps INFO @ Sat, 15 Sep 2018 10:40:45: #2.2 Generate R script for model : SRX2767196.10_model.r WARNING @ Sat, 15 Sep 2018 10:40:45: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 10:40:45: #2 You may need to consider one of the other alternative d(s): 57,165,188,211,231,247,273,292,353,398,421,444,486,509,530,552,594 WARNING @ Sat, 15 Sep 2018 10:40:45: #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 10:40:45: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:40:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:40:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:40:45: #1 tag size is determined as 150 bps INFO @ Sat, 15 Sep 2018 10:40:45: #1 tag size = 150 INFO @ Sat, 15 Sep 2018 10:40:45: #1 total tags in treatment: 837140 INFO @ Sat, 15 Sep 2018 10:40:45: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:40:45: #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 10:40:45: #1 tags after filtering in treatment: 136144 INFO @ Sat, 15 Sep 2018 10:40:45: #1 Redundant rate of treatment: 0.84 INFO @ Sat, 15 Sep 2018 10:40:45: #1 finished! INFO @ Sat, 15 Sep 2018 10:40:45: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:40:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:40:45: #2 number of paired peaks: 260 WARNING @ Sat, 15 Sep 2018 10:40:45: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Sat, 15 Sep 2018 10:40:45: start model_add_line... INFO @ Sat, 15 Sep 2018 10:40:45: start X-correlation... INFO @ Sat, 15 Sep 2018 10:40:45: end of X-cor INFO @ Sat, 15 Sep 2018 10:40:45: #2 finished! INFO @ Sat, 15 Sep 2018 10:40:45: #2 predicted fragment length is 165 bps INFO @ Sat, 15 Sep 2018 10:40:45: #2 alternative fragment length(s) may be 57,165,188,211,231,247,273,292,353,398,421,444,486,509,530,552,594 bps INFO @ Sat, 15 Sep 2018 10:40:45: #2.2 Generate R script for model : SRX2767196.05_model.r WARNING @ Sat, 15 Sep 2018 10:40:45: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 10:40:45: #2 You may need to consider one of the other alternative d(s): 57,165,188,211,231,247,273,292,353,398,421,444,486,509,530,552,594 WARNING @ Sat, 15 Sep 2018 10:40:45: #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 10:40:45: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:40:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:40:45: #4 Write output xls file... SRX2767196.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:40:45: #4 Write peak in narrowPeak format file... SRX2767196.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:40:45: #4 Write summits bed file... SRX2767196.10_summits.bed INFO @ Sat, 15 Sep 2018 10:40:45: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:40:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:40:46: #4 Write output xls file... SRX2767196.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:40:46: #4 Write peak in narrowPeak format file... SRX2767196.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:40:46: #4 Write summits bed file... SRX2767196.05_summits.bed INFO @ Sat, 15 Sep 2018 10:40:46: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 2 millis CompletedMACS2peakCalling