Job ID = 10937523 sra ファイルのダウンロード中... Completed: 438152K bytes transferred in 47 seconds (75988K 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 4591400 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010320/SRR5833319.sra Written 4591400 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010320/SRR5833319.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: 00:02:24 4591400 reads; of these: 4591400 (100.00%) were paired; of these: 3291037 (71.68%) aligned concordantly 0 times 678671 (14.78%) aligned concordantly exactly 1 time 621692 (13.54%) aligned concordantly >1 times ---- 3291037 pairs aligned concordantly 0 times; of these: 4032 (0.12%) aligned discordantly 1 time ---- 3287005 pairs aligned 0 times concordantly or discordantly; of these: 6574010 mates make up the pairs; of these: 6541342 (99.50%) aligned 0 times 12702 (0.19%) aligned exactly 1 time 19966 (0.30%) aligned >1 times 28.77% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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_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] 166261 / 1303549 = 0.1275 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 @ Fri, 10 Aug 2018 02:30:11: # Command line: callpeak -t SRX3010320.bam -f BAM -g 12100000 -n SRX3010320.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010320.10 # format = BAM # ChIP-seq file = ['SRX3010320.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 @ Fri, 10 Aug 2018 02:30:11: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:30:11: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:30:11: # Command line: callpeak -t SRX3010320.bam -f BAM -g 12100000 -n SRX3010320.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010320.05 # format = BAM # ChIP-seq file = ['SRX3010320.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 @ Fri, 10 Aug 2018 02:30:11: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:30:11: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:30:11: # Command line: callpeak -t SRX3010320.bam -f BAM -g 12100000 -n SRX3010320.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010320.20 # format = BAM # ChIP-seq file = ['SRX3010320.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 @ Fri, 10 Aug 2018 02:30:11: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:30:11: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:30:19: 1000000 INFO @ Fri, 10 Aug 2018 02:30:19: 1000000 INFO @ Fri, 10 Aug 2018 02:30:19: 1000000 INFO @ Fri, 10 Aug 2018 02:30:26: 2000000 INFO @ Fri, 10 Aug 2018 02:30:26: 2000000 INFO @ Fri, 10 Aug 2018 02:30:26: 2000000 INFO @ Fri, 10 Aug 2018 02:30:28: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:30:28: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:30:28: #1 total tags in treatment: 1134146 INFO @ Fri, 10 Aug 2018 02:30:28: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:30:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:30:28: #1 tags after filtering in treatment: 696769 INFO @ Fri, 10 Aug 2018 02:30:28: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 10 Aug 2018 02:30:28: #1 finished! INFO @ Fri, 10 Aug 2018 02:30:28: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:30:28: #2 number of paired peaks: 491 WARNING @ Fri, 10 Aug 2018 02:30:28: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Fri, 10 Aug 2018 02:30:28: start model_add_line... INFO @ Fri, 10 Aug 2018 02:30:28: start X-correlation... INFO @ Fri, 10 Aug 2018 02:30:28: end of X-cor INFO @ Fri, 10 Aug 2018 02:30:28: #2 finished! INFO @ Fri, 10 Aug 2018 02:30:28: #2 predicted fragment length is 189 bps INFO @ Fri, 10 Aug 2018 02:30:28: #2 alternative fragment length(s) may be 189 bps INFO @ Fri, 10 Aug 2018 02:30:28: #2.2 Generate R script for model : SRX3010320.20_model.r WARNING @ Fri, 10 Aug 2018 02:30:28: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 02:30:28: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Fri, 10 Aug 2018 02:30:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 02:30:28: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:30:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:30:29: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:30:29: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:30:29: #1 total tags in treatment: 1134146 INFO @ Fri, 10 Aug 2018 02:30:29: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:30:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:30:29: #1 tags after filtering in treatment: 696769 INFO @ Fri, 10 Aug 2018 02:30:29: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 10 Aug 2018 02:30:29: #1 finished! INFO @ Fri, 10 Aug 2018 02:30:29: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:30:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:30:29: #2 number of paired peaks: 491 WARNING @ Fri, 10 Aug 2018 02:30:29: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Fri, 10 Aug 2018 02:30:29: start model_add_line... INFO @ Fri, 10 Aug 2018 02:30:29: start X-correlation... INFO @ Fri, 10 Aug 2018 02:30:29: end of X-cor INFO @ Fri, 10 Aug 2018 02:30:29: #2 finished! INFO @ Fri, 10 Aug 2018 02:30:29: #2 predicted fragment length is 189 bps INFO @ Fri, 10 Aug 2018 02:30:29: #2 alternative fragment length(s) may be 189 bps INFO @ Fri, 10 Aug 2018 02:30:29: #2.2 Generate R script for model : SRX3010320.10_model.r WARNING @ Fri, 10 Aug 2018 02:30:29: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 02:30:29: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Fri, 10 Aug 2018 02:30:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 02:30:29: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:30:29: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:30:29: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:30:29: #1 total tags in treatment: 1134146 INFO @ Fri, 10 Aug 2018 02:30:29: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:30:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:30:29: #1 tags after filtering in treatment: 696769 INFO @ Fri, 10 Aug 2018 02:30:29: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 10 Aug 2018 02:30:29: #1 finished! INFO @ Fri, 10 Aug 2018 02:30:29: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:30:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:30:29: #2 number of paired peaks: 491 WARNING @ Fri, 10 Aug 2018 02:30:29: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Fri, 10 Aug 2018 02:30:29: start model_add_line... INFO @ Fri, 10 Aug 2018 02:30:29: start X-correlation... INFO @ Fri, 10 Aug 2018 02:30:29: end of X-cor INFO @ Fri, 10 Aug 2018 02:30:29: #2 finished! INFO @ Fri, 10 Aug 2018 02:30:29: #2 predicted fragment length is 189 bps INFO @ Fri, 10 Aug 2018 02:30:29: #2 alternative fragment length(s) may be 189 bps INFO @ Fri, 10 Aug 2018 02:30:29: #2.2 Generate R script for model : SRX3010320.05_model.r WARNING @ Fri, 10 Aug 2018 02:30:29: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 02:30:29: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Fri, 10 Aug 2018 02:30:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 02:30:29: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:30:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:30:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:30:32: #4 Write output xls file... SRX3010320.20_peaks.xls INFO @ Fri, 10 Aug 2018 02:30:32: #4 Write peak in narrowPeak format file... SRX3010320.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:30:32: #4 Write summits bed file... SRX3010320.20_summits.bed INFO @ Fri, 10 Aug 2018 02:30:32: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (377 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:30:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:30:32: #4 Write output xls file... SRX3010320.10_peaks.xls INFO @ Fri, 10 Aug 2018 02:30:32: #4 Write peak in narrowPeak format file... SRX3010320.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:30:32: #4 Write summits bed file... SRX3010320.10_summits.bed INFO @ Fri, 10 Aug 2018 02:30:32: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (415 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:30:33: #4 Write output xls file... SRX3010320.05_peaks.xls INFO @ Fri, 10 Aug 2018 02:30:33: #4 Write peak in narrowPeak format file... SRX3010320.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:30:33: #4 Write summits bed file... SRX3010320.05_summits.bed INFO @ Fri, 10 Aug 2018 02:30:33: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (473 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。