Job ID = 9158724 sra ファイルのダウンロード中... Completed: 89116K bytes transferred in 5 seconds (130114K bits/sec), in 1 file, 2 directories. 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... Written 1453382 spots for /home/okishinya/chipatlas/results/dm3/SRX2677156/SRR5382076.sra Written 1453382 spots total 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: 00:04:08 1453382 reads; of these: 1453382 (100.00%) were paired; of these: 169046 (11.63%) aligned concordantly 0 times 889445 (61.20%) aligned concordantly exactly 1 time 394891 (27.17%) aligned concordantly >1 times ---- 169046 pairs aligned concordantly 0 times; of these: 5338 (3.16%) aligned discordantly 1 time ---- 163708 pairs aligned 0 times concordantly or discordantly; of these: 327416 mates make up the pairs; of these: 305445 (93.29%) aligned 0 times 12927 (3.95%) aligned exactly 1 time 9044 (2.76%) aligned >1 times 89.49% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 137746 / 724403 = 0.1902 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 @ Tue, 27 Jun 2017 19:18:54: # Command line: callpeak -t SRX2677156.bam -f BAM -g dm -n SRX2677156.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2677156.05 # format = BAM # ChIP-seq file = ['SRX2677156.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 27 Jun 2017 19:18:54: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:18:54: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:18:54: # Command line: callpeak -t SRX2677156.bam -f BAM -g dm -n SRX2677156.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2677156.10 # format = BAM # ChIP-seq file = ['SRX2677156.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 27 Jun 2017 19:18:54: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:18:54: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:18:54: # Command line: callpeak -t SRX2677156.bam -f BAM -g dm -n SRX2677156.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2677156.20 # format = BAM # ChIP-seq file = ['SRX2677156.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 27 Jun 2017 19:18:54: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:18:54: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:19:03: 1000000 INFO @ Tue, 27 Jun 2017 19:19:03: 1000000 INFO @ Tue, 27 Jun 2017 19:19:03: 1000000 INFO @ Tue, 27 Jun 2017 19:19:12: 2000000 INFO @ Tue, 27 Jun 2017 19:19:13: 2000000 INFO @ Tue, 27 Jun 2017 19:19:14: 2000000 INFO @ Tue, 27 Jun 2017 19:19:15: #1 tag size is determined as 64 bps INFO @ Tue, 27 Jun 2017 19:19:15: #1 tag size = 64 INFO @ Tue, 27 Jun 2017 19:19:15: #1 total tags in treatment: 1146683 INFO @ Tue, 27 Jun 2017 19:19:15: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:19:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 19:19:15: #1 tags after filtering in treatment: 985072 INFO @ Tue, 27 Jun 2017 19:19:15: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 27 Jun 2017 19:19:15: #1 finished! INFO @ Tue, 27 Jun 2017 19:19:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:19:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:19:15: #2 number of paired peaks: 886 WARNING @ Tue, 27 Jun 2017 19:19:15: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Tue, 27 Jun 2017 19:19:15: start model_add_line... INFO @ Tue, 27 Jun 2017 19:19:15: start X-correlation... INFO @ Tue, 27 Jun 2017 19:19:15: end of X-cor INFO @ Tue, 27 Jun 2017 19:19:15: #2 finished! INFO @ Tue, 27 Jun 2017 19:19:15: #2 predicted fragment length is 98 bps INFO @ Tue, 27 Jun 2017 19:19:15: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 27 Jun 2017 19:19:15: #2.2 Generate R script for model : SRX2677156.10_model.r WARNING @ Tue, 27 Jun 2017 19:19:15: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:19:15: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Tue, 27 Jun 2017 19:19:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 19:19:15: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:19:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:19:16: #1 tag size is determined as 64 bps INFO @ Tue, 27 Jun 2017 19:19:16: #1 tag size = 64 INFO @ Tue, 27 Jun 2017 19:19:16: #1 total tags in treatment: 1146683 INFO @ Tue, 27 Jun 2017 19:19:16: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:19:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 19:19:16: #1 tags after filtering in treatment: 985072 INFO @ Tue, 27 Jun 2017 19:19:16: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 27 Jun 2017 19:19:16: #1 finished! INFO @ Tue, 27 Jun 2017 19:19:16: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:19:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:19:17: #2 number of paired peaks: 886 WARNING @ Tue, 27 Jun 2017 19:19:17: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Tue, 27 Jun 2017 19:19:17: start model_add_line... INFO @ Tue, 27 Jun 2017 19:19:17: start X-correlation... INFO @ Tue, 27 Jun 2017 19:19:17: end of X-cor INFO @ Tue, 27 Jun 2017 19:19:17: #2 finished! INFO @ Tue, 27 Jun 2017 19:19:17: #2 predicted fragment length is 98 bps INFO @ Tue, 27 Jun 2017 19:19:17: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 27 Jun 2017 19:19:17: #2.2 Generate R script for model : SRX2677156.05_model.r WARNING @ Tue, 27 Jun 2017 19:19:17: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:19:17: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Tue, 27 Jun 2017 19:19:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 19:19:17: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:19:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:19:17: #1 tag size is determined as 64 bps INFO @ Tue, 27 Jun 2017 19:19:17: #1 tag size = 64 INFO @ Tue, 27 Jun 2017 19:19:17: #1 total tags in treatment: 1146683 INFO @ Tue, 27 Jun 2017 19:19:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:19:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 19:19:17: #1 tags after filtering in treatment: 985072 INFO @ Tue, 27 Jun 2017 19:19:17: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 27 Jun 2017 19:19:17: #1 finished! INFO @ Tue, 27 Jun 2017 19:19:17: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:19:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:19:17: #2 number of paired peaks: 886 WARNING @ Tue, 27 Jun 2017 19:19:17: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Tue, 27 Jun 2017 19:19:17: start model_add_line... INFO @ Tue, 27 Jun 2017 19:19:17: start X-correlation... INFO @ Tue, 27 Jun 2017 19:19:17: end of X-cor INFO @ Tue, 27 Jun 2017 19:19:17: #2 finished! INFO @ Tue, 27 Jun 2017 19:19:17: #2 predicted fragment length is 98 bps INFO @ Tue, 27 Jun 2017 19:19:17: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 27 Jun 2017 19:19:17: #2.2 Generate R script for model : SRX2677156.20_model.r WARNING @ Tue, 27 Jun 2017 19:19:17: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:19:17: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Tue, 27 Jun 2017 19:19:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 19:19:17: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:19:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:19:18: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:19:19: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:19:19: #4 Write output xls file... SRX2677156.10_peaks.xls INFO @ Tue, 27 Jun 2017 19:19:19: #4 Write peak in narrowPeak format file... SRX2677156.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:19:19: #4 Write summits bed file... SRX2677156.10_summits.bed INFO @ Tue, 27 Jun 2017 19:19:19: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (357 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 19:19:19: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:19:20: #4 Write output xls file... SRX2677156.05_peaks.xls INFO @ Tue, 27 Jun 2017 19:19:20: #4 Write peak in narrowPeak format file... SRX2677156.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:19:20: #4 Write summits bed file... SRX2677156.05_summits.bed INFO @ Tue, 27 Jun 2017 19:19:20: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (616 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 19:19:21: #4 Write output xls file... SRX2677156.20_peaks.xls INFO @ Tue, 27 Jun 2017 19:19:21: #4 Write peak in narrowPeak format file... SRX2677156.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:19:21: #4 Write summits bed file... SRX2677156.20_summits.bed INFO @ Tue, 27 Jun 2017 19:19:21: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。