Job ID = 9158725 sra ファイルのダウンロード中... Completed: 203451K bytes transferred in 8 seconds (196185K 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 3173169 spots for /home/okishinya/chipatlas/results/dm3/SRX2677157/SRR5382077.sra Written 3173169 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:52 3173169 reads; of these: 3173169 (100.00%) were paired; of these: 307221 (9.68%) aligned concordantly 0 times 1947175 (61.36%) aligned concordantly exactly 1 time 918773 (28.95%) aligned concordantly >1 times ---- 307221 pairs aligned concordantly 0 times; of these: 26532 (8.64%) aligned discordantly 1 time ---- 280689 pairs aligned 0 times concordantly or discordantly; of these: 561378 mates make up the pairs; of these: 490554 (87.38%) aligned 0 times 38990 (6.95%) aligned exactly 1 time 31834 (5.67%) aligned >1 times 92.27% overall alignment rate Time searching: 00:09:53 Overall time: 00:09:53 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] 87415 / 2046048 = 0.0427 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 19:26:13: # Command line: callpeak -t SRX2677157.bam -f BAM -g dm -n SRX2677157.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2677157.20 # format = BAM # ChIP-seq file = ['SRX2677157.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 19:26:13: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:26:13: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:26:13: # Command line: callpeak -t SRX2677157.bam -f BAM -g dm -n SRX2677157.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2677157.10 # format = BAM # ChIP-seq file = ['SRX2677157.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 19:26:13: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:26:13: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:26:13: # Command line: callpeak -t SRX2677157.bam -f BAM -g dm -n SRX2677157.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2677157.05 # format = BAM # ChIP-seq file = ['SRX2677157.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 19:26:13: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:26:13: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:26:22: 1000000 INFO @ Tue, 27 Jun 2017 19:26:22: 1000000 INFO @ Tue, 27 Jun 2017 19:26:22: 1000000 INFO @ Tue, 27 Jun 2017 19:26:30: 2000000 INFO @ Tue, 27 Jun 2017 19:26:30: 2000000 INFO @ Tue, 27 Jun 2017 19:26:30: 2000000 INFO @ Tue, 27 Jun 2017 19:26:38: 3000000 INFO @ Tue, 27 Jun 2017 19:26:38: 3000000 INFO @ Tue, 27 Jun 2017 19:26:38: 3000000 INFO @ Tue, 27 Jun 2017 19:26:46: 4000000 INFO @ Tue, 27 Jun 2017 19:26:46: 4000000 INFO @ Tue, 27 Jun 2017 19:26:46: 4000000 INFO @ Tue, 27 Jun 2017 19:26:55: 5000000 INFO @ Tue, 27 Jun 2017 19:26:55: 5000000 INFO @ Tue, 27 Jun 2017 19:26:55: 5000000 INFO @ Tue, 27 Jun 2017 19:27:00: #1 tag size is determined as 70 bps INFO @ Tue, 27 Jun 2017 19:27:00: #1 tag size = 70 INFO @ Tue, 27 Jun 2017 19:27:00: #1 total tags in treatment: 2778715 INFO @ Tue, 27 Jun 2017 19:27:00: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:27:00: #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 19:27:00: #1 tag size is determined as 70 bps INFO @ Tue, 27 Jun 2017 19:27:00: #1 tag size = 70 INFO @ Tue, 27 Jun 2017 19:27:00: #1 total tags in treatment: 2778715 INFO @ Tue, 27 Jun 2017 19:27:00: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:27:00: #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 19:27:00: #1 tag size is determined as 70 bps INFO @ Tue, 27 Jun 2017 19:27:00: #1 tag size = 70 INFO @ Tue, 27 Jun 2017 19:27:00: #1 total tags in treatment: 2778715 INFO @ Tue, 27 Jun 2017 19:27:00: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:27:00: #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 19:27:00: #1 tags after filtering in treatment: 2567033 INFO @ Tue, 27 Jun 2017 19:27:00: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 27 Jun 2017 19:27:00: #1 finished! INFO @ Tue, 27 Jun 2017 19:27:00: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:27:00: #1 tags after filtering in treatment: 2567033 INFO @ Tue, 27 Jun 2017 19:27:00: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 27 Jun 2017 19:27:00: #1 finished! INFO @ Tue, 27 Jun 2017 19:27:00: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:27:00: #1 tags after filtering in treatment: 2567033 INFO @ Tue, 27 Jun 2017 19:27:00: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 27 Jun 2017 19:27:00: #1 finished! INFO @ Tue, 27 Jun 2017 19:27:00: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:27:00: #2 number of paired peaks: 587 WARNING @ Tue, 27 Jun 2017 19:27:00: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Tue, 27 Jun 2017 19:27:00: start model_add_line... INFO @ Tue, 27 Jun 2017 19:27:00: #2 number of paired peaks: 587 WARNING @ Tue, 27 Jun 2017 19:27:00: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Tue, 27 Jun 2017 19:27:00: start model_add_line... INFO @ Tue, 27 Jun 2017 19:27:00: start X-correlation... INFO @ Tue, 27 Jun 2017 19:27:01: start X-correlation... INFO @ Tue, 27 Jun 2017 19:27:01: end of X-cor INFO @ Tue, 27 Jun 2017 19:27:01: #2 finished! INFO @ Tue, 27 Jun 2017 19:27:01: #2 predicted fragment length is 115 bps INFO @ Tue, 27 Jun 2017 19:27:01: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 27 Jun 2017 19:27:01: #2.2 Generate R script for model : SRX2677157.05_model.r INFO @ Tue, 27 Jun 2017 19:27:01: end of X-cor INFO @ Tue, 27 Jun 2017 19:27:01: #2 finished! INFO @ Tue, 27 Jun 2017 19:27:01: #2 predicted fragment length is 115 bps INFO @ Tue, 27 Jun 2017 19:27:01: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 27 Jun 2017 19:27:01: #2.2 Generate R script for model : SRX2677157.20_model.r WARNING @ Tue, 27 Jun 2017 19:27:01: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:27:01: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Tue, 27 Jun 2017 19:27:01: #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 19:27:01: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:27:01: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 27 Jun 2017 19:27:01: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:27:01: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Tue, 27 Jun 2017 19:27:01: #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 19:27:01: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:27:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:27:01: #2 number of paired peaks: 587 WARNING @ Tue, 27 Jun 2017 19:27:01: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Tue, 27 Jun 2017 19:27:01: start model_add_line... INFO @ Tue, 27 Jun 2017 19:27:01: start X-correlation... INFO @ Tue, 27 Jun 2017 19:27:01: end of X-cor INFO @ Tue, 27 Jun 2017 19:27:01: #2 finished! INFO @ Tue, 27 Jun 2017 19:27:01: #2 predicted fragment length is 115 bps INFO @ Tue, 27 Jun 2017 19:27:01: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 27 Jun 2017 19:27:01: #2.2 Generate R script for model : SRX2677157.10_model.r WARNING @ Tue, 27 Jun 2017 19:27:01: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:27:01: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Tue, 27 Jun 2017 19:27:01: #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 19:27:01: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:27:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:27:07: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:27:07: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:27:07: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:27:10: #4 Write output xls file... SRX2677157.10_peaks.xls INFO @ Tue, 27 Jun 2017 19:27:10: #4 Write peak in narrowPeak format file... SRX2677157.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:27:10: #4 Write summits bed file... SRX2677157.10_summits.bed INFO @ Tue, 27 Jun 2017 19:27:10: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (574 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 19:27:10: #4 Write output xls file... SRX2677157.05_peaks.xls INFO @ Tue, 27 Jun 2017 19:27:10: #4 Write peak in narrowPeak format file... SRX2677157.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:27:10: #4 Write summits bed file... SRX2677157.05_summits.bed INFO @ Tue, 27 Jun 2017 19:27:10: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (876 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 19:27:10: #4 Write output xls file... SRX2677157.20_peaks.xls INFO @ Tue, 27 Jun 2017 19:27:10: #4 Write peak in narrowPeak format file... SRX2677157.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:27:10: #4 Write summits bed file... SRX2677157.20_summits.bed INFO @ Tue, 27 Jun 2017 19:27:10: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (349 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。