Job ID = 9158726 sra ファイルのダウンロード中... Completed: 107320K bytes transferred in 5 seconds (158624K 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 1686477 spots for /home/okishinya/chipatlas/results/dm3/SRX2677158/SRR5382078.sra Written 1686477 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: 00:06:35 1686477 reads; of these: 1686477 (100.00%) were paired; of these: 141929 (8.42%) aligned concordantly 0 times 934868 (55.43%) aligned concordantly exactly 1 time 609680 (36.15%) aligned concordantly >1 times ---- 141929 pairs aligned concordantly 0 times; of these: 13456 (9.48%) aligned discordantly 1 time ---- 128473 pairs aligned 0 times concordantly or discordantly; of these: 256946 mates make up the pairs; of these: 213236 (82.99%) aligned 0 times 20812 (8.10%) aligned exactly 1 time 22898 (8.91%) aligned >1 times 93.68% overall alignment rate Time searching: 00:06:35 Overall time: 00:06:35 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] 124243 / 1087921 = 0.1142 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 19:21:52: # Command line: callpeak -t SRX2677158.bam -f BAM -g dm -n SRX2677158.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2677158.10 # format = BAM # ChIP-seq file = ['SRX2677158.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 19:21:52: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:21:52: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:21:52: # Command line: callpeak -t SRX2677158.bam -f BAM -g dm -n SRX2677158.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2677158.20 # format = BAM # ChIP-seq file = ['SRX2677158.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 19:21:52: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:21:52: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:21:52: # Command line: callpeak -t SRX2677158.bam -f BAM -g dm -n SRX2677158.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2677158.05 # format = BAM # ChIP-seq file = ['SRX2677158.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 19:21:52: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:21:52: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:21:58: 1000000 INFO @ Tue, 27 Jun 2017 19:21:59: 1000000 INFO @ Tue, 27 Jun 2017 19:21:59: 1000000 INFO @ Tue, 27 Jun 2017 19:22:05: 2000000 INFO @ Tue, 27 Jun 2017 19:22:07: 2000000 INFO @ Tue, 27 Jun 2017 19:22:07: 2000000 INFO @ Tue, 27 Jun 2017 19:22:11: #1 tag size is determined as 69 bps INFO @ Tue, 27 Jun 2017 19:22:11: #1 tag size = 69 INFO @ Tue, 27 Jun 2017 19:22:11: #1 total tags in treatment: 1420488 INFO @ Tue, 27 Jun 2017 19:22:11: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:22:11: #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 19:22:11: #1 tags after filtering in treatment: 1289147 INFO @ Tue, 27 Jun 2017 19:22:11: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 27 Jun 2017 19:22:11: #1 finished! INFO @ Tue, 27 Jun 2017 19:22:11: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:22:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:22:11: #2 number of paired peaks: 768 WARNING @ Tue, 27 Jun 2017 19:22:11: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Tue, 27 Jun 2017 19:22:11: start model_add_line... INFO @ Tue, 27 Jun 2017 19:22:11: start X-correlation... INFO @ Tue, 27 Jun 2017 19:22:11: end of X-cor INFO @ Tue, 27 Jun 2017 19:22:11: #2 finished! INFO @ Tue, 27 Jun 2017 19:22:11: #2 predicted fragment length is 98 bps INFO @ Tue, 27 Jun 2017 19:22:11: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 27 Jun 2017 19:22:11: #2.2 Generate R script for model : SRX2677158.05_model.r WARNING @ Tue, 27 Jun 2017 19:22:11: #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 19:22:11: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Tue, 27 Jun 2017 19:22:11: #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 19:22:11: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:22:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:22:14: #1 tag size is determined as 69 bps INFO @ Tue, 27 Jun 2017 19:22:14: #1 tag size = 69 INFO @ Tue, 27 Jun 2017 19:22:14: #1 total tags in treatment: 1420488 INFO @ Tue, 27 Jun 2017 19:22:14: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:22:14: #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 19:22:14: #1 tag size is determined as 69 bps INFO @ Tue, 27 Jun 2017 19:22:14: #1 tag size = 69 INFO @ Tue, 27 Jun 2017 19:22:14: #1 total tags in treatment: 1420488 INFO @ Tue, 27 Jun 2017 19:22:14: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:22:14: #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 19:22:14: #1 tags after filtering in treatment: 1289147 INFO @ Tue, 27 Jun 2017 19:22:14: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 27 Jun 2017 19:22:14: #1 finished! INFO @ Tue, 27 Jun 2017 19:22:14: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:22:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:22:14: #1 tags after filtering in treatment: 1289147 INFO @ Tue, 27 Jun 2017 19:22:14: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 27 Jun 2017 19:22:14: #1 finished! INFO @ Tue, 27 Jun 2017 19:22:14: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:22:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:22:14: #2 number of paired peaks: 768 WARNING @ Tue, 27 Jun 2017 19:22:14: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Tue, 27 Jun 2017 19:22:14: start model_add_line... INFO @ Tue, 27 Jun 2017 19:22:14: #2 number of paired peaks: 768 WARNING @ Tue, 27 Jun 2017 19:22:14: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Tue, 27 Jun 2017 19:22:14: start model_add_line... INFO @ Tue, 27 Jun 2017 19:22:14: start X-correlation... INFO @ Tue, 27 Jun 2017 19:22:14: end of X-cor INFO @ Tue, 27 Jun 2017 19:22:14: #2 finished! INFO @ Tue, 27 Jun 2017 19:22:14: #2 predicted fragment length is 98 bps INFO @ Tue, 27 Jun 2017 19:22:14: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 27 Jun 2017 19:22:14: #2.2 Generate R script for model : SRX2677158.10_model.r INFO @ Tue, 27 Jun 2017 19:22:14: start X-correlation... INFO @ Tue, 27 Jun 2017 19:22:14: end of X-cor INFO @ Tue, 27 Jun 2017 19:22:14: #2 finished! INFO @ Tue, 27 Jun 2017 19:22:14: #2 predicted fragment length is 98 bps INFO @ Tue, 27 Jun 2017 19:22:14: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 27 Jun 2017 19:22:14: #2.2 Generate R script for model : SRX2677158.20_model.r WARNING @ Tue, 27 Jun 2017 19:22:14: #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 19:22:14: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Tue, 27 Jun 2017 19:22:14: #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 19:22:14: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:22:14: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 27 Jun 2017 19:22:14: #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 19:22:14: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Tue, 27 Jun 2017 19:22:14: #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 19:22:14: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:22:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:22:14: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:22:16: #4 Write output xls file... SRX2677158.05_peaks.xls INFO @ Tue, 27 Jun 2017 19:22:16: #4 Write peak in narrowPeak format file... SRX2677158.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:22:16: #4 Write summits bed file... SRX2677158.05_summits.bed INFO @ Tue, 27 Jun 2017 19:22:16: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (691 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 19:22:17: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:22:17: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:22:19: #4 Write output xls file... SRX2677158.20_peaks.xls INFO @ Tue, 27 Jun 2017 19:22:19: #4 Write peak in narrowPeak format file... SRX2677158.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:22:19: #4 Write summits bed file... SRX2677158.20_summits.bed INFO @ Tue, 27 Jun 2017 19:22:19: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 19:22:19: #4 Write output xls file... SRX2677158.10_peaks.xls INFO @ Tue, 27 Jun 2017 19:22:19: #4 Write peak in narrowPeak format file... SRX2677158.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:22:19: #4 Write summits bed file... SRX2677158.10_summits.bed INFO @ Tue, 27 Jun 2017 19:22:19: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (483 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。