Job ID = 9158728 sra ファイルのダウンロード中... Completed: 197293K bytes transferred in 8 seconds (186138K 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 3193217 spots for /home/okishinya/chipatlas/results/dm3/SRX2677159/SRR5382079.sra Written 3193217 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: 00:13:38 3193217 reads; of these: 3193217 (100.00%) were paired; of these: 245692 (7.69%) aligned concordantly 0 times 1694196 (53.06%) aligned concordantly exactly 1 time 1253329 (39.25%) aligned concordantly >1 times ---- 245692 pairs aligned concordantly 0 times; of these: 15638 (6.36%) aligned discordantly 1 time ---- 230054 pairs aligned 0 times concordantly or discordantly; of these: 460108 mates make up the pairs; of these: 387784 (84.28%) aligned 0 times 37416 (8.13%) aligned exactly 1 time 34908 (7.59%) aligned >1 times 93.93% overall alignment rate Time searching: 00:13:38 Overall time: 00:13:38 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] 298067 / 1903781 = 0.1566 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 19:29:55: # Command line: callpeak -t SRX2677159.bam -f BAM -g dm -n SRX2677159.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2677159.20 # format = BAM # ChIP-seq file = ['SRX2677159.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 19:29:55: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:29:55: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:29:55: # Command line: callpeak -t SRX2677159.bam -f BAM -g dm -n SRX2677159.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2677159.10 # format = BAM # ChIP-seq file = ['SRX2677159.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 19:29:55: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:29:55: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:29:55: # Command line: callpeak -t SRX2677159.bam -f BAM -g dm -n SRX2677159.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2677159.05 # format = BAM # ChIP-seq file = ['SRX2677159.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 19:29:55: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:29:55: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:30:03: 1000000 INFO @ Tue, 27 Jun 2017 19:30:03: 1000000 INFO @ Tue, 27 Jun 2017 19:30:04: 1000000 INFO @ Tue, 27 Jun 2017 19:30:12: 2000000 INFO @ Tue, 27 Jun 2017 19:30:12: 2000000 INFO @ Tue, 27 Jun 2017 19:30:13: 2000000 INFO @ Tue, 27 Jun 2017 19:30:21: 3000000 INFO @ Tue, 27 Jun 2017 19:30:21: 3000000 INFO @ Tue, 27 Jun 2017 19:30:22: 3000000 INFO @ Tue, 27 Jun 2017 19:30:29: 4000000 INFO @ Tue, 27 Jun 2017 19:30:29: 4000000 INFO @ Tue, 27 Jun 2017 19:30:31: 4000000 INFO @ Tue, 27 Jun 2017 19:30:38: 5000000 INFO @ Tue, 27 Jun 2017 19:30:38: 5000000 INFO @ Tue, 27 Jun 2017 19:30:40: 5000000 INFO @ Tue, 27 Jun 2017 19:30:41: #1 tag size is determined as 65 bps INFO @ Tue, 27 Jun 2017 19:30:41: #1 tag size is determined as 65 bps INFO @ Tue, 27 Jun 2017 19:30:41: #1 tag size = 65 INFO @ Tue, 27 Jun 2017 19:30:41: #1 tag size = 65 INFO @ Tue, 27 Jun 2017 19:30:41: #1 total tags in treatment: 2650004 INFO @ Tue, 27 Jun 2017 19:30:41: #1 total tags in treatment: 2650004 INFO @ Tue, 27 Jun 2017 19:30:41: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:30:41: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:30:41: #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 19:30:41: #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 19:30:41: #1 tags after filtering in treatment: 2289508 INFO @ Tue, 27 Jun 2017 19:30:41: #1 tags after filtering in treatment: 2289508 INFO @ Tue, 27 Jun 2017 19:30:41: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 27 Jun 2017 19:30:41: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 27 Jun 2017 19:30:41: #1 finished! INFO @ Tue, 27 Jun 2017 19:30:41: #1 finished! INFO @ Tue, 27 Jun 2017 19:30:41: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:30:41: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:30:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:30:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:30:41: #2 number of paired peaks: 801 WARNING @ Tue, 27 Jun 2017 19:30:41: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! INFO @ Tue, 27 Jun 2017 19:30:41: start model_add_line... INFO @ Tue, 27 Jun 2017 19:30:41: #2 number of paired peaks: 801 WARNING @ Tue, 27 Jun 2017 19:30:41: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! INFO @ Tue, 27 Jun 2017 19:30:41: start model_add_line... INFO @ Tue, 27 Jun 2017 19:30:41: start X-correlation... INFO @ Tue, 27 Jun 2017 19:30:41: start X-correlation... INFO @ Tue, 27 Jun 2017 19:30:41: end of X-cor INFO @ Tue, 27 Jun 2017 19:30:41: end of X-cor INFO @ Tue, 27 Jun 2017 19:30:41: #2 finished! INFO @ Tue, 27 Jun 2017 19:30:41: #2 finished! INFO @ Tue, 27 Jun 2017 19:30:41: #2 predicted fragment length is 101 bps INFO @ Tue, 27 Jun 2017 19:30:41: #2 predicted fragment length is 101 bps INFO @ Tue, 27 Jun 2017 19:30:41: #2 alternative fragment length(s) may be 101 bps INFO @ Tue, 27 Jun 2017 19:30:41: #2 alternative fragment length(s) may be 101 bps INFO @ Tue, 27 Jun 2017 19:30:41: #2.2 Generate R script for model : SRX2677159.10_model.r INFO @ Tue, 27 Jun 2017 19:30:41: #2.2 Generate R script for model : SRX2677159.20_model.r WARNING @ Tue, 27 Jun 2017 19:30:41: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:30:41: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:30:41: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Tue, 27 Jun 2017 19:30:41: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Tue, 27 Jun 2017 19:30:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Tue, 27 Jun 2017 19:30:41: #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 19:30:41: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:30:41: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:30:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:30:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:30:43: #1 tag size is determined as 65 bps INFO @ Tue, 27 Jun 2017 19:30:43: #1 tag size = 65 INFO @ Tue, 27 Jun 2017 19:30:43: #1 total tags in treatment: 2650004 INFO @ Tue, 27 Jun 2017 19:30:43: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:30:43: #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 19:30:43: #1 tags after filtering in treatment: 2289508 INFO @ Tue, 27 Jun 2017 19:30:43: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 27 Jun 2017 19:30:43: #1 finished! INFO @ Tue, 27 Jun 2017 19:30:43: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:30:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:30:44: #2 number of paired peaks: 801 WARNING @ Tue, 27 Jun 2017 19:30:44: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! INFO @ Tue, 27 Jun 2017 19:30:44: start model_add_line... INFO @ Tue, 27 Jun 2017 19:30:44: start X-correlation... INFO @ Tue, 27 Jun 2017 19:30:44: end of X-cor INFO @ Tue, 27 Jun 2017 19:30:44: #2 finished! INFO @ Tue, 27 Jun 2017 19:30:44: #2 predicted fragment length is 101 bps INFO @ Tue, 27 Jun 2017 19:30:44: #2 alternative fragment length(s) may be 101 bps INFO @ Tue, 27 Jun 2017 19:30:44: #2.2 Generate R script for model : SRX2677159.05_model.r WARNING @ Tue, 27 Jun 2017 19:30:44: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:30:44: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Tue, 27 Jun 2017 19:30:44: #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 19:30:44: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:30:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:30:47: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:30:47: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:30:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:30:50: #4 Write output xls file... SRX2677159.20_peaks.xls INFO @ Tue, 27 Jun 2017 19:30:50: #4 Write peak in narrowPeak format file... SRX2677159.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:30:50: #4 Write summits bed file... SRX2677159.20_summits.bed INFO @ Tue, 27 Jun 2017 19:30:50: Done! INFO @ Tue, 27 Jun 2017 19:30:50: #4 Write output xls file... SRX2677159.10_peaks.xls pass1 - making usageList (8 chroms): 0 millis INFO @ Tue, 27 Jun 2017 19:30:50: #4 Write peak in narrowPeak format file... SRX2677159.10_peaks.narrowPeak pass2 - checking and writing primary data (518 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 19:30:50: #4 Write summits bed file... SRX2677159.10_summits.bed INFO @ Tue, 27 Jun 2017 19:30:50: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (760 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 19:30:52: #4 Write output xls file... SRX2677159.05_peaks.xls INFO @ Tue, 27 Jun 2017 19:30:52: #4 Write peak in narrowPeak format file... SRX2677159.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:30:52: #4 Write summits bed file... SRX2677159.05_summits.bed INFO @ Tue, 27 Jun 2017 19:30:52: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1047 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。