Job ID = 9158494 sra ファイルのダウンロード中... Completed: 157142K bytes transferred in 4 seconds (275877K 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 521910 spots for /home/okishinya/chipatlas/results/dm3/SRX1426954/SRR2923829.sra Written 521910 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: 00:02:39 521910 reads; of these: 521910 (100.00%) were paired; of these: 461014 (88.33%) aligned concordantly 0 times 36923 (7.07%) aligned concordantly exactly 1 time 23973 (4.59%) aligned concordantly >1 times ---- 461014 pairs aligned concordantly 0 times; of these: 33515 (7.27%) aligned discordantly 1 time ---- 427499 pairs aligned 0 times concordantly or discordantly; of these: 854998 mates make up the pairs; of these: 816504 (95.50%) aligned 0 times 6345 (0.74%) aligned exactly 1 time 32149 (3.76%) aligned >1 times 21.78% overall alignment rate Time searching: 00:02:39 Overall time: 00:02:39 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] 2654 / 93459 = 0.0284 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 17:10:46: # Command line: callpeak -t SRX1426954.bam -f BAM -g dm -n SRX1426954.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1426954.05 # format = BAM # ChIP-seq file = ['SRX1426954.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 17:10:46: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:10:46: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:10:46: # Command line: callpeak -t SRX1426954.bam -f BAM -g dm -n SRX1426954.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1426954.10 # format = BAM # ChIP-seq file = ['SRX1426954.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 17:10:46: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:10:46: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:10:46: # Command line: callpeak -t SRX1426954.bam -f BAM -g dm -n SRX1426954.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1426954.20 # format = BAM # ChIP-seq file = ['SRX1426954.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 17:10:46: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:10:46: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:10:49: #1 tag size is determined as 251 bps INFO @ Tue, 27 Jun 2017 17:10:49: #1 tag size = 251 INFO @ Tue, 27 Jun 2017 17:10:49: #1 total tags in treatment: 58606 INFO @ Tue, 27 Jun 2017 17:10:49: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 17:10:49: #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 17:10:49: #1 tags after filtering in treatment: 56265 INFO @ Tue, 27 Jun 2017 17:10:49: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 27 Jun 2017 17:10:49: #1 finished! INFO @ Tue, 27 Jun 2017 17:10:49: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 17:10:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 17:10:50: #2 number of paired peaks: 2183 INFO @ Tue, 27 Jun 2017 17:10:50: start model_add_line... INFO @ Tue, 27 Jun 2017 17:10:50: start X-correlation... INFO @ Tue, 27 Jun 2017 17:10:50: end of X-cor INFO @ Tue, 27 Jun 2017 17:10:50: #2 finished! INFO @ Tue, 27 Jun 2017 17:10:50: #2 predicted fragment length is 295 bps INFO @ Tue, 27 Jun 2017 17:10:50: #2 alternative fragment length(s) may be 295 bps INFO @ Tue, 27 Jun 2017 17:10:50: #2.2 Generate R script for model : SRX1426954.05_model.r WARNING @ Tue, 27 Jun 2017 17:10:50: #2 Since the d (295) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 17:10:50: #2 You may need to consider one of the other alternative d(s): 295 WARNING @ Tue, 27 Jun 2017 17:10:50: #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 17:10:50: #3 Call peaks... INFO @ Tue, 27 Jun 2017 17:10:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 17:10:50: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 17:10:50: #4 Write output xls file... SRX1426954.05_peaks.xls INFO @ Tue, 27 Jun 2017 17:10:50: #4 Write peak in narrowPeak format file... SRX1426954.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 17:10:50: #4 Write summits bed file... SRX1426954.05_summits.bed INFO @ Tue, 27 Jun 2017 17:10:50: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (73 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 17:10:50: #1 tag size is determined as 251 bps INFO @ Tue, 27 Jun 2017 17:10:50: #1 tag size = 251 INFO @ Tue, 27 Jun 2017 17:10:50: #1 total tags in treatment: 58606 INFO @ Tue, 27 Jun 2017 17:10:50: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 17:10:50: #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 17:10:50: #1 tags after filtering in treatment: 56265 INFO @ Tue, 27 Jun 2017 17:10:50: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 27 Jun 2017 17:10:50: #1 finished! INFO @ Tue, 27 Jun 2017 17:10:50: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 17:10:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 17:10:50: #1 tag size is determined as 251 bps INFO @ Tue, 27 Jun 2017 17:10:50: #1 tag size = 251 INFO @ Tue, 27 Jun 2017 17:10:50: #1 total tags in treatment: 58606 INFO @ Tue, 27 Jun 2017 17:10:50: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 17:10:50: #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 17:10:50: #1 tags after filtering in treatment: 56265 INFO @ Tue, 27 Jun 2017 17:10:50: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 27 Jun 2017 17:10:50: #1 finished! INFO @ Tue, 27 Jun 2017 17:10:50: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 17:10:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 17:10:50: #2 number of paired peaks: 2183 INFO @ Tue, 27 Jun 2017 17:10:50: start model_add_line... INFO @ Tue, 27 Jun 2017 17:10:50: start X-correlation... INFO @ Tue, 27 Jun 2017 17:10:50: end of X-cor INFO @ Tue, 27 Jun 2017 17:10:50: #2 finished! INFO @ Tue, 27 Jun 2017 17:10:50: #2 predicted fragment length is 295 bps INFO @ Tue, 27 Jun 2017 17:10:50: #2 alternative fragment length(s) may be 295 bps INFO @ Tue, 27 Jun 2017 17:10:50: #2.2 Generate R script for model : SRX1426954.10_model.r INFO @ Tue, 27 Jun 2017 17:10:50: #2 number of paired peaks: 2183 INFO @ Tue, 27 Jun 2017 17:10:50: start model_add_line... INFO @ Tue, 27 Jun 2017 17:10:50: start X-correlation... WARNING @ Tue, 27 Jun 2017 17:10:50: #2 Since the d (295) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 17:10:50: #2 You may need to consider one of the other alternative d(s): 295 INFO @ Tue, 27 Jun 2017 17:10:50: end of X-cor WARNING @ Tue, 27 Jun 2017 17:10:50: #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 17:10:50: #2 finished! INFO @ Tue, 27 Jun 2017 17:10:50: #3 Call peaks... INFO @ Tue, 27 Jun 2017 17:10:50: #2 predicted fragment length is 295 bps INFO @ Tue, 27 Jun 2017 17:10:50: #2 alternative fragment length(s) may be 295 bps INFO @ Tue, 27 Jun 2017 17:10:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 17:10:50: #2.2 Generate R script for model : SRX1426954.20_model.r WARNING @ Tue, 27 Jun 2017 17:10:50: #2 Since the d (295) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 17:10:50: #2 You may need to consider one of the other alternative d(s): 295 WARNING @ Tue, 27 Jun 2017 17:10:50: #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 17:10:50: #3 Call peaks... INFO @ Tue, 27 Jun 2017 17:10:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 17:10:50: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 17:10:51: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 17:10:51: #4 Write output xls file... SRX1426954.10_peaks.xls INFO @ Tue, 27 Jun 2017 17:10:51: #4 Write peak in narrowPeak format file... SRX1426954.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 17:10:51: #4 Write summits bed file... SRX1426954.10_summits.bed INFO @ Tue, 27 Jun 2017 17:10:51: Done! INFO @ Tue, 27 Jun 2017 17:10:51: #4 Write output xls file... SRX1426954.20_peaks.xls INFO @ Tue, 27 Jun 2017 17:10:51: #4 Write peak in narrowPeak format file... SRX1426954.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 17:10:51: #4 Write summits bed file... SRX1426954.20_summits.bed INFO @ Tue, 27 Jun 2017 17:10:51: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (36 records, 4 fields): 1 millis CompletedMACS2peakCalling pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 0 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。