Job ID = 10480701 sra ファイルのダウンロード中... Completed: 340597K bytes transferred in 14 seconds (186199K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 12112903 spots for /home/okishinya/chipatlas/results/dm3/SRX3068972/SRR5907448.sra Written 12112903 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:00:01 Multiseed full-index search: 00:01:24 12112903 reads; of these: 12112903 (100.00%) were unpaired; of these: 10552734 (87.12%) aligned 0 times 1201364 (9.92%) aligned exactly 1 time 358805 (2.96%) aligned >1 times 12.88% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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_rmdupse_core] 383912 / 1560169 = 0.2461 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 @ Fri, 16 Mar 2018 07:42:15: # Command line: callpeak -t SRX3068972.bam -f BAM -g dm -n SRX3068972.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068972.20 # format = BAM # ChIP-seq file = ['SRX3068972.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 @ Fri, 16 Mar 2018 07:42:15: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:42:15: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:42:15: # Command line: callpeak -t SRX3068972.bam -f BAM -g dm -n SRX3068972.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068972.05 # format = BAM # ChIP-seq file = ['SRX3068972.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 @ Fri, 16 Mar 2018 07:42:15: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:42:15: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:42:15: # Command line: callpeak -t SRX3068972.bam -f BAM -g dm -n SRX3068972.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068972.10 # format = BAM # ChIP-seq file = ['SRX3068972.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 @ Fri, 16 Mar 2018 07:42:15: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:42:15: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:42:22: 1000000 INFO @ Fri, 16 Mar 2018 07:42:22: 1000000 INFO @ Fri, 16 Mar 2018 07:42:22: 1000000 INFO @ Fri, 16 Mar 2018 07:42:23: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:42:23: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:42:23: #1 total tags in treatment: 1176257 INFO @ Fri, 16 Mar 2018 07:42:23: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:42:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:42:23: #1 tags after filtering in treatment: 1176257 INFO @ Fri, 16 Mar 2018 07:42:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:42:23: #1 finished! INFO @ Fri, 16 Mar 2018 07:42:23: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:42:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:42:23: #2 number of paired peaks: 577 WARNING @ Fri, 16 Mar 2018 07:42:23: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Fri, 16 Mar 2018 07:42:23: start model_add_line... INFO @ Fri, 16 Mar 2018 07:42:23: start X-correlation... INFO @ Fri, 16 Mar 2018 07:42:23: end of X-cor INFO @ Fri, 16 Mar 2018 07:42:23: #2 finished! INFO @ Fri, 16 Mar 2018 07:42:23: #2 predicted fragment length is 52 bps INFO @ Fri, 16 Mar 2018 07:42:23: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 16 Mar 2018 07:42:23: #2.2 Generate R script for model : SRX3068972.05_model.r WARNING @ Fri, 16 Mar 2018 07:42:23: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:42:23: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 16 Mar 2018 07:42:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:42:23: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:42:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:42:24: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:42:24: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:42:24: #1 total tags in treatment: 1176257 INFO @ Fri, 16 Mar 2018 07:42:24: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:42:24: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:42:24: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:42:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:42:24: #1 total tags in treatment: 1176257 INFO @ Fri, 16 Mar 2018 07:42:24: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:42:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:42:24: #1 tags after filtering in treatment: 1176257 INFO @ Fri, 16 Mar 2018 07:42:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:42:24: #1 tags after filtering in treatment: 1176257 INFO @ Fri, 16 Mar 2018 07:42:24: #1 finished! INFO @ Fri, 16 Mar 2018 07:42:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:42:24: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:42:24: #1 finished! INFO @ Fri, 16 Mar 2018 07:42:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:42:24: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:42:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:42:24: #2 number of paired peaks: 577 WARNING @ Fri, 16 Mar 2018 07:42:24: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Fri, 16 Mar 2018 07:42:24: start model_add_line... INFO @ Fri, 16 Mar 2018 07:42:24: #2 number of paired peaks: 577 WARNING @ Fri, 16 Mar 2018 07:42:24: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Fri, 16 Mar 2018 07:42:24: start model_add_line... INFO @ Fri, 16 Mar 2018 07:42:24: start X-correlation... INFO @ Fri, 16 Mar 2018 07:42:24: end of X-cor INFO @ Fri, 16 Mar 2018 07:42:24: #2 finished! INFO @ Fri, 16 Mar 2018 07:42:24: #2 predicted fragment length is 52 bps INFO @ Fri, 16 Mar 2018 07:42:24: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 16 Mar 2018 07:42:24: #2.2 Generate R script for model : SRX3068972.20_model.r WARNING @ Fri, 16 Mar 2018 07:42:24: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:42:24: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 16 Mar 2018 07:42:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:42:24: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:42:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:42:24: start X-correlation... INFO @ Fri, 16 Mar 2018 07:42:24: end of X-cor INFO @ Fri, 16 Mar 2018 07:42:24: #2 finished! INFO @ Fri, 16 Mar 2018 07:42:24: #2 predicted fragment length is 52 bps INFO @ Fri, 16 Mar 2018 07:42:24: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 16 Mar 2018 07:42:24: #2.2 Generate R script for model : SRX3068972.10_model.r WARNING @ Fri, 16 Mar 2018 07:42:24: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:42:24: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 16 Mar 2018 07:42:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:42:24: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:42:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:42:26: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:42:27: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:42:27: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:42:28: #4 Write output xls file... SRX3068972.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:42:28: #4 Write peak in narrowPeak format file... SRX3068972.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:42:28: #4 Write summits bed file... SRX3068972.05_summits.bed INFO @ Fri, 16 Mar 2018 07:42:28: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (390 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:42:28: #4 Write output xls file... SRX3068972.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:42:28: #4 Write peak in narrowPeak format file... SRX3068972.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:42:28: #4 Write summits bed file... SRX3068972.10_summits.bed INFO @ Fri, 16 Mar 2018 07:42:28: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (275 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:42:28: #4 Write output xls file... SRX3068972.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:42:28: #4 Write peak in narrowPeak format file... SRX3068972.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:42:28: #4 Write summits bed file... SRX3068972.20_summits.bed INFO @ Fri, 16 Mar 2018 07:42:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (180 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。