Job ID = 9302862 sra ファイルのダウンロード中... Completed: 358354K bytes transferred in 5 seconds (495585K 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: SINGLE fastq に変換中... Written 12687346 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1514717/SRR3082932.sra Written 12687346 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: 00:02:19 12687346 reads; of these: 12687346 (100.00%) were unpaired; of these: 4653590 (36.68%) aligned 0 times 6498052 (51.22%) aligned exactly 1 time 1535704 (12.10%) aligned >1 times 63.32% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 6768729 / 8033756 = 0.8425 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, 28 Jul 2017 11:29:03: # Command line: callpeak -t SRX1514717.bam -f BAM -g 12100000 -n SRX1514717.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1514717.20 # format = BAM # ChIP-seq file = ['SRX1514717.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 28 Jul 2017 11:29:03: # Command line: callpeak -t SRX1514717.bam -f BAM -g 12100000 -n SRX1514717.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1514717.05 # format = BAM # ChIP-seq file = ['SRX1514717.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 28 Jul 2017 11:29:03: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:29:03: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:29:03: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:29:03: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:29:03: # Command line: callpeak -t SRX1514717.bam -f BAM -g 12100000 -n SRX1514717.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1514717.10 # format = BAM # ChIP-seq file = ['SRX1514717.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 28 Jul 2017 11:29:03: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:29:03: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:29:10: 1000000 INFO @ Fri, 28 Jul 2017 11:29:10: 1000000 INFO @ Fri, 28 Jul 2017 11:29:10: 1000000 INFO @ Fri, 28 Jul 2017 11:29:12: #1 tag size is determined as 49 bps INFO @ Fri, 28 Jul 2017 11:29:12: #1 tag size = 49 INFO @ Fri, 28 Jul 2017 11:29:12: #1 total tags in treatment: 1265027 INFO @ Fri, 28 Jul 2017 11:29:12: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:29:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:29:12: #1 tags after filtering in treatment: 1265027 INFO @ Fri, 28 Jul 2017 11:29:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 28 Jul 2017 11:29:12: #1 finished! INFO @ Fri, 28 Jul 2017 11:29:12: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:29:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:29:12: #1 tag size is determined as 49 bps INFO @ Fri, 28 Jul 2017 11:29:12: #1 tag size = 49 INFO @ Fri, 28 Jul 2017 11:29:12: #1 total tags in treatment: 1265027 INFO @ Fri, 28 Jul 2017 11:29:12: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:29:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:29:12: #1 tags after filtering in treatment: 1265027 INFO @ Fri, 28 Jul 2017 11:29:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 28 Jul 2017 11:29:12: #1 finished! INFO @ Fri, 28 Jul 2017 11:29:12: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:29:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:29:12: #1 tag size is determined as 49 bps INFO @ Fri, 28 Jul 2017 11:29:12: #1 tag size = 49 INFO @ Fri, 28 Jul 2017 11:29:12: #1 total tags in treatment: 1265027 INFO @ Fri, 28 Jul 2017 11:29:12: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:29:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:29:12: #1 tags after filtering in treatment: 1265027 INFO @ Fri, 28 Jul 2017 11:29:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 28 Jul 2017 11:29:12: #1 finished! INFO @ Fri, 28 Jul 2017 11:29:12: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:29:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:29:12: #2 number of paired peaks: 380 WARNING @ Fri, 28 Jul 2017 11:29:12: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Fri, 28 Jul 2017 11:29:12: start model_add_line... INFO @ Fri, 28 Jul 2017 11:29:12: start X-correlation... INFO @ Fri, 28 Jul 2017 11:29:12: #2 number of paired peaks: 380 WARNING @ Fri, 28 Jul 2017 11:29:12: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Fri, 28 Jul 2017 11:29:12: start model_add_line... INFO @ Fri, 28 Jul 2017 11:29:12: end of X-cor INFO @ Fri, 28 Jul 2017 11:29:12: #2 finished! INFO @ Fri, 28 Jul 2017 11:29:12: #2 predicted fragment length is 154 bps INFO @ Fri, 28 Jul 2017 11:29:12: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 28 Jul 2017 11:29:12: #2.2 Generate R script for model : SRX1514717.10_model.r INFO @ Fri, 28 Jul 2017 11:29:12: start X-correlation... INFO @ Fri, 28 Jul 2017 11:29:12: #3 Call peaks... INFO @ Fri, 28 Jul 2017 11:29:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 28 Jul 2017 11:29:12: end of X-cor INFO @ Fri, 28 Jul 2017 11:29:12: #2 finished! INFO @ Fri, 28 Jul 2017 11:29:12: #2 predicted fragment length is 154 bps INFO @ Fri, 28 Jul 2017 11:29:12: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 28 Jul 2017 11:29:12: #2.2 Generate R script for model : SRX1514717.20_model.r INFO @ Fri, 28 Jul 2017 11:29:12: #2 number of paired peaks: 380 WARNING @ Fri, 28 Jul 2017 11:29:12: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Fri, 28 Jul 2017 11:29:12: start model_add_line... INFO @ Fri, 28 Jul 2017 11:29:12: #3 Call peaks... INFO @ Fri, 28 Jul 2017 11:29:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 28 Jul 2017 11:29:12: start X-correlation... INFO @ Fri, 28 Jul 2017 11:29:12: end of X-cor INFO @ Fri, 28 Jul 2017 11:29:12: #2 finished! INFO @ Fri, 28 Jul 2017 11:29:12: #2 predicted fragment length is 154 bps INFO @ Fri, 28 Jul 2017 11:29:12: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 28 Jul 2017 11:29:12: #2.2 Generate R script for model : SRX1514717.05_model.r INFO @ Fri, 28 Jul 2017 11:29:12: #3 Call peaks... INFO @ Fri, 28 Jul 2017 11:29:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 28 Jul 2017 11:29:17: #3 Call peaks for each chromosome... INFO @ Fri, 28 Jul 2017 11:29:17: #3 Call peaks for each chromosome... INFO @ Fri, 28 Jul 2017 11:29:17: #3 Call peaks for each chromosome... INFO @ Fri, 28 Jul 2017 11:29:18: #4 Write output xls file... SRX1514717.05_peaks.xls INFO @ Fri, 28 Jul 2017 11:29:18: #4 Write output xls file... SRX1514717.20_peaks.xls INFO @ Fri, 28 Jul 2017 11:29:19: #4 Write peak in narrowPeak format file... SRX1514717.05_peaks.narrowPeak INFO @ Fri, 28 Jul 2017 11:29:19: #4 Write peak in narrowPeak format file... SRX1514717.20_peaks.narrowPeak INFO @ Fri, 28 Jul 2017 11:29:19: #4 Write summits bed file... SRX1514717.20_summits.bed INFO @ Fri, 28 Jul 2017 11:29:19: #4 Write summits bed file... SRX1514717.05_summits.bed INFO @ Fri, 28 Jul 2017 11:29:19: Done! INFO @ Fri, 28 Jul 2017 11:29:19: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (568 records, 4 fields): 3 millis pass1 - making usageList (17 chroms): 0 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (1281 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 28 Jul 2017 11:29:19: #4 Write output xls file... SRX1514717.10_peaks.xls INFO @ Fri, 28 Jul 2017 11:29:19: #4 Write peak in narrowPeak format file... SRX1514717.10_peaks.narrowPeak INFO @ Fri, 28 Jul 2017 11:29:19: #4 Write summits bed file... SRX1514717.10_summits.bed INFO @ Fri, 28 Jul 2017 11:29:19: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (888 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。