Job ID = 1296388 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 27,420,659 reads read : 54,841,318 reads written : 54,841,318 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory 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: 00:06:39 27420659 reads; of these: 27420659 (100.00%) were paired; of these: 26044152 (94.98%) aligned concordantly 0 times 1095698 (4.00%) aligned concordantly exactly 1 time 280809 (1.02%) aligned concordantly >1 times ---- 26044152 pairs aligned concordantly 0 times; of these: 2706 (0.01%) aligned discordantly 1 time ---- 26041446 pairs aligned 0 times concordantly or discordantly; of these: 52082892 mates make up the pairs; of these: 51600288 (99.07%) aligned 0 times 152391 (0.29%) aligned exactly 1 time 330213 (0.63%) aligned >1 times 5.91% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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] 63984 / 1376848 = 0.0465 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 @ Mon, 03 Jun 2019 16:19:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.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 @ Mon, 03 Jun 2019 16:19:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:19:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:19:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.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 @ Mon, 03 Jun 2019 16:19:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:19:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:19:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.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 @ Mon, 03 Jun 2019 16:19:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:19:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:19:58: 1000000 INFO @ Mon, 03 Jun 2019 16:19:59: 1000000 INFO @ Mon, 03 Jun 2019 16:19:59: 1000000 INFO @ Mon, 03 Jun 2019 16:20:05: 2000000 INFO @ Mon, 03 Jun 2019 16:20:07: 2000000 INFO @ Mon, 03 Jun 2019 16:20:08: 2000000 INFO @ Mon, 03 Jun 2019 16:20:11: 3000000 INFO @ Mon, 03 Jun 2019 16:20:12: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 16:20:12: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 16:20:12: #1 total tags in treatment: 1312614 INFO @ Mon, 03 Jun 2019 16:20:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:20:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 16:20:12: #1 tags after filtering in treatment: 1271185 INFO @ Mon, 03 Jun 2019 16:20:12: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 16:20:12: #1 finished! INFO @ Mon, 03 Jun 2019 16:20:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:20:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:20:12: #2 number of paired peaks: 3032 INFO @ Mon, 03 Jun 2019 16:20:12: start model_add_line... INFO @ Mon, 03 Jun 2019 16:20:12: start X-correlation... INFO @ Mon, 03 Jun 2019 16:20:12: end of X-cor INFO @ Mon, 03 Jun 2019 16:20:12: #2 finished! INFO @ Mon, 03 Jun 2019 16:20:12: #2 predicted fragment length is 147 bps INFO @ Mon, 03 Jun 2019 16:20:12: #2 alternative fragment length(s) may be 4,147,171 bps INFO @ Mon, 03 Jun 2019 16:20:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.10_model.r INFO @ Mon, 03 Jun 2019 16:20:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:20:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:20:15: 3000000 INFO @ Mon, 03 Jun 2019 16:20:16: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 16:20:16: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 16:20:16: #1 total tags in treatment: 1312614 INFO @ Mon, 03 Jun 2019 16:20:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:20:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 16:20:16: #1 tags after filtering in treatment: 1271185 INFO @ Mon, 03 Jun 2019 16:20:16: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 16:20:16: #1 finished! INFO @ Mon, 03 Jun 2019 16:20:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:20:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:20:16: 3000000 INFO @ Mon, 03 Jun 2019 16:20:16: #2 number of paired peaks: 3032 INFO @ Mon, 03 Jun 2019 16:20:16: start model_add_line... INFO @ Mon, 03 Jun 2019 16:20:16: start X-correlation... INFO @ Mon, 03 Jun 2019 16:20:16: end of X-cor INFO @ Mon, 03 Jun 2019 16:20:16: #2 finished! INFO @ Mon, 03 Jun 2019 16:20:16: #2 predicted fragment length is 147 bps INFO @ Mon, 03 Jun 2019 16:20:16: #2 alternative fragment length(s) may be 4,147,171 bps INFO @ Mon, 03 Jun 2019 16:20:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.05_model.r INFO @ Mon, 03 Jun 2019 16:20:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:20:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:20:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:20:17: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 16:20:17: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 16:20:17: #1 total tags in treatment: 1312614 INFO @ Mon, 03 Jun 2019 16:20:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:20:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 16:20:17: #1 tags after filtering in treatment: 1271185 INFO @ Mon, 03 Jun 2019 16:20:17: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 16:20:17: #1 finished! INFO @ Mon, 03 Jun 2019 16:20:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:20:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:20:17: #2 number of paired peaks: 3032 INFO @ Mon, 03 Jun 2019 16:20:17: start model_add_line... INFO @ Mon, 03 Jun 2019 16:20:17: start X-correlation... INFO @ Mon, 03 Jun 2019 16:20:17: end of X-cor INFO @ Mon, 03 Jun 2019 16:20:17: #2 finished! INFO @ Mon, 03 Jun 2019 16:20:17: #2 predicted fragment length is 147 bps INFO @ Mon, 03 Jun 2019 16:20:17: #2 alternative fragment length(s) may be 4,147,171 bps INFO @ Mon, 03 Jun 2019 16:20:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.20_model.r INFO @ Mon, 03 Jun 2019 16:20:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:20:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:20:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:20:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:20:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.10_summits.bed INFO @ Mon, 03 Jun 2019 16:20:18: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (107 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:20:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:20:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:20:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:20:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:20:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.05_summits.bed INFO @ Mon, 03 Jun 2019 16:20:22: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (235 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:20:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:20:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:20:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650751/SRX4650751.20_summits.bed INFO @ Mon, 03 Jun 2019 16:20:23: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (45 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。