Job ID = 1307281 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 42,878,672 reads read : 85,757,344 reads written : 85,757,344 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: 00:11:36 42878672 reads; of these: 42878672 (100.00%) were paired; of these: 40470106 (94.38%) aligned concordantly 0 times 1790344 (4.18%) aligned concordantly exactly 1 time 618222 (1.44%) aligned concordantly >1 times ---- 40470106 pairs aligned concordantly 0 times; of these: 4203 (0.01%) aligned discordantly 1 time ---- 40465903 pairs aligned 0 times concordantly or discordantly; of these: 80931806 mates make up the pairs; of these: 80634155 (99.63%) aligned 0 times 114792 (0.14%) aligned exactly 1 time 182859 (0.23%) aligned >1 times 5.97% overall alignment rate Time searching: 00:11:36 Overall time: 00:11:36 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] 80939 / 2411338 = 0.0336 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 22:49:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.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 22:49:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:49:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:49:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.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 22:49:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:49:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:49:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.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 22:49:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:49:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:49:25: 1000000 INFO @ Mon, 03 Jun 2019 22:49:26: 1000000 INFO @ Mon, 03 Jun 2019 22:49:26: 1000000 INFO @ Mon, 03 Jun 2019 22:49:33: 2000000 INFO @ Mon, 03 Jun 2019 22:49:34: 2000000 INFO @ Mon, 03 Jun 2019 22:49:35: 2000000 INFO @ Mon, 03 Jun 2019 22:49:40: 3000000 INFO @ Mon, 03 Jun 2019 22:49:41: 3000000 INFO @ Mon, 03 Jun 2019 22:49:43: 3000000 INFO @ Mon, 03 Jun 2019 22:49:48: 4000000 INFO @ Mon, 03 Jun 2019 22:49:49: 4000000 INFO @ Mon, 03 Jun 2019 22:49:51: 4000000 INFO @ Mon, 03 Jun 2019 22:49:55: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 22:49:55: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 22:49:55: #1 total tags in treatment: 2327744 INFO @ Mon, 03 Jun 2019 22:49:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:49:55: #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 22:49:55: #1 tags after filtering in treatment: 2220817 INFO @ Mon, 03 Jun 2019 22:49:55: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 22:49:55: #1 finished! INFO @ Mon, 03 Jun 2019 22:49:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:49:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:49:55: #2 number of paired peaks: 1018 INFO @ Mon, 03 Jun 2019 22:49:55: start model_add_line... INFO @ Mon, 03 Jun 2019 22:49:55: start X-correlation... INFO @ Mon, 03 Jun 2019 22:49:55: end of X-cor INFO @ Mon, 03 Jun 2019 22:49:55: #2 finished! INFO @ Mon, 03 Jun 2019 22:49:55: #2 predicted fragment length is 107 bps INFO @ Mon, 03 Jun 2019 22:49:55: #2 alternative fragment length(s) may be 91,107 bps INFO @ Mon, 03 Jun 2019 22:49:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.10_model.r INFO @ Mon, 03 Jun 2019 22:49:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:49:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:49:56: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 22:49:56: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 22:49:56: #1 total tags in treatment: 2327744 INFO @ Mon, 03 Jun 2019 22:49:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:49:56: #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 22:49:56: #1 tags after filtering in treatment: 2220817 INFO @ Mon, 03 Jun 2019 22:49:56: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 22:49:56: #1 finished! INFO @ Mon, 03 Jun 2019 22:49:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:49:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:49:56: #2 number of paired peaks: 1018 INFO @ Mon, 03 Jun 2019 22:49:56: start model_add_line... INFO @ Mon, 03 Jun 2019 22:49:56: start X-correlation... INFO @ Mon, 03 Jun 2019 22:49:56: end of X-cor INFO @ Mon, 03 Jun 2019 22:49:56: #2 finished! INFO @ Mon, 03 Jun 2019 22:49:56: #2 predicted fragment length is 107 bps INFO @ Mon, 03 Jun 2019 22:49:56: #2 alternative fragment length(s) may be 91,107 bps INFO @ Mon, 03 Jun 2019 22:49:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.05_model.r INFO @ Mon, 03 Jun 2019 22:49:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:49:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:49:58: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 22:49:58: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 22:49:58: #1 total tags in treatment: 2327744 INFO @ Mon, 03 Jun 2019 22:49:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:49:58: #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 22:49:58: #1 tags after filtering in treatment: 2220817 INFO @ Mon, 03 Jun 2019 22:49:58: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 22:49:58: #1 finished! INFO @ Mon, 03 Jun 2019 22:49:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:49:59: #2 number of paired peaks: 1018 INFO @ Mon, 03 Jun 2019 22:49:59: start model_add_line... INFO @ Mon, 03 Jun 2019 22:49:59: start X-correlation... INFO @ Mon, 03 Jun 2019 22:49:59: end of X-cor INFO @ Mon, 03 Jun 2019 22:49:59: #2 finished! INFO @ Mon, 03 Jun 2019 22:49:59: #2 predicted fragment length is 107 bps INFO @ Mon, 03 Jun 2019 22:49:59: #2 alternative fragment length(s) may be 91,107 bps INFO @ Mon, 03 Jun 2019 22:49:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.20_model.r INFO @ Mon, 03 Jun 2019 22:49:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:49:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:50:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:50:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:50:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:50:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:50:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.10_summits.bed INFO @ Mon, 03 Jun 2019 22:50:05: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (190 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:50:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:50:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:50:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:50:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.05_summits.bed INFO @ Mon, 03 Jun 2019 22:50:06: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (343 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:50:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:50:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:50:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5299376/SRX5299376.20_summits.bed INFO @ Mon, 03 Jun 2019 22:50:09: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (89 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。