Job ID = 1295868 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 32,278,008 reads read : 64,556,016 reads written : 64,556,016 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: 00:07:28 32278008 reads; of these: 32278008 (100.00%) were paired; of these: 31435730 (97.39%) aligned concordantly 0 times 686571 (2.13%) aligned concordantly exactly 1 time 155707 (0.48%) aligned concordantly >1 times ---- 31435730 pairs aligned concordantly 0 times; of these: 859 (0.00%) aligned discordantly 1 time ---- 31434871 pairs aligned 0 times concordantly or discordantly; of these: 62869742 mates make up the pairs; of these: 62699324 (99.73%) aligned 0 times 54918 (0.09%) aligned exactly 1 time 115500 (0.18%) aligned >1 times 2.88% overall alignment rate Time searching: 00:07:28 Overall time: 00:07:28 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] 24402 / 842337 = 0.0290 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 16:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.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 16:13:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:13:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.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 16:13:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:13:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.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 16:13:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:13:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:13:18: 1000000 INFO @ Mon, 03 Jun 2019 16:13:19: 1000000 INFO @ Mon, 03 Jun 2019 16:13:19: 1000000 INFO @ Mon, 03 Jun 2019 16:13:27: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 16:13:27: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 16:13:27: #1 total tags in treatment: 817906 INFO @ Mon, 03 Jun 2019 16:13:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:13:27: #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 16:13:27: #1 tags after filtering in treatment: 798574 INFO @ Mon, 03 Jun 2019 16:13:27: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 16:13:27: #1 finished! INFO @ Mon, 03 Jun 2019 16:13:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:13:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:13:28: #2 number of paired peaks: 1659 INFO @ Mon, 03 Jun 2019 16:13:28: start model_add_line... INFO @ Mon, 03 Jun 2019 16:13:28: start X-correlation... INFO @ Mon, 03 Jun 2019 16:13:28: end of X-cor INFO @ Mon, 03 Jun 2019 16:13:28: #2 finished! INFO @ Mon, 03 Jun 2019 16:13:28: #2 predicted fragment length is 140 bps INFO @ Mon, 03 Jun 2019 16:13:28: #2 alternative fragment length(s) may be 116,140 bps INFO @ Mon, 03 Jun 2019 16:13:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.05_model.r INFO @ Mon, 03 Jun 2019 16:13:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:13:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:13:30: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 16:13:30: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 16:13:30: #1 total tags in treatment: 817906 INFO @ Mon, 03 Jun 2019 16:13:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:13:30: #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 16:13:30: #1 tags after filtering in treatment: 798574 INFO @ Mon, 03 Jun 2019 16:13:30: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 16:13:30: #1 finished! INFO @ Mon, 03 Jun 2019 16:13:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:13:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:13:30: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 16:13:30: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 16:13:30: #1 total tags in treatment: 817906 INFO @ Mon, 03 Jun 2019 16:13:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:13:30: #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 16:13:30: #2 number of paired peaks: 1659 INFO @ Mon, 03 Jun 2019 16:13:30: start model_add_line... INFO @ Mon, 03 Jun 2019 16:13:30: #1 tags after filtering in treatment: 798574 INFO @ Mon, 03 Jun 2019 16:13:30: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 16:13:30: #1 finished! INFO @ Mon, 03 Jun 2019 16:13:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:13:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:13:30: start X-correlation... INFO @ Mon, 03 Jun 2019 16:13:30: end of X-cor INFO @ Mon, 03 Jun 2019 16:13:30: #2 finished! INFO @ Mon, 03 Jun 2019 16:13:30: #2 predicted fragment length is 140 bps INFO @ Mon, 03 Jun 2019 16:13:30: #2 alternative fragment length(s) may be 116,140 bps INFO @ Mon, 03 Jun 2019 16:13:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.10_model.r INFO @ Mon, 03 Jun 2019 16:13:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:13:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:13:30: #2 number of paired peaks: 1659 INFO @ Mon, 03 Jun 2019 16:13:30: start model_add_line... INFO @ Mon, 03 Jun 2019 16:13:30: start X-correlation... INFO @ Mon, 03 Jun 2019 16:13:30: end of X-cor INFO @ Mon, 03 Jun 2019 16:13:30: #2 finished! INFO @ Mon, 03 Jun 2019 16:13:30: #2 predicted fragment length is 140 bps INFO @ Mon, 03 Jun 2019 16:13:30: #2 alternative fragment length(s) may be 116,140 bps INFO @ Mon, 03 Jun 2019 16:13:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.20_model.r INFO @ Mon, 03 Jun 2019 16:13:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:13:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:13:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:13:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:13:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:13:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.05_summits.bed INFO @ Mon, 03 Jun 2019 16:13:33: Done! pass1 - making usageList (11 chroms): 3 millis pass2 - checking and writing primary data (315 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:13:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:13:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:13:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:13:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:13:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.10_summits.bed INFO @ Mon, 03 Jun 2019 16:13:35: Done! INFO @ Mon, 03 Jun 2019 16:13:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:13:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:13:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650731/SRX4650731.20_summits.bed INFO @ Mon, 03 Jun 2019 16:13:35: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (129 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (23 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。