Job ID = 1307271 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 39,908,225 reads read : 79,816,450 reads written : 79,816,450 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: 00:11:10 39908225 reads; of these: 39908225 (100.00%) were paired; of these: 36790755 (92.19%) aligned concordantly 0 times 2345017 (5.88%) aligned concordantly exactly 1 time 772453 (1.94%) aligned concordantly >1 times ---- 36790755 pairs aligned concordantly 0 times; of these: 3350 (0.01%) aligned discordantly 1 time ---- 36787405 pairs aligned 0 times concordantly or discordantly; of these: 73574810 mates make up the pairs; of these: 73260510 (99.57%) aligned 0 times 131267 (0.18%) aligned exactly 1 time 183033 (0.25%) aligned >1 times 8.21% overall alignment rate Time searching: 00:11:10 Overall time: 00:11:10 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] 129108 / 3119223 = 0.0414 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 22:47:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.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 22:47:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:47:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:47:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.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 22:47:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:47:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:47:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.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 22:47:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:47:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:47:52: 1000000 INFO @ Mon, 03 Jun 2019 22:47:53: 1000000 INFO @ Mon, 03 Jun 2019 22:47:54: 1000000 INFO @ Mon, 03 Jun 2019 22:47:59: 2000000 INFO @ Mon, 03 Jun 2019 22:48:01: 2000000 INFO @ Mon, 03 Jun 2019 22:48:02: 2000000 INFO @ Mon, 03 Jun 2019 22:48:05: 3000000 INFO @ Mon, 03 Jun 2019 22:48:08: 3000000 INFO @ Mon, 03 Jun 2019 22:48:09: 3000000 INFO @ Mon, 03 Jun 2019 22:48:12: 4000000 INFO @ Mon, 03 Jun 2019 22:48:15: 4000000 INFO @ Mon, 03 Jun 2019 22:48:17: 4000000 INFO @ Mon, 03 Jun 2019 22:48:18: 5000000 INFO @ Mon, 03 Jun 2019 22:48:22: 5000000 INFO @ Mon, 03 Jun 2019 22:48:24: 5000000 INFO @ Mon, 03 Jun 2019 22:48:25: 6000000 INFO @ Mon, 03 Jun 2019 22:48:27: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 22:48:27: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 22:48:27: #1 total tags in treatment: 2988503 INFO @ Mon, 03 Jun 2019 22:48:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:48:27: #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 22:48:27: #1 tags after filtering in treatment: 2827872 INFO @ Mon, 03 Jun 2019 22:48:27: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 22:48:27: #1 finished! INFO @ Mon, 03 Jun 2019 22:48:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:48:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:48:27: #2 number of paired peaks: 1014 INFO @ Mon, 03 Jun 2019 22:48:27: start model_add_line... INFO @ Mon, 03 Jun 2019 22:48:27: start X-correlation... INFO @ Mon, 03 Jun 2019 22:48:27: end of X-cor INFO @ Mon, 03 Jun 2019 22:48:27: #2 finished! INFO @ Mon, 03 Jun 2019 22:48:27: #2 predicted fragment length is 111 bps INFO @ Mon, 03 Jun 2019 22:48:27: #2 alternative fragment length(s) may be 111,597 bps INFO @ Mon, 03 Jun 2019 22:48:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.05_model.r INFO @ Mon, 03 Jun 2019 22:48:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:48:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:48:30: 6000000 INFO @ Mon, 03 Jun 2019 22:48:32: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 22:48:32: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 22:48:32: #1 total tags in treatment: 2988503 INFO @ Mon, 03 Jun 2019 22:48:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:48:32: #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 22:48:32: #1 tags after filtering in treatment: 2827872 INFO @ Mon, 03 Jun 2019 22:48:32: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 22:48:32: #1 finished! INFO @ Mon, 03 Jun 2019 22:48:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:48:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:48:32: 6000000 INFO @ Mon, 03 Jun 2019 22:48:32: #2 number of paired peaks: 1014 INFO @ Mon, 03 Jun 2019 22:48:32: start model_add_line... INFO @ Mon, 03 Jun 2019 22:48:32: start X-correlation... INFO @ Mon, 03 Jun 2019 22:48:32: end of X-cor INFO @ Mon, 03 Jun 2019 22:48:32: #2 finished! INFO @ Mon, 03 Jun 2019 22:48:32: #2 predicted fragment length is 111 bps INFO @ Mon, 03 Jun 2019 22:48:32: #2 alternative fragment length(s) may be 111,597 bps INFO @ Mon, 03 Jun 2019 22:48:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.20_model.r INFO @ Mon, 03 Jun 2019 22:48:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:48:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:48:34: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 22:48:34: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 22:48:34: #1 total tags in treatment: 2988503 INFO @ Mon, 03 Jun 2019 22:48:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:48:34: #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 22:48:34: #1 tags after filtering in treatment: 2827872 INFO @ Mon, 03 Jun 2019 22:48:34: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 22:48:34: #1 finished! INFO @ Mon, 03 Jun 2019 22:48:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:48:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:48:35: #2 number of paired peaks: 1014 INFO @ Mon, 03 Jun 2019 22:48:35: start model_add_line... INFO @ Mon, 03 Jun 2019 22:48:35: start X-correlation... INFO @ Mon, 03 Jun 2019 22:48:35: end of X-cor INFO @ Mon, 03 Jun 2019 22:48:35: #2 finished! INFO @ Mon, 03 Jun 2019 22:48:35: #2 predicted fragment length is 111 bps INFO @ Mon, 03 Jun 2019 22:48:35: #2 alternative fragment length(s) may be 111,597 bps INFO @ Mon, 03 Jun 2019 22:48:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.10_model.r INFO @ Mon, 03 Jun 2019 22:48:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:48:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:48:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:48:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:48:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:48:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.05_summits.bed INFO @ Mon, 03 Jun 2019 22:48:40: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (409 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:48:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:48:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:48:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:48:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:48:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.20_summits.bed INFO @ Mon, 03 Jun 2019 22:48:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:48:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:48:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:48:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5299375/SRX5299375.10_summits.bed INFO @ Mon, 03 Jun 2019 22:48:48: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (212 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。