Job ID = 1295478 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,934,944 reads read : 7,869,888 reads written : 7,869,888 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: 00:08:05 3934944 reads; of these: 3934944 (100.00%) were paired; of these: 1106107 (28.11%) aligned concordantly 0 times 1978482 (50.28%) aligned concordantly exactly 1 time 850355 (21.61%) aligned concordantly >1 times ---- 1106107 pairs aligned concordantly 0 times; of these: 3067 (0.28%) aligned discordantly 1 time ---- 1103040 pairs aligned 0 times concordantly or discordantly; of these: 2206080 mates make up the pairs; of these: 2016891 (91.42%) aligned 0 times 89631 (4.06%) aligned exactly 1 time 99558 (4.51%) aligned >1 times 74.37% overall alignment rate Time searching: 00:08:05 Overall time: 00:08:05 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] 63975 / 2830325 = 0.0226 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 14:07:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.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 14:07:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:07:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:07:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.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 14:07:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:07:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:07:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.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 14:07:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:07:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:07:35: 1000000 INFO @ Mon, 03 Jun 2019 14:07:37: 1000000 INFO @ Mon, 03 Jun 2019 14:07:38: 1000000 INFO @ Mon, 03 Jun 2019 14:07:42: 2000000 INFO @ Mon, 03 Jun 2019 14:07:45: 2000000 INFO @ Mon, 03 Jun 2019 14:07:48: 2000000 INFO @ Mon, 03 Jun 2019 14:07:49: 3000000 INFO @ Mon, 03 Jun 2019 14:07:55: 3000000 INFO @ Mon, 03 Jun 2019 14:07:56: 4000000 INFO @ Mon, 03 Jun 2019 14:07:58: 3000000 INFO @ Mon, 03 Jun 2019 14:08:03: 4000000 INFO @ Mon, 03 Jun 2019 14:08:04: 5000000 INFO @ Mon, 03 Jun 2019 14:08:08: 4000000 INFO @ Mon, 03 Jun 2019 14:08:09: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 14:08:09: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 14:08:09: #1 total tags in treatment: 2764891 INFO @ Mon, 03 Jun 2019 14:08:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:08:09: #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 14:08:10: #1 tags after filtering in treatment: 2045338 INFO @ Mon, 03 Jun 2019 14:08:10: #1 Redundant rate of treatment: 0.26 INFO @ Mon, 03 Jun 2019 14:08:10: #1 finished! INFO @ Mon, 03 Jun 2019 14:08:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:08:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:08:10: #2 number of paired peaks: 7499 INFO @ Mon, 03 Jun 2019 14:08:10: start model_add_line... INFO @ Mon, 03 Jun 2019 14:08:10: start X-correlation... INFO @ Mon, 03 Jun 2019 14:08:10: end of X-cor INFO @ Mon, 03 Jun 2019 14:08:10: #2 finished! INFO @ Mon, 03 Jun 2019 14:08:10: #2 predicted fragment length is 147 bps INFO @ Mon, 03 Jun 2019 14:08:10: #2 alternative fragment length(s) may be 147 bps INFO @ Mon, 03 Jun 2019 14:08:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.05_model.r INFO @ Mon, 03 Jun 2019 14:08:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:08:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:08:12: 5000000 INFO @ Mon, 03 Jun 2019 14:08:18: 5000000 INFO @ Mon, 03 Jun 2019 14:08:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:08:19: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 14:08:19: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 14:08:19: #1 total tags in treatment: 2764891 INFO @ Mon, 03 Jun 2019 14:08:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:08:19: #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 14:08:19: #1 tags after filtering in treatment: 2045338 INFO @ Mon, 03 Jun 2019 14:08:19: #1 Redundant rate of treatment: 0.26 INFO @ Mon, 03 Jun 2019 14:08:19: #1 finished! INFO @ Mon, 03 Jun 2019 14:08:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:08:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:08:19: #2 number of paired peaks: 7499 INFO @ Mon, 03 Jun 2019 14:08:19: start model_add_line... INFO @ Mon, 03 Jun 2019 14:08:20: start X-correlation... INFO @ Mon, 03 Jun 2019 14:08:20: end of X-cor INFO @ Mon, 03 Jun 2019 14:08:20: #2 finished! INFO @ Mon, 03 Jun 2019 14:08:20: #2 predicted fragment length is 147 bps INFO @ Mon, 03 Jun 2019 14:08:20: #2 alternative fragment length(s) may be 147 bps INFO @ Mon, 03 Jun 2019 14:08:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.20_model.r INFO @ Mon, 03 Jun 2019 14:08:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:08:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:08:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:08:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:08:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.05_summits.bed INFO @ Mon, 03 Jun 2019 14:08:22: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (8056 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:08:24: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 14:08:24: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 14:08:24: #1 total tags in treatment: 2764891 INFO @ Mon, 03 Jun 2019 14:08:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:08:24: #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 14:08:24: #1 tags after filtering in treatment: 2045338 INFO @ Mon, 03 Jun 2019 14:08:24: #1 Redundant rate of treatment: 0.26 INFO @ Mon, 03 Jun 2019 14:08:24: #1 finished! INFO @ Mon, 03 Jun 2019 14:08:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:08:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:08:25: #2 number of paired peaks: 7499 INFO @ Mon, 03 Jun 2019 14:08:25: start model_add_line... INFO @ Mon, 03 Jun 2019 14:08:25: start X-correlation... INFO @ Mon, 03 Jun 2019 14:08:25: end of X-cor INFO @ Mon, 03 Jun 2019 14:08:25: #2 finished! INFO @ Mon, 03 Jun 2019 14:08:25: #2 predicted fragment length is 147 bps INFO @ Mon, 03 Jun 2019 14:08:25: #2 alternative fragment length(s) may be 147 bps INFO @ Mon, 03 Jun 2019 14:08:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.10_model.r INFO @ Mon, 03 Jun 2019 14:08:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:08:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:08:28: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 14:08:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:08:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:08:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.20_summits.bed INFO @ Mon, 03 Jun 2019 14:08:32: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4966 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:08:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:08:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:08:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:08:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393680/SRX3393680.10_summits.bed INFO @ Mon, 03 Jun 2019 14:08:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6626 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。