Job ID = 1296455 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,666,885 reads read : 15,333,770 reads written : 15,333,770 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: 00:01:40 7666885 reads; of these: 7666885 (100.00%) were paired; of these: 7553736 (98.52%) aligned concordantly 0 times 82024 (1.07%) aligned concordantly exactly 1 time 31125 (0.41%) aligned concordantly >1 times ---- 7553736 pairs aligned concordantly 0 times; of these: 501 (0.01%) aligned discordantly 1 time ---- 7553235 pairs aligned 0 times concordantly or discordantly; of these: 15106470 mates make up the pairs; of these: 14940237 (98.90%) aligned 0 times 43395 (0.29%) aligned exactly 1 time 122838 (0.81%) aligned >1 times 2.57% overall alignment rate Time searching: 00:01:40 Overall time: 00:01:40 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] 2306 / 113321 = 0.0203 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 16:24:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.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 16:24:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:24:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:24:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.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 16:24:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:24:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:24:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.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 16:24:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:24:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:24:31: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 16:24:31: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 16:24:31: #1 total tags in treatment: 110850 INFO @ Mon, 03 Jun 2019 16:24:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:24:31: #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 16:24:31: #1 tags after filtering in treatment: 110095 INFO @ Mon, 03 Jun 2019 16:24:31: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 03 Jun 2019 16:24:31: #1 finished! INFO @ Mon, 03 Jun 2019 16:24:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:24:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:24:32: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 16:24:32: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 16:24:32: #1 total tags in treatment: 110850 INFO @ Mon, 03 Jun 2019 16:24:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:24:32: #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 16:24:32: #1 tags after filtering in treatment: 110095 INFO @ Mon, 03 Jun 2019 16:24:32: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 03 Jun 2019 16:24:32: #1 finished! INFO @ Mon, 03 Jun 2019 16:24:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:24:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:24:32: #2 number of paired peaks: 5459 INFO @ Mon, 03 Jun 2019 16:24:32: start model_add_line... INFO @ Mon, 03 Jun 2019 16:24:32: start X-correlation... INFO @ Mon, 03 Jun 2019 16:24:32: end of X-cor INFO @ Mon, 03 Jun 2019 16:24:32: #2 finished! INFO @ Mon, 03 Jun 2019 16:24:32: #2 predicted fragment length is 297 bps INFO @ Mon, 03 Jun 2019 16:24:32: #2 alternative fragment length(s) may be 297 bps INFO @ Mon, 03 Jun 2019 16:24:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.10_model.r INFO @ Mon, 03 Jun 2019 16:24:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:24:32: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 16:24:32: #2 number of paired peaks: 5459 INFO @ Mon, 03 Jun 2019 16:24:32: start model_add_line... INFO @ Mon, 03 Jun 2019 16:24:32: start X-correlation... INFO @ Mon, 03 Jun 2019 16:24:32: end of X-cor INFO @ Mon, 03 Jun 2019 16:24:32: #2 finished! INFO @ Mon, 03 Jun 2019 16:24:32: #2 predicted fragment length is 297 bps INFO @ Mon, 03 Jun 2019 16:24:32: #2 alternative fragment length(s) may be 297 bps INFO @ Mon, 03 Jun 2019 16:24:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.05_model.r INFO @ Mon, 03 Jun 2019 16:24:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:24:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:24:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:24:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:24:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:24:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.10_summits.bed INFO @ Mon, 03 Jun 2019 16:24:32: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:24:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:24:33: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 16:24:33: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 16:24:33: #1 total tags in treatment: 110850 INFO @ Mon, 03 Jun 2019 16:24:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:24:33: #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 16:24:33: #1 tags after filtering in treatment: 110095 INFO @ Mon, 03 Jun 2019 16:24:33: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 03 Jun 2019 16:24:33: #1 finished! INFO @ Mon, 03 Jun 2019 16:24:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:24:33: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 16:24:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:24:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:24:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.05_summits.bed INFO @ Mon, 03 Jun 2019 16:24:33: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (34 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:24:33: #2 number of paired peaks: 5459 INFO @ Mon, 03 Jun 2019 16:24:33: start model_add_line... INFO @ Mon, 03 Jun 2019 16:24:33: start X-correlation... INFO @ Mon, 03 Jun 2019 16:24:33: end of X-cor INFO @ Mon, 03 Jun 2019 16:24:33: #2 finished! INFO @ Mon, 03 Jun 2019 16:24:33: #2 predicted fragment length is 297 bps INFO @ Mon, 03 Jun 2019 16:24:33: #2 alternative fragment length(s) may be 297 bps INFO @ Mon, 03 Jun 2019 16:24:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.20_model.r INFO @ Mon, 03 Jun 2019 16:24:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:24:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:24:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:24:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:24:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:24:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650779/SRX4650779.20_summits.bed INFO @ Mon, 03 Jun 2019 16:24:34: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling