Job ID = 1296669 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 31,453,904 reads read : 62,907,808 reads written : 62,907,808 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: 00:06:41 31453904 reads; of these: 31453904 (100.00%) were paired; of these: 30896515 (98.23%) aligned concordantly 0 times 430507 (1.37%) aligned concordantly exactly 1 time 126882 (0.40%) aligned concordantly >1 times ---- 30896515 pairs aligned concordantly 0 times; of these: 2089 (0.01%) aligned discordantly 1 time ---- 30894426 pairs aligned 0 times concordantly or discordantly; of these: 61788852 mates make up the pairs; of these: 61323518 (99.25%) aligned 0 times 100944 (0.16%) aligned exactly 1 time 364390 (0.59%) aligned >1 times 2.52% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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] 26409 / 557727 = 0.0474 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 16:51:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.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 16:51:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:51:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:51:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.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 16:51:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:51:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:51:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.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 16:51:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:51:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:51:47: 1000000 INFO @ Mon, 03 Jun 2019 16:51:48: 1000000 INFO @ Mon, 03 Jun 2019 16:51:48: 1000000 INFO @ Mon, 03 Jun 2019 16:51:51: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 16:51:51: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 16:51:51: #1 total tags in treatment: 531130 INFO @ Mon, 03 Jun 2019 16:51:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:51:51: #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 16:51:51: #1 tags after filtering in treatment: 521723 INFO @ Mon, 03 Jun 2019 16:51:51: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 16:51:51: #1 finished! INFO @ Mon, 03 Jun 2019 16:51:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:51:51: #2 number of paired peaks: 2110 INFO @ Mon, 03 Jun 2019 16:51:51: start model_add_line... INFO @ Mon, 03 Jun 2019 16:51:51: start X-correlation... INFO @ Mon, 03 Jun 2019 16:51:51: end of X-cor INFO @ Mon, 03 Jun 2019 16:51:51: #2 finished! INFO @ Mon, 03 Jun 2019 16:51:51: #2 predicted fragment length is 189 bps INFO @ Mon, 03 Jun 2019 16:51:51: #2 alternative fragment length(s) may be 102,189,246,253,269 bps INFO @ Mon, 03 Jun 2019 16:51:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.20_model.r INFO @ Mon, 03 Jun 2019 16:51:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:51:52: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 16:51:52: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 16:51:52: #1 total tags in treatment: 531130 INFO @ Mon, 03 Jun 2019 16:51:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:51:52: #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 16:51:52: #1 tags after filtering in treatment: 521723 INFO @ Mon, 03 Jun 2019 16:51:52: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 16:51:52: #1 finished! INFO @ Mon, 03 Jun 2019 16:51:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:51:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:51:52: #2 number of paired peaks: 2110 INFO @ Mon, 03 Jun 2019 16:51:52: start model_add_line... INFO @ Mon, 03 Jun 2019 16:51:52: start X-correlation... INFO @ Mon, 03 Jun 2019 16:51:52: end of X-cor INFO @ Mon, 03 Jun 2019 16:51:52: #2 finished! INFO @ Mon, 03 Jun 2019 16:51:52: #2 predicted fragment length is 189 bps INFO @ Mon, 03 Jun 2019 16:51:52: #2 alternative fragment length(s) may be 102,189,246,253,269 bps INFO @ Mon, 03 Jun 2019 16:51:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.10_model.r INFO @ Mon, 03 Jun 2019 16:51:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:51:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:51:53: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 16:51:53: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 16:51:53: #1 total tags in treatment: 531130 INFO @ Mon, 03 Jun 2019 16:51:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:51:53: #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 16:51:53: #1 tags after filtering in treatment: 521723 INFO @ Mon, 03 Jun 2019 16:51:53: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 16:51:53: #1 finished! INFO @ Mon, 03 Jun 2019 16:51:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:51:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:51:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:51:53: #2 number of paired peaks: 2110 INFO @ Mon, 03 Jun 2019 16:51:53: start model_add_line... INFO @ Mon, 03 Jun 2019 16:51:53: start X-correlation... INFO @ Mon, 03 Jun 2019 16:51:53: end of X-cor INFO @ Mon, 03 Jun 2019 16:51:53: #2 finished! INFO @ Mon, 03 Jun 2019 16:51:53: #2 predicted fragment length is 189 bps INFO @ Mon, 03 Jun 2019 16:51:53: #2 alternative fragment length(s) may be 102,189,246,253,269 bps INFO @ Mon, 03 Jun 2019 16:51:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.05_model.r INFO @ Mon, 03 Jun 2019 16:51:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:51:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:51:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:51:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:51:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.20_summits.bed INFO @ Mon, 03 Jun 2019 16:51:54: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:51:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:51:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:51:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:51:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:51:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.10_summits.bed INFO @ Mon, 03 Jun 2019 16:51:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (58 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:51:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:51:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:51:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650808/SRX4650808.05_summits.bed INFO @ Mon, 03 Jun 2019 16:51:55: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (127 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。