Job ID = 2590992 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,422,315 reads read : 2,844,630 reads written : 2,844,630 rm: cannot remove ‘[DSE]RR*’: 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: 00:01:56 1422315 reads; of these: 1422315 (100.00%) were paired; of these: 432391 (30.40%) aligned concordantly 0 times 901670 (63.39%) aligned concordantly exactly 1 time 88254 (6.20%) aligned concordantly >1 times ---- 432391 pairs aligned concordantly 0 times; of these: 84280 (19.49%) aligned discordantly 1 time ---- 348111 pairs aligned 0 times concordantly or discordantly; of these: 696222 mates make up the pairs; of these: 426194 (61.22%) aligned 0 times 233280 (33.51%) aligned exactly 1 time 36748 (5.28%) aligned >1 times 85.02% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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] 818640 / 1071657 = 0.7639 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 @ Tue, 13 Aug 2019 00:23:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.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 @ Tue, 13 Aug 2019 00:23:23: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:23:23: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:23:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.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 @ Tue, 13 Aug 2019 00:23:24: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:23:24: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:23:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.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 @ Tue, 13 Aug 2019 00:23:25: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:23:25: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:23:33: #1 tag size is determined as 75 bps INFO @ Tue, 13 Aug 2019 00:23:33: #1 tag size = 75 INFO @ Tue, 13 Aug 2019 00:23:33: #1 total tags in treatment: 225966 INFO @ Tue, 13 Aug 2019 00:23:33: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:23:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:23:33: #1 tags after filtering in treatment: 183445 INFO @ Tue, 13 Aug 2019 00:23:33: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 13 Aug 2019 00:23:33: #1 finished! INFO @ Tue, 13 Aug 2019 00:23:33: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:23:33: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 13 Aug 2019 00:23:33: #2 number of paired peaks: 8415 INFO @ Tue, 13 Aug 2019 00:23:33: start model_add_line... INFO @ Tue, 13 Aug 2019 00:23:33: start X-correlation... INFO @ Tue, 13 Aug 2019 00:23:33: end of X-cor INFO @ Tue, 13 Aug 2019 00:23:33: #2 finished! INFO @ Tue, 13 Aug 2019 00:23:33: #2 predicted fragment length is 290 bps INFO @ Tue, 13 Aug 2019 00:23:33: #2 alternative fragment length(s) may be 7,240,290 bps INFO @ Tue, 13 Aug 2019 00:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.05_model.r INFO @ Tue, 13 Aug 2019 00:23:33: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:23:34: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:23:34: #1 tag size is determined as 75 bps INFO @ Tue, 13 Aug 2019 00:23:34: #1 tag size = 75 INFO @ Tue, 13 Aug 2019 00:23:34: #1 total tags in treatment: 225966 INFO @ Tue, 13 Aug 2019 00:23:34: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:23:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:23:34: #1 tags after filtering in treatment: 183445 INFO @ Tue, 13 Aug 2019 00:23:34: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 13 Aug 2019 00:23:34: #1 finished! INFO @ Tue, 13 Aug 2019 00:23:34: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:23:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:23:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:23:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:23:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.05_summits.bed INFO @ Tue, 13 Aug 2019 00:23:34: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (257 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:23:34: #2 number of paired peaks: 8415 INFO @ Tue, 13 Aug 2019 00:23:34: start model_add_line... INFO @ Tue, 13 Aug 2019 00:23:34: start X-correlation... INFO @ Tue, 13 Aug 2019 00:23:34: end of X-cor INFO @ Tue, 13 Aug 2019 00:23:34: #2 finished! INFO @ Tue, 13 Aug 2019 00:23:34: #2 predicted fragment length is 290 bps INFO @ Tue, 13 Aug 2019 00:23:34: #2 alternative fragment length(s) may be 7,240,290 bps INFO @ Tue, 13 Aug 2019 00:23:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.10_model.r INFO @ Tue, 13 Aug 2019 00:23:34: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:23:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 13 Aug 2019 00:23:35: #1 tag size is determined as 75 bps INFO @ Tue, 13 Aug 2019 00:23:35: #1 tag size = 75 INFO @ Tue, 13 Aug 2019 00:23:35: #1 total tags in treatment: 225966 INFO @ Tue, 13 Aug 2019 00:23:35: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:23:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:23:35: #1 tags after filtering in treatment: 183445 INFO @ Tue, 13 Aug 2019 00:23:35: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 13 Aug 2019 00:23:35: #1 finished! INFO @ Tue, 13 Aug 2019 00:23:35: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:23:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:23:35: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:23:35: #2 number of paired peaks: 8415 INFO @ Tue, 13 Aug 2019 00:23:35: start model_add_line... INFO @ Tue, 13 Aug 2019 00:23:35: start X-correlation... INFO @ Tue, 13 Aug 2019 00:23:35: end of X-cor INFO @ Tue, 13 Aug 2019 00:23:35: #2 finished! INFO @ Tue, 13 Aug 2019 00:23:35: #2 predicted fragment length is 290 bps INFO @ Tue, 13 Aug 2019 00:23:35: #2 alternative fragment length(s) may be 7,240,290 bps INFO @ Tue, 13 Aug 2019 00:23:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.20_model.r INFO @ Tue, 13 Aug 2019 00:23:35: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:23:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:23:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:23:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:23:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.10_summits.bed INFO @ Tue, 13 Aug 2019 00:23:35: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (66 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:23:35: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:23:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:23:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:23:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441121/SRX6441121.20_summits.bed INFO @ Tue, 13 Aug 2019 00:23:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 3 millis CompletedMACS2peakCalling