Job ID = 1295659 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,979,395 reads read : 17,958,790 reads written : 17,958,790 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: 00:32:25 8979395 reads; of these: 8979395 (100.00%) were paired; of these: 4460371 (49.67%) aligned concordantly 0 times 491866 (5.48%) aligned concordantly exactly 1 time 4027158 (44.85%) aligned concordantly >1 times ---- 4460371 pairs aligned concordantly 0 times; of these: 115155 (2.58%) aligned discordantly 1 time ---- 4345216 pairs aligned 0 times concordantly or discordantly; of these: 8690432 mates make up the pairs; of these: 7642042 (87.94%) aligned 0 times 364456 (4.19%) aligned exactly 1 time 683934 (7.87%) aligned >1 times 57.45% overall alignment rate Time searching: 00:32:25 Overall time: 00:32:25 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] 1903750 / 4511383 = 0.4220 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 15:31:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.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 15:31:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:31:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:31:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.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 15:31:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:31:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:31:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.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 15:31:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:31:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:31:46: 1000000 INFO @ Mon, 03 Jun 2019 15:31:46: 1000000 INFO @ Mon, 03 Jun 2019 15:31:46: 1000000 INFO @ Mon, 03 Jun 2019 15:31:54: 2000000 INFO @ Mon, 03 Jun 2019 15:31:54: 2000000 INFO @ Mon, 03 Jun 2019 15:31:55: 2000000 INFO @ Mon, 03 Jun 2019 15:32:02: 3000000 INFO @ Mon, 03 Jun 2019 15:32:02: 3000000 INFO @ Mon, 03 Jun 2019 15:32:03: 3000000 INFO @ Mon, 03 Jun 2019 15:32:10: 4000000 INFO @ Mon, 03 Jun 2019 15:32:10: 4000000 INFO @ Mon, 03 Jun 2019 15:32:11: 4000000 INFO @ Mon, 03 Jun 2019 15:32:19: 5000000 INFO @ Mon, 03 Jun 2019 15:32:20: 5000000 INFO @ Mon, 03 Jun 2019 15:32:20: 5000000 INFO @ Mon, 03 Jun 2019 15:32:26: 6000000 INFO @ Mon, 03 Jun 2019 15:32:30: 6000000 INFO @ Mon, 03 Jun 2019 15:32:30: 6000000 INFO @ Mon, 03 Jun 2019 15:32:31: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:32:31: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:32:31: #1 total tags in treatment: 2615957 INFO @ Mon, 03 Jun 2019 15:32:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:32:31: #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 15:32:31: #1 tags after filtering in treatment: 2156605 INFO @ Mon, 03 Jun 2019 15:32:31: #1 Redundant rate of treatment: 0.18 INFO @ Mon, 03 Jun 2019 15:32:31: #1 finished! INFO @ Mon, 03 Jun 2019 15:32:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:32:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:32:31: #2 number of paired peaks: 8997 INFO @ Mon, 03 Jun 2019 15:32:31: start model_add_line... INFO @ Mon, 03 Jun 2019 15:32:31: start X-correlation... INFO @ Mon, 03 Jun 2019 15:32:31: end of X-cor INFO @ Mon, 03 Jun 2019 15:32:31: #2 finished! INFO @ Mon, 03 Jun 2019 15:32:31: #2 predicted fragment length is 175 bps INFO @ Mon, 03 Jun 2019 15:32:31: #2 alternative fragment length(s) may be 175 bps INFO @ Mon, 03 Jun 2019 15:32:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.05_model.r INFO @ Mon, 03 Jun 2019 15:32:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:32:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:32:34: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:32:34: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:32:34: #1 total tags in treatment: 2615957 INFO @ Mon, 03 Jun 2019 15:32:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:32:34: #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 15:32:34: #1 tags after filtering in treatment: 2156605 INFO @ Mon, 03 Jun 2019 15:32:34: #1 Redundant rate of treatment: 0.18 INFO @ Mon, 03 Jun 2019 15:32:34: #1 finished! INFO @ Mon, 03 Jun 2019 15:32:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:32:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:32:35: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:32:35: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:32:35: #1 total tags in treatment: 2615957 INFO @ Mon, 03 Jun 2019 15:32:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:32:35: #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 15:32:35: #1 tags after filtering in treatment: 2156605 INFO @ Mon, 03 Jun 2019 15:32:35: #1 Redundant rate of treatment: 0.18 INFO @ Mon, 03 Jun 2019 15:32:35: #1 finished! INFO @ Mon, 03 Jun 2019 15:32:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:32:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:32:35: #2 number of paired peaks: 8997 INFO @ Mon, 03 Jun 2019 15:32:35: start model_add_line... INFO @ Mon, 03 Jun 2019 15:32:35: start X-correlation... INFO @ Mon, 03 Jun 2019 15:32:35: end of X-cor INFO @ Mon, 03 Jun 2019 15:32:35: #2 finished! INFO @ Mon, 03 Jun 2019 15:32:35: #2 predicted fragment length is 175 bps INFO @ Mon, 03 Jun 2019 15:32:35: #2 alternative fragment length(s) may be 175 bps INFO @ Mon, 03 Jun 2019 15:32:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.20_model.r INFO @ Mon, 03 Jun 2019 15:32:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:32:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:32:35: #2 number of paired peaks: 8997 INFO @ Mon, 03 Jun 2019 15:32:35: start model_add_line... INFO @ Mon, 03 Jun 2019 15:32:35: start X-correlation... INFO @ Mon, 03 Jun 2019 15:32:35: end of X-cor INFO @ Mon, 03 Jun 2019 15:32:35: #2 finished! INFO @ Mon, 03 Jun 2019 15:32:35: #2 predicted fragment length is 175 bps INFO @ Mon, 03 Jun 2019 15:32:35: #2 alternative fragment length(s) may be 175 bps INFO @ Mon, 03 Jun 2019 15:32:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.10_model.r INFO @ Mon, 03 Jun 2019 15:32:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:32:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:32:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:32:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:32:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:32:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.05_summits.bed INFO @ Mon, 03 Jun 2019 15:32:43: Done! pass1 - making usageList (15 chroms): 4 millis INFO @ Mon, 03 Jun 2019 15:32:43: #3 Call peaks for each chromosome... pass2 - checking and writing primary data (7246 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:32:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:32:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:32:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:32:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.10_summits.bed INFO @ Mon, 03 Jun 2019 15:32:47: Done! INFO @ Mon, 03 Jun 2019 15:32:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:32:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:32:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3961893/SRX3961893.20_summits.bed INFO @ Mon, 03 Jun 2019 15:32:47: Done! pass1 - making usageList (14 chroms): 2 millis pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1336 records, 4 fields): 6 millis pass2 - checking and writing primary data (4066 records, 4 fields): 33 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。