Job ID = 1297754 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 35,858,108 reads read : 71,716,216 reads written : 71,716,216 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: 00:09:18 35858108 reads; of these: 35858108 (100.00%) were paired; of these: 33556175 (93.58%) aligned concordantly 0 times 1840364 (5.13%) aligned concordantly exactly 1 time 461569 (1.29%) aligned concordantly >1 times ---- 33556175 pairs aligned concordantly 0 times; of these: 7653 (0.02%) aligned discordantly 1 time ---- 33548522 pairs aligned 0 times concordantly or discordantly; of these: 67097044 mates make up the pairs; of these: 66362630 (98.91%) aligned 0 times 340632 (0.51%) aligned exactly 1 time 393782 (0.59%) aligned >1 times 7.46% overall alignment rate Time searching: 00:09:18 Overall time: 00:09:18 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] 113834 / 2303565 = 0.0494 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 17:24:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.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 17:24:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:24:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:24:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.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 17:24:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:24:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:24:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.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 17:24:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:24:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:24:11: 1000000 INFO @ Mon, 03 Jun 2019 17:24:11: 1000000 INFO @ Mon, 03 Jun 2019 17:24:11: 1000000 INFO @ Mon, 03 Jun 2019 17:24:17: 2000000 INFO @ Mon, 03 Jun 2019 17:24:18: 2000000 INFO @ Mon, 03 Jun 2019 17:24:18: 2000000 INFO @ Mon, 03 Jun 2019 17:24:24: 3000000 INFO @ Mon, 03 Jun 2019 17:24:25: 3000000 INFO @ Mon, 03 Jun 2019 17:24:25: 3000000 INFO @ Mon, 03 Jun 2019 17:24:31: 4000000 INFO @ Mon, 03 Jun 2019 17:24:31: 4000000 INFO @ Mon, 03 Jun 2019 17:24:31: 4000000 INFO @ Mon, 03 Jun 2019 17:24:37: 5000000 INFO @ Mon, 03 Jun 2019 17:24:37: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:24:37: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:24:37: #1 total tags in treatment: 2188223 INFO @ Mon, 03 Jun 2019 17:24:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:24:37: #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 17:24:37: #1 tags after filtering in treatment: 2092445 INFO @ Mon, 03 Jun 2019 17:24:37: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 03 Jun 2019 17:24:37: #1 finished! INFO @ Mon, 03 Jun 2019 17:24:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:24:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:24:38: 5000000 INFO @ Mon, 03 Jun 2019 17:24:38: 5000000 INFO @ Mon, 03 Jun 2019 17:24:38: #2 number of paired peaks: 2249 INFO @ Mon, 03 Jun 2019 17:24:38: start model_add_line... INFO @ Mon, 03 Jun 2019 17:24:38: start X-correlation... INFO @ Mon, 03 Jun 2019 17:24:38: end of X-cor INFO @ Mon, 03 Jun 2019 17:24:38: #2 finished! INFO @ Mon, 03 Jun 2019 17:24:38: #2 predicted fragment length is 146 bps INFO @ Mon, 03 Jun 2019 17:24:38: #2 alternative fragment length(s) may be 4,146 bps INFO @ Mon, 03 Jun 2019 17:24:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.10_model.r INFO @ Mon, 03 Jun 2019 17:24:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:24:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:24:39: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:24:39: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:24:39: #1 total tags in treatment: 2188223 INFO @ Mon, 03 Jun 2019 17:24:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:24:39: #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 17:24:39: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:24:39: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:24:39: #1 total tags in treatment: 2188223 INFO @ Mon, 03 Jun 2019 17:24:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:24:39: #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 17:24:39: #1 tags after filtering in treatment: 2092445 INFO @ Mon, 03 Jun 2019 17:24:39: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 03 Jun 2019 17:24:39: #1 finished! INFO @ Mon, 03 Jun 2019 17:24:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:24:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:24:39: #1 tags after filtering in treatment: 2092445 INFO @ Mon, 03 Jun 2019 17:24:39: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 03 Jun 2019 17:24:39: #1 finished! INFO @ Mon, 03 Jun 2019 17:24:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:24:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:24:39: #2 number of paired peaks: 2249 INFO @ Mon, 03 Jun 2019 17:24:39: start model_add_line... INFO @ Mon, 03 Jun 2019 17:24:39: #2 number of paired peaks: 2249 INFO @ Mon, 03 Jun 2019 17:24:39: start model_add_line... INFO @ Mon, 03 Jun 2019 17:24:39: start X-correlation... INFO @ Mon, 03 Jun 2019 17:24:39: start X-correlation... INFO @ Mon, 03 Jun 2019 17:24:39: end of X-cor INFO @ Mon, 03 Jun 2019 17:24:39: #2 finished! INFO @ Mon, 03 Jun 2019 17:24:39: #2 predicted fragment length is 146 bps INFO @ Mon, 03 Jun 2019 17:24:39: #2 alternative fragment length(s) may be 4,146 bps INFO @ Mon, 03 Jun 2019 17:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.20_model.r INFO @ Mon, 03 Jun 2019 17:24:39: end of X-cor INFO @ Mon, 03 Jun 2019 17:24:39: #2 finished! INFO @ Mon, 03 Jun 2019 17:24:39: #2 predicted fragment length is 146 bps INFO @ Mon, 03 Jun 2019 17:24:39: #2 alternative fragment length(s) may be 4,146 bps INFO @ Mon, 03 Jun 2019 17:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.05_model.r INFO @ Mon, 03 Jun 2019 17:24:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:24:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:24:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:24:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:24:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:24:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:24:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:24:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.10_summits.bed INFO @ Mon, 03 Jun 2019 17:24:47: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:24:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:24:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:24:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:24:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.20_summits.bed INFO @ Mon, 03 Jun 2019 17:24:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:24:49: Done! INFO @ Mon, 03 Jun 2019 17:24:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650867/SRX4650867.05_summits.bed INFO @ Mon, 03 Jun 2019 17:24:49: Done! pass1 - making usageList (6 chroms): 1 millis pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (66 records, 4 fields): 1 millis pass2 - checking and writing primary data (375 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。