Job ID = 1297307 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 42,909,089 reads read : 85,818,178 reads written : 85,818,178 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: 00:08:44 42909089 reads; of these: 42909089 (100.00%) were paired; of these: 41312675 (96.28%) aligned concordantly 0 times 1240840 (2.89%) aligned concordantly exactly 1 time 355574 (0.83%) aligned concordantly >1 times ---- 41312675 pairs aligned concordantly 0 times; of these: 2784 (0.01%) aligned discordantly 1 time ---- 41309891 pairs aligned 0 times concordantly or discordantly; of these: 82619782 mates make up the pairs; of these: 82168315 (99.45%) aligned 0 times 156328 (0.19%) aligned exactly 1 time 295139 (0.36%) aligned >1 times 4.25% overall alignment rate Time searching: 00:08:44 Overall time: 00:08:44 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] 80042 / 1596910 = 0.0501 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 17:18:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.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 17:18:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:18:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:18:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.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 17:18:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:18:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:18:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.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 17:18:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:18:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:19:01: 1000000 INFO @ Mon, 03 Jun 2019 17:19:02: 1000000 INFO @ Mon, 03 Jun 2019 17:19:03: 1000000 INFO @ Mon, 03 Jun 2019 17:19:07: 2000000 INFO @ Mon, 03 Jun 2019 17:19:10: 2000000 INFO @ Mon, 03 Jun 2019 17:19:11: 2000000 INFO @ Mon, 03 Jun 2019 17:19:13: 3000000 INFO @ Mon, 03 Jun 2019 17:19:16: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 17:19:16: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 17:19:16: #1 total tags in treatment: 1516509 INFO @ Mon, 03 Jun 2019 17:19:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:19:16: #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 17:19:16: #1 tags after filtering in treatment: 1463798 INFO @ Mon, 03 Jun 2019 17:19:16: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 17:19:16: #1 finished! INFO @ Mon, 03 Jun 2019 17:19:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:19:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:19:17: #2 number of paired peaks: 2586 INFO @ Mon, 03 Jun 2019 17:19:17: start model_add_line... INFO @ Mon, 03 Jun 2019 17:19:17: start X-correlation... INFO @ Mon, 03 Jun 2019 17:19:17: end of X-cor INFO @ Mon, 03 Jun 2019 17:19:17: #2 finished! INFO @ Mon, 03 Jun 2019 17:19:17: #2 predicted fragment length is 148 bps INFO @ Mon, 03 Jun 2019 17:19:17: #2 alternative fragment length(s) may be 4,148 bps INFO @ Mon, 03 Jun 2019 17:19:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.20_model.r INFO @ Mon, 03 Jun 2019 17:19:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:19:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:19:17: 3000000 INFO @ Mon, 03 Jun 2019 17:19:19: 3000000 INFO @ Mon, 03 Jun 2019 17:19:20: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 17:19:20: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 17:19:20: #1 total tags in treatment: 1516509 INFO @ Mon, 03 Jun 2019 17:19:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:19:20: #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 17:19:20: #1 tags after filtering in treatment: 1463798 INFO @ Mon, 03 Jun 2019 17:19:20: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 17:19:20: #1 finished! INFO @ Mon, 03 Jun 2019 17:19:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:19:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:19:21: #2 number of paired peaks: 2586 INFO @ Mon, 03 Jun 2019 17:19:21: start model_add_line... INFO @ Mon, 03 Jun 2019 17:19:21: start X-correlation... INFO @ Mon, 03 Jun 2019 17:19:21: end of X-cor INFO @ Mon, 03 Jun 2019 17:19:21: #2 finished! INFO @ Mon, 03 Jun 2019 17:19:21: #2 predicted fragment length is 148 bps INFO @ Mon, 03 Jun 2019 17:19:21: #2 alternative fragment length(s) may be 4,148 bps INFO @ Mon, 03 Jun 2019 17:19:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.05_model.r INFO @ Mon, 03 Jun 2019 17:19:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:19:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:19:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:19:23: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 17:19:23: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 17:19:23: #1 total tags in treatment: 1516509 INFO @ Mon, 03 Jun 2019 17:19:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:19:23: #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 17:19:23: #1 tags after filtering in treatment: 1463798 INFO @ Mon, 03 Jun 2019 17:19:23: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 17:19:23: #1 finished! INFO @ Mon, 03 Jun 2019 17:19:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:19:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:19:23: #2 number of paired peaks: 2586 INFO @ Mon, 03 Jun 2019 17:19:23: start model_add_line... INFO @ Mon, 03 Jun 2019 17:19:23: start X-correlation... INFO @ Mon, 03 Jun 2019 17:19:23: end of X-cor INFO @ Mon, 03 Jun 2019 17:19:23: #2 finished! INFO @ Mon, 03 Jun 2019 17:19:23: #2 predicted fragment length is 148 bps INFO @ Mon, 03 Jun 2019 17:19:23: #2 alternative fragment length(s) may be 4,148 bps INFO @ Mon, 03 Jun 2019 17:19:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.10_model.r INFO @ Mon, 03 Jun 2019 17:19:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:19:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:19:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:19:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:19:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.20_summits.bed INFO @ Mon, 03 Jun 2019 17:19:24: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (75 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:19:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:19:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:19:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:19:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.05_summits.bed INFO @ Mon, 03 Jun 2019 17:19:28: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (272 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:19:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:19:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:19:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:19:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650845/SRX4650845.10_summits.bed INFO @ Mon, 03 Jun 2019 17:19:31: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (159 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。