Job ID = 1298087 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 45,387,988 reads read : 90,775,976 reads written : 90,775,976 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: 00:13:18 45387988 reads; of these: 45387988 (100.00%) were paired; of these: 42520959 (93.68%) aligned concordantly 0 times 2239678 (4.93%) aligned concordantly exactly 1 time 627351 (1.38%) aligned concordantly >1 times ---- 42520959 pairs aligned concordantly 0 times; of these: 11360 (0.03%) aligned discordantly 1 time ---- 42509599 pairs aligned 0 times concordantly or discordantly; of these: 85019198 mates make up the pairs; of these: 83891486 (98.67%) aligned 0 times 410185 (0.48%) aligned exactly 1 time 717527 (0.84%) aligned >1 times 7.58% overall alignment rate Time searching: 00:13:18 Overall time: 00:13:18 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] 139925 / 2871459 = 0.0487 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 17:46:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.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 17:46:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:46:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:46:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.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 17:46:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:46:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:46:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.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 17:46:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:46:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:46:12: 1000000 INFO @ Mon, 03 Jun 2019 17:46:14: 1000000 INFO @ Mon, 03 Jun 2019 17:46:14: 1000000 INFO @ Mon, 03 Jun 2019 17:46:21: 2000000 INFO @ Mon, 03 Jun 2019 17:46:26: 2000000 INFO @ Mon, 03 Jun 2019 17:46:26: 2000000 INFO @ Mon, 03 Jun 2019 17:46:30: 3000000 INFO @ Mon, 03 Jun 2019 17:46:38: 3000000 INFO @ Mon, 03 Jun 2019 17:46:38: 3000000 INFO @ Mon, 03 Jun 2019 17:46:39: 4000000 INFO @ Mon, 03 Jun 2019 17:46:48: 5000000 INFO @ Mon, 03 Jun 2019 17:46:49: 4000000 INFO @ Mon, 03 Jun 2019 17:46:49: 4000000 INFO @ Mon, 03 Jun 2019 17:46:57: 6000000 INFO @ Mon, 03 Jun 2019 17:47:01: 5000000 INFO @ Mon, 03 Jun 2019 17:47:01: 5000000 INFO @ Mon, 03 Jun 2019 17:47:02: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:47:02: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:47:02: #1 total tags in treatment: 2727303 INFO @ Mon, 03 Jun 2019 17:47:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:47:02: #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 17:47:02: #1 tags after filtering in treatment: 2592188 INFO @ Mon, 03 Jun 2019 17:47:02: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 17:47:02: #1 finished! INFO @ Mon, 03 Jun 2019 17:47:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:47:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:47:03: #2 number of paired peaks: 1792 INFO @ Mon, 03 Jun 2019 17:47:03: start model_add_line... INFO @ Mon, 03 Jun 2019 17:47:03: start X-correlation... INFO @ Mon, 03 Jun 2019 17:47:03: end of X-cor INFO @ Mon, 03 Jun 2019 17:47:03: #2 finished! INFO @ Mon, 03 Jun 2019 17:47:03: #2 predicted fragment length is 145 bps INFO @ Mon, 03 Jun 2019 17:47:03: #2 alternative fragment length(s) may be 4,145 bps INFO @ Mon, 03 Jun 2019 17:47:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.05_model.r INFO @ Mon, 03 Jun 2019 17:47:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:47:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:47:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:47:12: 6000000 INFO @ Mon, 03 Jun 2019 17:47:12: 6000000 INFO @ Mon, 03 Jun 2019 17:47:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:47:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:47:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.05_summits.bed INFO @ Mon, 03 Jun 2019 17:47:15: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (441 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:47:19: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:47:19: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:47:19: #1 total tags in treatment: 2727303 INFO @ Mon, 03 Jun 2019 17:47:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:47:19: #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 17:47:19: #1 tags after filtering in treatment: 2592188 INFO @ Mon, 03 Jun 2019 17:47:19: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 17:47:19: #1 finished! INFO @ Mon, 03 Jun 2019 17:47:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:47:19: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:47:19: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:47:19: #1 total tags in treatment: 2727303 INFO @ Mon, 03 Jun 2019 17:47:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:47:19: #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 17:47:19: #1 tags after filtering in treatment: 2592188 INFO @ Mon, 03 Jun 2019 17:47:19: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 17:47:19: #1 finished! INFO @ Mon, 03 Jun 2019 17:47:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:47:19: #2 number of paired peaks: 1792 INFO @ Mon, 03 Jun 2019 17:47:19: start model_add_line... INFO @ Mon, 03 Jun 2019 17:47:19: start X-correlation... INFO @ Mon, 03 Jun 2019 17:47:19: end of X-cor INFO @ Mon, 03 Jun 2019 17:47:19: #2 finished! INFO @ Mon, 03 Jun 2019 17:47:19: #2 predicted fragment length is 145 bps INFO @ Mon, 03 Jun 2019 17:47:19: #2 alternative fragment length(s) may be 4,145 bps INFO @ Mon, 03 Jun 2019 17:47:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.10_model.r INFO @ Mon, 03 Jun 2019 17:47:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:47:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:47:19: #2 number of paired peaks: 1792 INFO @ Mon, 03 Jun 2019 17:47:19: start model_add_line... INFO @ Mon, 03 Jun 2019 17:47:19: start X-correlation... INFO @ Mon, 03 Jun 2019 17:47:19: end of X-cor INFO @ Mon, 03 Jun 2019 17:47:19: #2 finished! INFO @ Mon, 03 Jun 2019 17:47:19: #2 predicted fragment length is 145 bps INFO @ Mon, 03 Jun 2019 17:47:19: #2 alternative fragment length(s) may be 4,145 bps INFO @ Mon, 03 Jun 2019 17:47:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.20_model.r INFO @ Mon, 03 Jun 2019 17:47:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:47:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:47:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:47:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:47:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:47:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:47:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.10_summits.bed INFO @ Mon, 03 Jun 2019 17:47:31: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (208 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:47:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:47:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:47:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650884/SRX4650884.20_summits.bed INFO @ Mon, 03 Jun 2019 17:47:31: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (106 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。