Job ID = 1293338 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 96,820,528 reads read : 193,641,056 reads written : 193,641,056 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: 01:13:51 96820528 reads; of these: 96820528 (100.00%) were paired; of these: 63369007 (65.45%) aligned concordantly 0 times 26839681 (27.72%) aligned concordantly exactly 1 time 6611840 (6.83%) aligned concordantly >1 times ---- 63369007 pairs aligned concordantly 0 times; of these: 1025112 (1.62%) aligned discordantly 1 time ---- 62343895 pairs aligned 0 times concordantly or discordantly; of these: 124687790 mates make up the pairs; of these: 122767377 (98.46%) aligned 0 times 1285990 (1.03%) aligned exactly 1 time 634423 (0.51%) aligned >1 times 36.60% overall alignment rate Time searching: 01:13:51 Overall time: 01:13:51 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_sort_core] merging from 32 files... [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] 31573645 / 34456552 = 0.9163 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 01:30:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.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 01:30:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:30:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:30:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.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 01:30:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:30:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:30:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.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 01:30:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:30:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:30:26: 1000000 INFO @ Mon, 03 Jun 2019 01:30:29: 1000000 INFO @ Mon, 03 Jun 2019 01:30:29: 1000000 INFO @ Mon, 03 Jun 2019 01:30:33: 2000000 INFO @ Mon, 03 Jun 2019 01:30:40: 2000000 INFO @ Mon, 03 Jun 2019 01:30:40: 3000000 INFO @ Mon, 03 Jun 2019 01:30:41: 2000000 INFO @ Mon, 03 Jun 2019 01:30:47: 4000000 INFO @ Mon, 03 Jun 2019 01:30:51: 3000000 INFO @ Mon, 03 Jun 2019 01:30:51: 3000000 INFO @ Mon, 03 Jun 2019 01:30:55: 5000000 INFO @ Mon, 03 Jun 2019 01:31:01: 4000000 INFO @ Mon, 03 Jun 2019 01:31:01: 4000000 INFO @ Mon, 03 Jun 2019 01:31:02: 6000000 INFO @ Mon, 03 Jun 2019 01:31:09: 7000000 INFO @ Mon, 03 Jun 2019 01:31:11: 5000000 INFO @ Mon, 03 Jun 2019 01:31:11: 5000000 INFO @ Mon, 03 Jun 2019 01:31:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 01:31:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 01:31:14: #1 total tags in treatment: 2810082 INFO @ Mon, 03 Jun 2019 01:31:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:31:14: #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 01:31:14: #1 tags after filtering in treatment: 2637616 INFO @ Mon, 03 Jun 2019 01:31:14: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 03 Jun 2019 01:31:14: #1 finished! INFO @ Mon, 03 Jun 2019 01:31:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:31:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:31:15: #2 number of paired peaks: 4500 INFO @ Mon, 03 Jun 2019 01:31:15: start model_add_line... INFO @ Mon, 03 Jun 2019 01:31:15: start X-correlation... INFO @ Mon, 03 Jun 2019 01:31:15: end of X-cor INFO @ Mon, 03 Jun 2019 01:31:15: #2 finished! INFO @ Mon, 03 Jun 2019 01:31:15: #2 predicted fragment length is 215 bps INFO @ Mon, 03 Jun 2019 01:31:15: #2 alternative fragment length(s) may be 215 bps INFO @ Mon, 03 Jun 2019 01:31:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.05_model.r INFO @ Mon, 03 Jun 2019 01:31:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:31:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:31:22: 6000000 INFO @ Mon, 03 Jun 2019 01:31:22: 6000000 INFO @ Mon, 03 Jun 2019 01:31:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:31:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:31:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:31:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.05_summits.bed INFO @ Mon, 03 Jun 2019 01:31:29: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4964 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:31:31: 7000000 INFO @ Mon, 03 Jun 2019 01:31:32: 7000000 INFO @ Mon, 03 Jun 2019 01:31:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 01:31:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 01:31:38: #1 total tags in treatment: 2810082 INFO @ Mon, 03 Jun 2019 01:31:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:31:38: #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 01:31:38: #1 tags after filtering in treatment: 2637616 INFO @ Mon, 03 Jun 2019 01:31:38: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 03 Jun 2019 01:31:38: #1 finished! INFO @ Mon, 03 Jun 2019 01:31:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:31:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:31:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 01:31:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 01:31:38: #1 total tags in treatment: 2810082 INFO @ Mon, 03 Jun 2019 01:31:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:31:38: #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 01:31:38: #1 tags after filtering in treatment: 2637616 INFO @ Mon, 03 Jun 2019 01:31:38: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 03 Jun 2019 01:31:38: #1 finished! INFO @ Mon, 03 Jun 2019 01:31:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:31:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:31:39: #2 number of paired peaks: 4500 INFO @ Mon, 03 Jun 2019 01:31:39: start model_add_line... INFO @ Mon, 03 Jun 2019 01:31:39: start X-correlation... INFO @ Mon, 03 Jun 2019 01:31:39: end of X-cor INFO @ Mon, 03 Jun 2019 01:31:39: #2 finished! INFO @ Mon, 03 Jun 2019 01:31:39: #2 predicted fragment length is 215 bps INFO @ Mon, 03 Jun 2019 01:31:39: #2 alternative fragment length(s) may be 215 bps INFO @ Mon, 03 Jun 2019 01:31:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.10_model.r INFO @ Mon, 03 Jun 2019 01:31:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:31:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:31:39: #2 number of paired peaks: 4500 INFO @ Mon, 03 Jun 2019 01:31:39: start model_add_line... INFO @ Mon, 03 Jun 2019 01:31:39: start X-correlation... INFO @ Mon, 03 Jun 2019 01:31:39: end of X-cor INFO @ Mon, 03 Jun 2019 01:31:39: #2 finished! INFO @ Mon, 03 Jun 2019 01:31:39: #2 predicted fragment length is 215 bps INFO @ Mon, 03 Jun 2019 01:31:39: #2 alternative fragment length(s) may be 215 bps INFO @ Mon, 03 Jun 2019 01:31:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.20_model.r INFO @ Mon, 03 Jun 2019 01:31:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:31:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:31:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:31:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:31:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:31:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:31:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.10_summits.bed INFO @ Mon, 03 Jun 2019 01:31:52: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2563 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:31:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:31:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:31:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818265/ERX1818265.20_summits.bed INFO @ Mon, 03 Jun 2019 01:31:52: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (909 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。