Job ID = 1294116 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,269,050 reads read : 30,269,050 reads written : 30,269,050 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: 00:08:35 30269050 reads; of these: 30269050 (100.00%) were unpaired; of these: 1637526 (5.41%) aligned 0 times 23531051 (77.74%) aligned exactly 1 time 5100473 (16.85%) aligned >1 times 94.59% overall alignment rate Time searching: 00:08:35 Overall time: 00:08:35 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 8 files... [bam_rmdupse_core] 18016837 / 28631524 = 0.6293 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 05:28:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.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 05:28:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:28:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:28:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.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 05:28:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:28:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:28:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.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 05:28:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:28:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:28:39: 1000000 INFO @ Mon, 03 Jun 2019 05:28:42: 1000000 INFO @ Mon, 03 Jun 2019 05:28:42: 1000000 INFO @ Mon, 03 Jun 2019 05:28:46: 2000000 INFO @ Mon, 03 Jun 2019 05:28:52: 2000000 INFO @ Mon, 03 Jun 2019 05:28:52: 2000000 INFO @ Mon, 03 Jun 2019 05:28:53: 3000000 INFO @ Mon, 03 Jun 2019 05:29:00: 4000000 INFO @ Mon, 03 Jun 2019 05:29:02: 3000000 INFO @ Mon, 03 Jun 2019 05:29:02: 3000000 INFO @ Mon, 03 Jun 2019 05:29:07: 5000000 INFO @ Mon, 03 Jun 2019 05:29:11: 4000000 INFO @ Mon, 03 Jun 2019 05:29:11: 4000000 INFO @ Mon, 03 Jun 2019 05:29:14: 6000000 INFO @ Mon, 03 Jun 2019 05:29:21: 5000000 INFO @ Mon, 03 Jun 2019 05:29:21: 5000000 INFO @ Mon, 03 Jun 2019 05:29:21: 7000000 INFO @ Mon, 03 Jun 2019 05:29:28: 8000000 INFO @ Mon, 03 Jun 2019 05:29:31: 6000000 INFO @ Mon, 03 Jun 2019 05:29:31: 6000000 INFO @ Mon, 03 Jun 2019 05:29:36: 9000000 INFO @ Mon, 03 Jun 2019 05:29:42: 7000000 INFO @ Mon, 03 Jun 2019 05:29:43: 7000000 INFO @ Mon, 03 Jun 2019 05:29:43: 10000000 INFO @ Mon, 03 Jun 2019 05:29:48: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:29:48: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:29:48: #1 total tags in treatment: 10614687 INFO @ Mon, 03 Jun 2019 05:29:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:29:48: #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 05:29:48: #1 tags after filtering in treatment: 10614687 INFO @ Mon, 03 Jun 2019 05:29:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:29:48: #1 finished! INFO @ Mon, 03 Jun 2019 05:29:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:29:49: #2 number of paired peaks: 2503 INFO @ Mon, 03 Jun 2019 05:29:49: start model_add_line... INFO @ Mon, 03 Jun 2019 05:29:49: start X-correlation... INFO @ Mon, 03 Jun 2019 05:29:49: end of X-cor INFO @ Mon, 03 Jun 2019 05:29:49: #2 finished! INFO @ Mon, 03 Jun 2019 05:29:49: #2 predicted fragment length is 127 bps INFO @ Mon, 03 Jun 2019 05:29:49: #2 alternative fragment length(s) may be 127 bps INFO @ Mon, 03 Jun 2019 05:29:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.05_model.r INFO @ Mon, 03 Jun 2019 05:29:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:29:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:29:52: 8000000 INFO @ Mon, 03 Jun 2019 05:29:53: 8000000 INFO @ Mon, 03 Jun 2019 05:30:02: 9000000 INFO @ Mon, 03 Jun 2019 05:30:04: 9000000 INFO @ Mon, 03 Jun 2019 05:30:12: 10000000 INFO @ Mon, 03 Jun 2019 05:30:14: 10000000 INFO @ Mon, 03 Jun 2019 05:30:18: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:30:18: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:30:18: #1 total tags in treatment: 10614687 INFO @ Mon, 03 Jun 2019 05:30:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:30:18: #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 05:30:18: #1 tags after filtering in treatment: 10614687 INFO @ Mon, 03 Jun 2019 05:30:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:30:18: #1 finished! INFO @ Mon, 03 Jun 2019 05:30:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:30:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:30:20: #2 number of paired peaks: 2503 INFO @ Mon, 03 Jun 2019 05:30:20: start model_add_line... INFO @ Mon, 03 Jun 2019 05:30:20: start X-correlation... INFO @ Mon, 03 Jun 2019 05:30:20: end of X-cor INFO @ Mon, 03 Jun 2019 05:30:20: #2 finished! INFO @ Mon, 03 Jun 2019 05:30:20: #2 predicted fragment length is 127 bps INFO @ Mon, 03 Jun 2019 05:30:20: #2 alternative fragment length(s) may be 127 bps INFO @ Mon, 03 Jun 2019 05:30:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.20_model.r INFO @ Mon, 03 Jun 2019 05:30:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:30:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:30:20: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:30:20: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:30:20: #1 total tags in treatment: 10614687 INFO @ Mon, 03 Jun 2019 05:30:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:30:20: #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 05:30:20: #1 tags after filtering in treatment: 10614687 INFO @ Mon, 03 Jun 2019 05:30:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:30:20: #1 finished! INFO @ Mon, 03 Jun 2019 05:30:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:30:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:30:22: #2 number of paired peaks: 2503 INFO @ Mon, 03 Jun 2019 05:30:22: start model_add_line... INFO @ Mon, 03 Jun 2019 05:30:22: start X-correlation... INFO @ Mon, 03 Jun 2019 05:30:22: end of X-cor INFO @ Mon, 03 Jun 2019 05:30:22: #2 finished! INFO @ Mon, 03 Jun 2019 05:30:22: #2 predicted fragment length is 127 bps INFO @ Mon, 03 Jun 2019 05:30:22: #2 alternative fragment length(s) may be 127 bps INFO @ Mon, 03 Jun 2019 05:30:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.10_model.r INFO @ Mon, 03 Jun 2019 05:30:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:30:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:30:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:30:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:30:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.05_summits.bed INFO @ Mon, 03 Jun 2019 05:30:38: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (13955 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:30:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:30:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:31:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:31:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:31:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.20_summits.bed INFO @ Mon, 03 Jun 2019 05:31:08: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7195 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:31:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:31:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:31:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX191908/SRX191908.10_summits.bed INFO @ Mon, 03 Jun 2019 05:31:11: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (10417 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。