Job ID = 1294462 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,097,573 reads read : 17,097,573 reads written : 17,097,573 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: 00:04:06 17097573 reads; of these: 17097573 (100.00%) were unpaired; of these: 1210897 (7.08%) aligned 0 times 14828697 (86.73%) aligned exactly 1 time 1057979 (6.19%) aligned >1 times 92.92% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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] 2222073 / 15886676 = 0.1399 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 08:21:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.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 08:21:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:21:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:21:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.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 08:21:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:21:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:21:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.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 08:21:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:21:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:21:38: 1000000 INFO @ Mon, 03 Jun 2019 08:21:38: 1000000 INFO @ Mon, 03 Jun 2019 08:21:38: 1000000 INFO @ Mon, 03 Jun 2019 08:21:47: 2000000 INFO @ Mon, 03 Jun 2019 08:21:48: 2000000 INFO @ Mon, 03 Jun 2019 08:21:48: 2000000 INFO @ Mon, 03 Jun 2019 08:21:56: 3000000 INFO @ Mon, 03 Jun 2019 08:21:57: 3000000 INFO @ Mon, 03 Jun 2019 08:21:57: 3000000 INFO @ Mon, 03 Jun 2019 08:22:05: 4000000 INFO @ Mon, 03 Jun 2019 08:22:06: 4000000 INFO @ Mon, 03 Jun 2019 08:22:06: 4000000 INFO @ Mon, 03 Jun 2019 08:22:16: 5000000 INFO @ Mon, 03 Jun 2019 08:22:16: 5000000 INFO @ Mon, 03 Jun 2019 08:22:16: 5000000 INFO @ Mon, 03 Jun 2019 08:22:25: 6000000 INFO @ Mon, 03 Jun 2019 08:22:25: 6000000 INFO @ Mon, 03 Jun 2019 08:22:25: 6000000 INFO @ Mon, 03 Jun 2019 08:22:34: 7000000 INFO @ Mon, 03 Jun 2019 08:22:35: 7000000 INFO @ Mon, 03 Jun 2019 08:22:35: 7000000 INFO @ Mon, 03 Jun 2019 08:22:43: 8000000 INFO @ Mon, 03 Jun 2019 08:22:44: 8000000 INFO @ Mon, 03 Jun 2019 08:22:44: 8000000 INFO @ Mon, 03 Jun 2019 08:22:52: 9000000 INFO @ Mon, 03 Jun 2019 08:22:53: 9000000 INFO @ Mon, 03 Jun 2019 08:22:53: 9000000 INFO @ Mon, 03 Jun 2019 08:23:00: 10000000 INFO @ Mon, 03 Jun 2019 08:23:02: 10000000 INFO @ Mon, 03 Jun 2019 08:23:02: 10000000 INFO @ Mon, 03 Jun 2019 08:23:09: 11000000 INFO @ Mon, 03 Jun 2019 08:23:10: 11000000 INFO @ Mon, 03 Jun 2019 08:23:11: 11000000 INFO @ Mon, 03 Jun 2019 08:23:18: 12000000 INFO @ Mon, 03 Jun 2019 08:23:19: 12000000 INFO @ Mon, 03 Jun 2019 08:23:20: 12000000 INFO @ Mon, 03 Jun 2019 08:23:27: 13000000 INFO @ Mon, 03 Jun 2019 08:23:28: 13000000 INFO @ Mon, 03 Jun 2019 08:23:29: 13000000 INFO @ Mon, 03 Jun 2019 08:23:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:23:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:23:33: #1 total tags in treatment: 13664603 INFO @ Mon, 03 Jun 2019 08:23:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:23:33: #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 08:23:33: #1 tags after filtering in treatment: 13664603 INFO @ Mon, 03 Jun 2019 08:23:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:23:33: #1 finished! INFO @ Mon, 03 Jun 2019 08:23:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:23:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:23:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:23:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:23:34: #1 total tags in treatment: 13664603 INFO @ Mon, 03 Jun 2019 08:23:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:23:34: #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 08:23:34: #1 tags after filtering in treatment: 13664603 INFO @ Mon, 03 Jun 2019 08:23:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:23:34: #1 finished! INFO @ Mon, 03 Jun 2019 08:23:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:23:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:23:34: #2 number of paired peaks: 3406 INFO @ Mon, 03 Jun 2019 08:23:34: start model_add_line... INFO @ Mon, 03 Jun 2019 08:23:35: start X-correlation... INFO @ Mon, 03 Jun 2019 08:23:35: end of X-cor INFO @ Mon, 03 Jun 2019 08:23:35: #2 finished! INFO @ Mon, 03 Jun 2019 08:23:35: #2 predicted fragment length is 190 bps INFO @ Mon, 03 Jun 2019 08:23:35: #2 alternative fragment length(s) may be 4,190 bps INFO @ Mon, 03 Jun 2019 08:23:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.05_model.r INFO @ Mon, 03 Jun 2019 08:23:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:23:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:23:36: #2 number of paired peaks: 3406 INFO @ Mon, 03 Jun 2019 08:23:36: start model_add_line... INFO @ Mon, 03 Jun 2019 08:23:36: start X-correlation... INFO @ Mon, 03 Jun 2019 08:23:36: end of X-cor INFO @ Mon, 03 Jun 2019 08:23:36: #2 finished! INFO @ Mon, 03 Jun 2019 08:23:36: #2 predicted fragment length is 190 bps INFO @ Mon, 03 Jun 2019 08:23:36: #2 alternative fragment length(s) may be 4,190 bps INFO @ Mon, 03 Jun 2019 08:23:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.10_model.r INFO @ Mon, 03 Jun 2019 08:23:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:23:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:23:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:23:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:23:37: #1 total tags in treatment: 13664603 INFO @ Mon, 03 Jun 2019 08:23:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:23:37: #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 08:23:37: #1 tags after filtering in treatment: 13664603 INFO @ Mon, 03 Jun 2019 08:23:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:23:37: #1 finished! INFO @ Mon, 03 Jun 2019 08:23:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:23:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:23:39: #2 number of paired peaks: 3406 INFO @ Mon, 03 Jun 2019 08:23:39: start model_add_line... INFO @ Mon, 03 Jun 2019 08:23:39: start X-correlation... INFO @ Mon, 03 Jun 2019 08:23:39: end of X-cor INFO @ Mon, 03 Jun 2019 08:23:39: #2 finished! INFO @ Mon, 03 Jun 2019 08:23:39: #2 predicted fragment length is 190 bps INFO @ Mon, 03 Jun 2019 08:23:39: #2 alternative fragment length(s) may be 4,190 bps INFO @ Mon, 03 Jun 2019 08:23:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.20_model.r INFO @ Mon, 03 Jun 2019 08:23:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:23:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:24:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:24:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:24:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:24:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:24:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:24:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.05_summits.bed INFO @ Mon, 03 Jun 2019 08:24:38: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (9010 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:24:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:24:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:24:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.10_summits.bed INFO @ Mon, 03 Jun 2019 08:24:39: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (4456 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:24:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:24:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:24:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287663/SRX287663.20_summits.bed INFO @ Mon, 03 Jun 2019 08:24:44: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1652 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。