Job ID = 1301496 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,504,702 reads read : 22,504,702 reads written : 22,504,702 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: 00:05:51 22504702 reads; of these: 22504702 (100.00%) were unpaired; of these: 1528519 (6.79%) aligned 0 times 18741371 (83.28%) aligned exactly 1 time 2234812 (9.93%) aligned >1 times 93.21% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 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 12 files... [bam_rmdupse_core] 8091810 / 20976183 = 0.3858 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 20:13:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.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 20:13:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:13:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:13:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.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 20:13:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:13:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:13:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.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 20:13:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:13:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:13:50: 1000000 INFO @ Mon, 03 Jun 2019 20:13:50: 1000000 INFO @ Mon, 03 Jun 2019 20:13:53: 1000000 INFO @ Mon, 03 Jun 2019 20:13:59: 2000000 INFO @ Mon, 03 Jun 2019 20:13:59: 2000000 INFO @ Mon, 03 Jun 2019 20:14:03: 2000000 INFO @ Mon, 03 Jun 2019 20:14:07: 3000000 INFO @ Mon, 03 Jun 2019 20:14:07: 3000000 INFO @ Mon, 03 Jun 2019 20:14:14: 3000000 INFO @ Mon, 03 Jun 2019 20:14:15: 4000000 INFO @ Mon, 03 Jun 2019 20:14:15: 4000000 INFO @ Mon, 03 Jun 2019 20:14:23: 5000000 INFO @ Mon, 03 Jun 2019 20:14:23: 5000000 INFO @ Mon, 03 Jun 2019 20:14:24: 4000000 INFO @ Mon, 03 Jun 2019 20:14:31: 6000000 INFO @ Mon, 03 Jun 2019 20:14:31: 6000000 INFO @ Mon, 03 Jun 2019 20:14:34: 5000000 INFO @ Mon, 03 Jun 2019 20:14:39: 7000000 INFO @ Mon, 03 Jun 2019 20:14:39: 7000000 INFO @ Mon, 03 Jun 2019 20:14:45: 6000000 INFO @ Mon, 03 Jun 2019 20:14:47: 8000000 INFO @ Mon, 03 Jun 2019 20:14:47: 8000000 INFO @ Mon, 03 Jun 2019 20:14:55: 7000000 INFO @ Mon, 03 Jun 2019 20:14:55: 9000000 INFO @ Mon, 03 Jun 2019 20:14:55: 9000000 INFO @ Mon, 03 Jun 2019 20:15:03: 10000000 INFO @ Mon, 03 Jun 2019 20:15:03: 10000000 INFO @ Mon, 03 Jun 2019 20:15:05: 8000000 INFO @ Mon, 03 Jun 2019 20:15:11: 11000000 INFO @ Mon, 03 Jun 2019 20:15:11: 11000000 INFO @ Mon, 03 Jun 2019 20:15:15: 9000000 INFO @ Mon, 03 Jun 2019 20:15:19: 12000000 INFO @ Mon, 03 Jun 2019 20:15:19: 12000000 INFO @ Mon, 03 Jun 2019 20:15:25: 10000000 INFO @ Mon, 03 Jun 2019 20:15:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:15:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:15:26: #1 total tags in treatment: 12884373 INFO @ Mon, 03 Jun 2019 20:15:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:15:26: #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 20:15:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:15:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:15:26: #1 total tags in treatment: 12884373 INFO @ Mon, 03 Jun 2019 20:15:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:15:26: #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 20:15:26: #1 tags after filtering in treatment: 12884373 INFO @ Mon, 03 Jun 2019 20:15:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:15:26: #1 finished! INFO @ Mon, 03 Jun 2019 20:15:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:15:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:15:27: #1 tags after filtering in treatment: 12884373 INFO @ Mon, 03 Jun 2019 20:15:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:15:27: #1 finished! INFO @ Mon, 03 Jun 2019 20:15:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:15:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:15:28: #2 number of paired peaks: 7871 INFO @ Mon, 03 Jun 2019 20:15:28: start model_add_line... INFO @ Mon, 03 Jun 2019 20:15:29: #2 number of paired peaks: 7871 INFO @ Mon, 03 Jun 2019 20:15:29: start model_add_line... INFO @ Mon, 03 Jun 2019 20:15:29: start X-correlation... INFO @ Mon, 03 Jun 2019 20:15:29: end of X-cor INFO @ Mon, 03 Jun 2019 20:15:29: #2 finished! INFO @ Mon, 03 Jun 2019 20:15:29: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 20:15:29: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 20:15:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.20_model.r INFO @ Mon, 03 Jun 2019 20:15:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:15:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:15:29: start X-correlation... INFO @ Mon, 03 Jun 2019 20:15:29: end of X-cor INFO @ Mon, 03 Jun 2019 20:15:29: #2 finished! INFO @ Mon, 03 Jun 2019 20:15:29: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 20:15:29: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 20:15:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.05_model.r INFO @ Mon, 03 Jun 2019 20:15:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:15:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:15:35: 11000000 INFO @ Mon, 03 Jun 2019 20:15:45: 12000000 INFO @ Mon, 03 Jun 2019 20:15:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:15:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:15:53: #1 total tags in treatment: 12884373 INFO @ Mon, 03 Jun 2019 20:15:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:15:53: #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 20:15:53: #1 tags after filtering in treatment: 12884373 INFO @ Mon, 03 Jun 2019 20:15:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:15:53: #1 finished! INFO @ Mon, 03 Jun 2019 20:15:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:15:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:15:55: #2 number of paired peaks: 7871 INFO @ Mon, 03 Jun 2019 20:15:55: start model_add_line... INFO @ Mon, 03 Jun 2019 20:15:56: start X-correlation... INFO @ Mon, 03 Jun 2019 20:15:56: end of X-cor INFO @ Mon, 03 Jun 2019 20:15:56: #2 finished! INFO @ Mon, 03 Jun 2019 20:15:56: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 20:15:56: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 20:15:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.10_model.r INFO @ Mon, 03 Jun 2019 20:15:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:15:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:16:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:16:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:16:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:16:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:16:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.20_summits.bed INFO @ Mon, 03 Jun 2019 20:16:39: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5252 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:16:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:16:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:16:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.05_summits.bed INFO @ Mon, 03 Jun 2019 20:16:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8354 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:16:45: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 20:17:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:17:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:17:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485220/SRX485220.10_summits.bed INFO @ Mon, 03 Jun 2019 20:17:12: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6884 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。