Job ID = 2590263 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,472,062 reads read : 31,472,062 reads written : 31,472,062 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR100232.sra.cache’: 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: 00:10:03 31472062 reads; of these: 31472062 (100.00%) were unpaired; of these: 4684447 (14.88%) aligned 0 times 25217797 (80.13%) aligned exactly 1 time 1569818 (4.99%) aligned >1 times 85.12% overall alignment rate Time searching: 00:10:03 Overall time: 00:10:03 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] 12010824 / 26787615 = 0.4484 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, 12 Aug 2019 20:40:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.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, 12 Aug 2019 20:40:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:40:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:40:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.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, 12 Aug 2019 20:40:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:40:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:40:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.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, 12 Aug 2019 20:40:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:40:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:40:42: 1000000 INFO @ Mon, 12 Aug 2019 20:40:42: 1000000 INFO @ Mon, 12 Aug 2019 20:40:44: 1000000 INFO @ Mon, 12 Aug 2019 20:40:50: 2000000 INFO @ Mon, 12 Aug 2019 20:40:51: 2000000 INFO @ Mon, 12 Aug 2019 20:40:52: 2000000 INFO @ Mon, 12 Aug 2019 20:40:58: 3000000 INFO @ Mon, 12 Aug 2019 20:40:59: 3000000 INFO @ Mon, 12 Aug 2019 20:41:00: 3000000 INFO @ Mon, 12 Aug 2019 20:41:05: 4000000 INFO @ Mon, 12 Aug 2019 20:41:06: 4000000 INFO @ Mon, 12 Aug 2019 20:41:08: 4000000 INFO @ Mon, 12 Aug 2019 20:41:13: 5000000 INFO @ Mon, 12 Aug 2019 20:41:15: 5000000 INFO @ Mon, 12 Aug 2019 20:41:16: 5000000 INFO @ Mon, 12 Aug 2019 20:41:20: 6000000 INFO @ Mon, 12 Aug 2019 20:41:23: 6000000 INFO @ Mon, 12 Aug 2019 20:41:24: 6000000 INFO @ Mon, 12 Aug 2019 20:41:28: 7000000 INFO @ Mon, 12 Aug 2019 20:41:33: 7000000 INFO @ Mon, 12 Aug 2019 20:41:33: 7000000 INFO @ Mon, 12 Aug 2019 20:41:35: 8000000 INFO @ Mon, 12 Aug 2019 20:41:41: 8000000 INFO @ Mon, 12 Aug 2019 20:41:42: 8000000 INFO @ Mon, 12 Aug 2019 20:41:43: 9000000 INFO @ Mon, 12 Aug 2019 20:41:49: 9000000 INFO @ Mon, 12 Aug 2019 20:41:50: 10000000 INFO @ Mon, 12 Aug 2019 20:41:51: 9000000 INFO @ Mon, 12 Aug 2019 20:41:58: 10000000 INFO @ Mon, 12 Aug 2019 20:41:58: 11000000 INFO @ Mon, 12 Aug 2019 20:42:00: 10000000 INFO @ Mon, 12 Aug 2019 20:42:06: 11000000 INFO @ Mon, 12 Aug 2019 20:42:06: 12000000 INFO @ Mon, 12 Aug 2019 20:42:09: 11000000 INFO @ Mon, 12 Aug 2019 20:42:14: 13000000 INFO @ Mon, 12 Aug 2019 20:42:15: 12000000 INFO @ Mon, 12 Aug 2019 20:42:18: 12000000 INFO @ Mon, 12 Aug 2019 20:42:21: 14000000 INFO @ Mon, 12 Aug 2019 20:42:23: 13000000 INFO @ Mon, 12 Aug 2019 20:42:27: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:42:27: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:42:27: #1 total tags in treatment: 14776791 INFO @ Mon, 12 Aug 2019 20:42:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:42:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:42:27: 13000000 INFO @ Mon, 12 Aug 2019 20:42:27: #1 tags after filtering in treatment: 14776791 INFO @ Mon, 12 Aug 2019 20:42:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:42:27: #1 finished! INFO @ Mon, 12 Aug 2019 20:42:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:42:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:42:29: #2 number of paired peaks: 2437 INFO @ Mon, 12 Aug 2019 20:42:29: start model_add_line... INFO @ Mon, 12 Aug 2019 20:42:30: start X-correlation... INFO @ Mon, 12 Aug 2019 20:42:30: end of X-cor INFO @ Mon, 12 Aug 2019 20:42:30: #2 finished! INFO @ Mon, 12 Aug 2019 20:42:30: #2 predicted fragment length is 356 bps INFO @ Mon, 12 Aug 2019 20:42:30: #2 alternative fragment length(s) may be 356 bps INFO @ Mon, 12 Aug 2019 20:42:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.10_model.r INFO @ Mon, 12 Aug 2019 20:42:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:42:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:42:31: 14000000 INFO @ Mon, 12 Aug 2019 20:42:37: 14000000 INFO @ Mon, 12 Aug 2019 20:42:37: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:42:37: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:42:37: #1 total tags in treatment: 14776791 INFO @ Mon, 12 Aug 2019 20:42:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:42:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:42:38: #1 tags after filtering in treatment: 14776791 INFO @ Mon, 12 Aug 2019 20:42:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:42:38: #1 finished! INFO @ Mon, 12 Aug 2019 20:42:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:42:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:42:40: #2 number of paired peaks: 2437 INFO @ Mon, 12 Aug 2019 20:42:40: start model_add_line... INFO @ Mon, 12 Aug 2019 20:42:40: start X-correlation... INFO @ Mon, 12 Aug 2019 20:42:40: end of X-cor INFO @ Mon, 12 Aug 2019 20:42:40: #2 finished! INFO @ Mon, 12 Aug 2019 20:42:40: #2 predicted fragment length is 356 bps INFO @ Mon, 12 Aug 2019 20:42:40: #2 alternative fragment length(s) may be 356 bps INFO @ Mon, 12 Aug 2019 20:42:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.20_model.r INFO @ Mon, 12 Aug 2019 20:42:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:42:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:42:44: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:42:44: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:42:44: #1 total tags in treatment: 14776791 INFO @ Mon, 12 Aug 2019 20:42:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:42:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:42:44: #1 tags after filtering in treatment: 14776791 INFO @ Mon, 12 Aug 2019 20:42:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:42:44: #1 finished! INFO @ Mon, 12 Aug 2019 20:42:44: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:42:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:42:46: #2 number of paired peaks: 2437 INFO @ Mon, 12 Aug 2019 20:42:46: start model_add_line... INFO @ Mon, 12 Aug 2019 20:42:46: start X-correlation... INFO @ Mon, 12 Aug 2019 20:42:46: end of X-cor INFO @ Mon, 12 Aug 2019 20:42:46: #2 finished! INFO @ Mon, 12 Aug 2019 20:42:46: #2 predicted fragment length is 356 bps INFO @ Mon, 12 Aug 2019 20:42:46: #2 alternative fragment length(s) may be 356 bps INFO @ Mon, 12 Aug 2019 20:42:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.05_model.r INFO @ Mon, 12 Aug 2019 20:42:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:42:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:43:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:43:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:43:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:43:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:43:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:43:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.10_summits.bed INFO @ Mon, 12 Aug 2019 20:43:47: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (9842 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:43:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:43:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:43:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.20_summits.bed INFO @ Mon, 12 Aug 2019 20:43:57: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6010 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:44:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:44:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:44:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX042251/SRX042251.05_summits.bed INFO @ Mon, 12 Aug 2019 20:44:11: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (13512 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。