Job ID = 2590661 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,869,632 reads read : 43,739,264 reads written : 21,869,632 reads 0-length : 21,869,632 rm: cannot remove ‘[DSE]RR*’: 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: 00:07:35 21869632 reads; of these: 21869632 (100.00%) were unpaired; of these: 1667392 (7.62%) aligned 0 times 15851105 (72.48%) aligned exactly 1 time 4351135 (19.90%) aligned >1 times 92.38% overall alignment rate Time searching: 00:07:35 Overall time: 00:07:35 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 12 files... [bam_rmdupse_core] 9546900 / 20202240 = 0.4726 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 23:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.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 23:14:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:14:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:14:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.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 23:14:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:14:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:14:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.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 23:14:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:14:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:14:41: 1000000 INFO @ Mon, 12 Aug 2019 23:14:43: 1000000 INFO @ Mon, 12 Aug 2019 23:14:45: 1000000 INFO @ Mon, 12 Aug 2019 23:14:48: 2000000 INFO @ Mon, 12 Aug 2019 23:14:50: 2000000 INFO @ Mon, 12 Aug 2019 23:14:53: 2000000 INFO @ Mon, 12 Aug 2019 23:14:55: 3000000 INFO @ Mon, 12 Aug 2019 23:14:58: 3000000 INFO @ Mon, 12 Aug 2019 23:15:01: 3000000 INFO @ Mon, 12 Aug 2019 23:15:02: 4000000 INFO @ Mon, 12 Aug 2019 23:15:05: 4000000 INFO @ Mon, 12 Aug 2019 23:15:09: 4000000 INFO @ Mon, 12 Aug 2019 23:15:09: 5000000 INFO @ Mon, 12 Aug 2019 23:15:13: 5000000 INFO @ Mon, 12 Aug 2019 23:15:16: 6000000 INFO @ Mon, 12 Aug 2019 23:15:17: 5000000 INFO @ Mon, 12 Aug 2019 23:15:20: 6000000 INFO @ Mon, 12 Aug 2019 23:15:23: 7000000 INFO @ Mon, 12 Aug 2019 23:15:25: 6000000 INFO @ Mon, 12 Aug 2019 23:15:28: 7000000 INFO @ Mon, 12 Aug 2019 23:15:30: 8000000 INFO @ Mon, 12 Aug 2019 23:15:33: 7000000 INFO @ Mon, 12 Aug 2019 23:15:35: 8000000 INFO @ Mon, 12 Aug 2019 23:15:37: 9000000 INFO @ Mon, 12 Aug 2019 23:15:42: 8000000 INFO @ Mon, 12 Aug 2019 23:15:43: 9000000 INFO @ Mon, 12 Aug 2019 23:15:44: 10000000 INFO @ Mon, 12 Aug 2019 23:15:49: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:15:49: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:15:49: #1 total tags in treatment: 10655340 INFO @ Mon, 12 Aug 2019 23:15:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:15:49: #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 23:15:49: #1 tags after filtering in treatment: 10655340 INFO @ Mon, 12 Aug 2019 23:15:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:15:49: #1 finished! INFO @ Mon, 12 Aug 2019 23:15:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:15:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:15:50: 9000000 INFO @ Mon, 12 Aug 2019 23:15:50: 10000000 INFO @ Mon, 12 Aug 2019 23:15:50: #2 number of paired peaks: 2802 INFO @ Mon, 12 Aug 2019 23:15:50: start model_add_line... INFO @ Mon, 12 Aug 2019 23:15:50: start X-correlation... INFO @ Mon, 12 Aug 2019 23:15:50: end of X-cor INFO @ Mon, 12 Aug 2019 23:15:50: #2 finished! INFO @ Mon, 12 Aug 2019 23:15:50: #2 predicted fragment length is 217 bps INFO @ Mon, 12 Aug 2019 23:15:50: #2 alternative fragment length(s) may be 217 bps INFO @ Mon, 12 Aug 2019 23:15:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.05_model.r INFO @ Mon, 12 Aug 2019 23:15:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:15:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:15:55: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:15:55: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:15:55: #1 total tags in treatment: 10655340 INFO @ Mon, 12 Aug 2019 23:15:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:15:55: #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 23:15:55: #1 tags after filtering in treatment: 10655340 INFO @ Mon, 12 Aug 2019 23:15:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:15:55: #1 finished! INFO @ Mon, 12 Aug 2019 23:15:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:15:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:15:56: #2 number of paired peaks: 2802 INFO @ Mon, 12 Aug 2019 23:15:56: start model_add_line... INFO @ Mon, 12 Aug 2019 23:15:57: start X-correlation... INFO @ Mon, 12 Aug 2019 23:15:57: end of X-cor INFO @ Mon, 12 Aug 2019 23:15:57: #2 finished! INFO @ Mon, 12 Aug 2019 23:15:57: #2 predicted fragment length is 217 bps INFO @ Mon, 12 Aug 2019 23:15:57: #2 alternative fragment length(s) may be 217 bps INFO @ Mon, 12 Aug 2019 23:15:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.10_model.r INFO @ Mon, 12 Aug 2019 23:15:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:15:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:15:58: 10000000 INFO @ Mon, 12 Aug 2019 23:16:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:16:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:16:03: #1 total tags in treatment: 10655340 INFO @ Mon, 12 Aug 2019 23:16:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:16:03: #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 23:16:03: #1 tags after filtering in treatment: 10655340 INFO @ Mon, 12 Aug 2019 23:16:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:16:03: #1 finished! INFO @ Mon, 12 Aug 2019 23:16:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:16:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:16:04: #2 number of paired peaks: 2802 INFO @ Mon, 12 Aug 2019 23:16:04: start model_add_line... INFO @ Mon, 12 Aug 2019 23:16:05: start X-correlation... INFO @ Mon, 12 Aug 2019 23:16:05: end of X-cor INFO @ Mon, 12 Aug 2019 23:16:05: #2 finished! INFO @ Mon, 12 Aug 2019 23:16:05: #2 predicted fragment length is 217 bps INFO @ Mon, 12 Aug 2019 23:16:05: #2 alternative fragment length(s) may be 217 bps INFO @ Mon, 12 Aug 2019 23:16:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.20_model.r INFO @ Mon, 12 Aug 2019 23:16:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:16:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:16:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:16:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:16:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:16:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:16:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:16:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.05_summits.bed INFO @ Mon, 12 Aug 2019 23:16:42: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10191 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:16:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:16:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:16:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.10_summits.bed INFO @ Mon, 12 Aug 2019 23:16:48: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7321 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:16:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:16:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:16:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011012/SRX5011012.20_summits.bed INFO @ Mon, 12 Aug 2019 23:16:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4350 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。