Job ID = 2590667 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,584,442 reads read : 41,168,884 reads written : 20,584,442 reads 0-length : 20,584,442 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: 00:00:01 Multiseed full-index search: 00:08:06 20584442 reads; of these: 20584442 (100.00%) were unpaired; of these: 2013184 (9.78%) aligned 0 times 13772709 (66.91%) aligned exactly 1 time 4798549 (23.31%) aligned >1 times 90.22% overall alignment rate Time searching: 00:08:07 Overall time: 00:08:07 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] 9133679 / 18571258 = 0.4918 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 23:16:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.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 23:16:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:16:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:16:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.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 23:16:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:16:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:16:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.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 23:16:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:16:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:16:30: 1000000 INFO @ Mon, 12 Aug 2019 23:16:31: 1000000 INFO @ Mon, 12 Aug 2019 23:16:31: 1000000 INFO @ Mon, 12 Aug 2019 23:16:36: 2000000 INFO @ Mon, 12 Aug 2019 23:16:37: 2000000 INFO @ Mon, 12 Aug 2019 23:16:38: 2000000 INFO @ Mon, 12 Aug 2019 23:16:43: 3000000 INFO @ Mon, 12 Aug 2019 23:16:44: 3000000 INFO @ Mon, 12 Aug 2019 23:16:45: 3000000 INFO @ Mon, 12 Aug 2019 23:16:49: 4000000 INFO @ Mon, 12 Aug 2019 23:16:50: 4000000 INFO @ Mon, 12 Aug 2019 23:16:51: 4000000 INFO @ Mon, 12 Aug 2019 23:16:56: 5000000 INFO @ Mon, 12 Aug 2019 23:16:57: 5000000 INFO @ Mon, 12 Aug 2019 23:16:58: 5000000 INFO @ Mon, 12 Aug 2019 23:17:02: 6000000 INFO @ Mon, 12 Aug 2019 23:17:03: 6000000 INFO @ Mon, 12 Aug 2019 23:17:04: 6000000 INFO @ Mon, 12 Aug 2019 23:17:09: 7000000 INFO @ Mon, 12 Aug 2019 23:17:10: 7000000 INFO @ Mon, 12 Aug 2019 23:17:11: 7000000 INFO @ Mon, 12 Aug 2019 23:17:15: 8000000 INFO @ Mon, 12 Aug 2019 23:17:16: 8000000 INFO @ Mon, 12 Aug 2019 23:17:17: 8000000 INFO @ Mon, 12 Aug 2019 23:17:22: 9000000 INFO @ Mon, 12 Aug 2019 23:17:23: 9000000 INFO @ Mon, 12 Aug 2019 23:17:24: 9000000 INFO @ Mon, 12 Aug 2019 23:17:25: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:17:25: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:17:25: #1 total tags in treatment: 9437579 INFO @ Mon, 12 Aug 2019 23:17:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:17:25: #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 23:17:25: #1 tags after filtering in treatment: 9437579 INFO @ Mon, 12 Aug 2019 23:17:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:17:25: #1 finished! INFO @ Mon, 12 Aug 2019 23:17:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:17:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:17:26: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:17:26: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:17:26: #1 total tags in treatment: 9437579 INFO @ Mon, 12 Aug 2019 23:17:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:17:26: #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 23:17:26: #1 tags after filtering in treatment: 9437579 INFO @ Mon, 12 Aug 2019 23:17:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:17:26: #1 finished! INFO @ Mon, 12 Aug 2019 23:17:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:17:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:17:26: #2 number of paired peaks: 1574 INFO @ Mon, 12 Aug 2019 23:17:26: start model_add_line... INFO @ Mon, 12 Aug 2019 23:17:26: start X-correlation... INFO @ Mon, 12 Aug 2019 23:17:26: end of X-cor INFO @ Mon, 12 Aug 2019 23:17:26: #2 finished! INFO @ Mon, 12 Aug 2019 23:17:26: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 23:17:26: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 12 Aug 2019 23:17:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.05_model.r INFO @ Mon, 12 Aug 2019 23:17:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:17:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:17:27: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:17:27: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:17:27: #1 total tags in treatment: 9437579 INFO @ Mon, 12 Aug 2019 23:17:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:17:27: #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 23:17:27: #1 tags after filtering in treatment: 9437579 INFO @ Mon, 12 Aug 2019 23:17:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:17:27: #1 finished! INFO @ Mon, 12 Aug 2019 23:17:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:17:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:17:27: #2 number of paired peaks: 1574 INFO @ Mon, 12 Aug 2019 23:17:27: start model_add_line... INFO @ Mon, 12 Aug 2019 23:17:27: start X-correlation... INFO @ Mon, 12 Aug 2019 23:17:27: end of X-cor INFO @ Mon, 12 Aug 2019 23:17:27: #2 finished! INFO @ Mon, 12 Aug 2019 23:17:27: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 23:17:27: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 12 Aug 2019 23:17:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.10_model.r INFO @ Mon, 12 Aug 2019 23:17:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:17:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:17:28: #2 number of paired peaks: 1574 INFO @ Mon, 12 Aug 2019 23:17:28: start model_add_line... INFO @ Mon, 12 Aug 2019 23:17:28: start X-correlation... INFO @ Mon, 12 Aug 2019 23:17:28: end of X-cor INFO @ Mon, 12 Aug 2019 23:17:28: #2 finished! INFO @ Mon, 12 Aug 2019 23:17:28: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 23:17:28: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 12 Aug 2019 23:17:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.20_model.r INFO @ Mon, 12 Aug 2019 23:17:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:17:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:17:54: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:17:55: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:17:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:18:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:18:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:18:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.05_summits.bed INFO @ Mon, 12 Aug 2019 23:18:09: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8878 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:18:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:18:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:18:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.10_summits.bed INFO @ Mon, 12 Aug 2019 23:18:09: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5311 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:18:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:18:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:18:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011016/SRX5011016.20_summits.bed INFO @ Mon, 12 Aug 2019 23:18:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2532 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。