Job ID = 4178547 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,877,859 reads read : 35,755,718 reads written : 17,877,859 reads 0-length : 17,877,859 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: 00:04:09 17877859 reads; of these: 17877859 (100.00%) were unpaired; of these: 3243175 (18.14%) aligned 0 times 12175855 (68.11%) aligned exactly 1 time 2458829 (13.75%) aligned >1 times 81.86% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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] 7574634 / 14634684 = 0.5176 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:05:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.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 @ Thu, 05 Dec 2019 13:05:42: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:05:42: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:05:48: 1000000 INFO @ Thu, 05 Dec 2019 13:05:54: 2000000 INFO @ Thu, 05 Dec 2019 13:05:59: 3000000 INFO @ Thu, 05 Dec 2019 13:06:05: 4000000 INFO @ Thu, 05 Dec 2019 13:06:10: 5000000 INFO @ Thu, 05 Dec 2019 13:06:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.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 @ Thu, 05 Dec 2019 13:06:12: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:06:12: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:06:16: 6000000 INFO @ Thu, 05 Dec 2019 13:06:18: 1000000 INFO @ Thu, 05 Dec 2019 13:06:22: 7000000 INFO @ Thu, 05 Dec 2019 13:06:23: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:06:23: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:06:23: #1 total tags in treatment: 7060050 INFO @ Thu, 05 Dec 2019 13:06:23: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:06:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:06:23: #1 tags after filtering in treatment: 7060050 INFO @ Thu, 05 Dec 2019 13:06:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:06:23: #1 finished! INFO @ Thu, 05 Dec 2019 13:06:23: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:06:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:06:23: #2 number of paired peaks: 460 WARNING @ Thu, 05 Dec 2019 13:06:23: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Thu, 05 Dec 2019 13:06:23: start model_add_line... INFO @ Thu, 05 Dec 2019 13:06:23: start X-correlation... INFO @ Thu, 05 Dec 2019 13:06:23: end of X-cor INFO @ Thu, 05 Dec 2019 13:06:23: #2 finished! INFO @ Thu, 05 Dec 2019 13:06:23: #2 predicted fragment length is 110 bps INFO @ Thu, 05 Dec 2019 13:06:23: #2 alternative fragment length(s) may be 110 bps INFO @ Thu, 05 Dec 2019 13:06:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.05_model.r INFO @ Thu, 05 Dec 2019 13:06:23: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:06:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:06:24: 2000000 INFO @ Thu, 05 Dec 2019 13:06:30: 3000000 INFO @ Thu, 05 Dec 2019 13:06:36: 4000000 INFO @ Thu, 05 Dec 2019 13:06:37: #3 Call peaks for each chromosome... BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:06:42: 5000000 INFO @ Thu, 05 Dec 2019 13:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.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 @ Thu, 05 Dec 2019 13:06:43: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:06:43: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:06:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:06:47: 6000000 INFO @ Thu, 05 Dec 2019 13:06:49: 1000000 INFO @ Thu, 05 Dec 2019 13:06:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:06:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.05_summits.bed INFO @ Thu, 05 Dec 2019 13:06:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2218 records, 4 fields): 66 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:06:53: 7000000 INFO @ Thu, 05 Dec 2019 13:06:53: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:06:53: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:06:53: #1 total tags in treatment: 7060050 INFO @ Thu, 05 Dec 2019 13:06:53: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:06:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:06:54: #1 tags after filtering in treatment: 7060050 INFO @ Thu, 05 Dec 2019 13:06:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:06:54: #1 finished! INFO @ Thu, 05 Dec 2019 13:06:54: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:06:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:06:54: #2 number of paired peaks: 460 WARNING @ Thu, 05 Dec 2019 13:06:54: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Thu, 05 Dec 2019 13:06:54: start model_add_line... INFO @ Thu, 05 Dec 2019 13:06:54: start X-correlation... INFO @ Thu, 05 Dec 2019 13:06:54: end of X-cor INFO @ Thu, 05 Dec 2019 13:06:54: #2 finished! INFO @ Thu, 05 Dec 2019 13:06:54: #2 predicted fragment length is 110 bps INFO @ Thu, 05 Dec 2019 13:06:54: #2 alternative fragment length(s) may be 110 bps INFO @ Thu, 05 Dec 2019 13:06:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.10_model.r INFO @ Thu, 05 Dec 2019 13:06:54: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:06:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:06:55: 2000000 INFO @ Thu, 05 Dec 2019 13:07:01: 3000000 INFO @ Thu, 05 Dec 2019 13:07:07: 4000000 INFO @ Thu, 05 Dec 2019 13:07:08: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:07:12: 5000000 INFO @ Thu, 05 Dec 2019 13:07:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:07:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:07:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.10_summits.bed INFO @ Thu, 05 Dec 2019 13:07:15: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1080 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:07:18: 6000000 INFO @ Thu, 05 Dec 2019 13:07:24: 7000000 INFO @ Thu, 05 Dec 2019 13:07:25: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:07:25: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:07:25: #1 total tags in treatment: 7060050 INFO @ Thu, 05 Dec 2019 13:07:25: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:07:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:07:25: #1 tags after filtering in treatment: 7060050 INFO @ Thu, 05 Dec 2019 13:07:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:07:25: #1 finished! INFO @ Thu, 05 Dec 2019 13:07:25: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:07:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:07:25: #2 number of paired peaks: 460 WARNING @ Thu, 05 Dec 2019 13:07:25: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Thu, 05 Dec 2019 13:07:25: start model_add_line... INFO @ Thu, 05 Dec 2019 13:07:25: start X-correlation... INFO @ Thu, 05 Dec 2019 13:07:25: end of X-cor INFO @ Thu, 05 Dec 2019 13:07:25: #2 finished! INFO @ Thu, 05 Dec 2019 13:07:25: #2 predicted fragment length is 110 bps INFO @ Thu, 05 Dec 2019 13:07:25: #2 alternative fragment length(s) may be 110 bps INFO @ Thu, 05 Dec 2019 13:07:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.20_model.r INFO @ Thu, 05 Dec 2019 13:07:25: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:07:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:07:39: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:07:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:07:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:07:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827819/SRX5827819.20_summits.bed INFO @ Thu, 05 Dec 2019 13:07:46: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (560 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。