Job ID = 2590184 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,611,426 reads read : 22,611,426 reads written : 22,611,426 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: 00:06:01 22611426 reads; of these: 22611426 (100.00%) were unpaired; of these: 914884 (4.05%) aligned 0 times 17441508 (77.14%) aligned exactly 1 time 4255034 (18.82%) aligned >1 times 95.95% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 7458153 / 21696542 = 0.3437 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 20:16:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.bam'] # control file = None # effective genome size = 9.00e+07 # 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 20:16:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:16:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:16:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.bam'] # control file = None # effective genome size = 9.00e+07 # 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 20:16:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:16:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:16:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.bam'] # control file = None # effective genome size = 9.00e+07 # 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 20:16:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:16:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:16:18: 1000000 INFO @ Mon, 12 Aug 2019 20:16:20: 1000000 INFO @ Mon, 12 Aug 2019 20:16:21: 1000000 INFO @ Mon, 12 Aug 2019 20:16:26: 2000000 INFO @ Mon, 12 Aug 2019 20:16:29: 2000000 INFO @ Mon, 12 Aug 2019 20:16:31: 2000000 INFO @ Mon, 12 Aug 2019 20:16:35: 3000000 INFO @ Mon, 12 Aug 2019 20:16:37: 3000000 INFO @ Mon, 12 Aug 2019 20:16:41: 3000000 INFO @ Mon, 12 Aug 2019 20:16:43: 4000000 INFO @ Mon, 12 Aug 2019 20:16:46: 4000000 INFO @ Mon, 12 Aug 2019 20:16:51: 4000000 INFO @ Mon, 12 Aug 2019 20:16:52: 5000000 INFO @ Mon, 12 Aug 2019 20:16:54: 5000000 INFO @ Mon, 12 Aug 2019 20:17:00: 6000000 INFO @ Mon, 12 Aug 2019 20:17:01: 5000000 INFO @ Mon, 12 Aug 2019 20:17:03: 6000000 INFO @ Mon, 12 Aug 2019 20:17:09: 7000000 INFO @ Mon, 12 Aug 2019 20:17:11: 6000000 INFO @ Mon, 12 Aug 2019 20:17:11: 7000000 INFO @ Mon, 12 Aug 2019 20:17:17: 8000000 INFO @ Mon, 12 Aug 2019 20:17:20: 8000000 INFO @ Mon, 12 Aug 2019 20:17:21: 7000000 INFO @ Mon, 12 Aug 2019 20:17:25: 9000000 INFO @ Mon, 12 Aug 2019 20:17:28: 9000000 INFO @ Mon, 12 Aug 2019 20:17:31: 8000000 INFO @ Mon, 12 Aug 2019 20:17:34: 10000000 INFO @ Mon, 12 Aug 2019 20:17:36: 10000000 INFO @ Mon, 12 Aug 2019 20:17:41: 9000000 INFO @ Mon, 12 Aug 2019 20:17:42: 11000000 INFO @ Mon, 12 Aug 2019 20:17:45: 11000000 INFO @ Mon, 12 Aug 2019 20:17:51: 12000000 INFO @ Mon, 12 Aug 2019 20:17:51: 10000000 INFO @ Mon, 12 Aug 2019 20:17:53: 12000000 INFO @ Mon, 12 Aug 2019 20:17:59: 13000000 INFO @ Mon, 12 Aug 2019 20:18:01: 11000000 INFO @ Mon, 12 Aug 2019 20:18:02: 13000000 INFO @ Mon, 12 Aug 2019 20:18:07: 14000000 INFO @ Mon, 12 Aug 2019 20:18:10: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:18:10: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:18:10: #1 total tags in treatment: 14238389 INFO @ Mon, 12 Aug 2019 20:18:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:18:10: #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 20:18:10: #1 tags after filtering in treatment: 14238389 INFO @ Mon, 12 Aug 2019 20:18:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:18:10: #1 finished! INFO @ Mon, 12 Aug 2019 20:18:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:18:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:18:10: 14000000 INFO @ Mon, 12 Aug 2019 20:18:11: 12000000 INFO @ Mon, 12 Aug 2019 20:18:11: #2 number of paired peaks: 677 WARNING @ Mon, 12 Aug 2019 20:18:11: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Mon, 12 Aug 2019 20:18:11: start model_add_line... INFO @ Mon, 12 Aug 2019 20:18:11: start X-correlation... INFO @ Mon, 12 Aug 2019 20:18:11: end of X-cor INFO @ Mon, 12 Aug 2019 20:18:11: #2 finished! INFO @ Mon, 12 Aug 2019 20:18:11: #2 predicted fragment length is 117 bps INFO @ Mon, 12 Aug 2019 20:18:11: #2 alternative fragment length(s) may be 117 bps INFO @ Mon, 12 Aug 2019 20:18:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.05_model.r INFO @ Mon, 12 Aug 2019 20:18:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:18:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:18:12: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:18:12: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:18:12: #1 total tags in treatment: 14238389 INFO @ Mon, 12 Aug 2019 20:18:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:18:12: #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 20:18:12: #1 tags after filtering in treatment: 14238389 INFO @ Mon, 12 Aug 2019 20:18:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:18:12: #1 finished! INFO @ Mon, 12 Aug 2019 20:18:12: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:18:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:18:14: #2 number of paired peaks: 677 WARNING @ Mon, 12 Aug 2019 20:18:14: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Mon, 12 Aug 2019 20:18:14: start model_add_line... INFO @ Mon, 12 Aug 2019 20:18:14: start X-correlation... INFO @ Mon, 12 Aug 2019 20:18:14: end of X-cor INFO @ Mon, 12 Aug 2019 20:18:14: #2 finished! INFO @ Mon, 12 Aug 2019 20:18:14: #2 predicted fragment length is 117 bps INFO @ Mon, 12 Aug 2019 20:18:14: #2 alternative fragment length(s) may be 117 bps INFO @ Mon, 12 Aug 2019 20:18:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.20_model.r INFO @ Mon, 12 Aug 2019 20:18:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:18:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:18:20: 13000000 INFO @ Mon, 12 Aug 2019 20:18:29: 14000000 INFO @ Mon, 12 Aug 2019 20:18:32: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:18:32: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:18:32: #1 total tags in treatment: 14238389 INFO @ Mon, 12 Aug 2019 20:18:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:18:32: #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 20:18:32: #1 tags after filtering in treatment: 14238389 INFO @ Mon, 12 Aug 2019 20:18:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:18:32: #1 finished! INFO @ Mon, 12 Aug 2019 20:18:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:18:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:18:33: #2 number of paired peaks: 677 WARNING @ Mon, 12 Aug 2019 20:18:33: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Mon, 12 Aug 2019 20:18:33: start model_add_line... INFO @ Mon, 12 Aug 2019 20:18:33: start X-correlation... INFO @ Mon, 12 Aug 2019 20:18:33: end of X-cor INFO @ Mon, 12 Aug 2019 20:18:33: #2 finished! INFO @ Mon, 12 Aug 2019 20:18:33: #2 predicted fragment length is 117 bps INFO @ Mon, 12 Aug 2019 20:18:33: #2 alternative fragment length(s) may be 117 bps INFO @ Mon, 12 Aug 2019 20:18:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.10_model.r INFO @ Mon, 12 Aug 2019 20:18:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:18:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:18:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:18:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:19:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:19:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:19:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.05_summits.bed INFO @ Mon, 12 Aug 2019 20:19:07: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2639 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:19:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:19:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:19:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.20_summits.bed INFO @ Mon, 12 Aug 2019 20:19:09: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1165 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:19:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:19:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:19:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:19:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495072/SRX495072.10_summits.bed INFO @ Mon, 12 Aug 2019 20:19:29: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1808 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。