Job ID = 2589273 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,765,642 reads read : 8,765,642 reads written : 8,765,642 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR217347.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: 00:01:12 8765642 reads; of these: 8765642 (100.00%) were unpaired; of these: 2859025 (32.62%) aligned 0 times 5010300 (57.16%) aligned exactly 1 time 896317 (10.23%) aligned >1 times 67.38% overall alignment rate Time searching: 00:01:12 Overall time: 00:01:12 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_rmdupse_core] 1019125 / 5906617 = 0.1725 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 17:19:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.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 17:19:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:19:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:19:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.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 17:19:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:19:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:19:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.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 17:19:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:19:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:20:06: 1000000 INFO @ Mon, 12 Aug 2019 17:20:08: 1000000 INFO @ Mon, 12 Aug 2019 17:20:08: 1000000 INFO @ Mon, 12 Aug 2019 17:20:15: 2000000 INFO @ Mon, 12 Aug 2019 17:20:17: 2000000 INFO @ Mon, 12 Aug 2019 17:20:17: 2000000 INFO @ Mon, 12 Aug 2019 17:20:25: 3000000 INFO @ Mon, 12 Aug 2019 17:20:25: 3000000 INFO @ Mon, 12 Aug 2019 17:20:26: 3000000 INFO @ Mon, 12 Aug 2019 17:20:34: 4000000 INFO @ Mon, 12 Aug 2019 17:20:34: 4000000 INFO @ Mon, 12 Aug 2019 17:20:35: 4000000 INFO @ Mon, 12 Aug 2019 17:20:42: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:20:42: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:20:42: #1 total tags in treatment: 4887492 INFO @ Mon, 12 Aug 2019 17:20:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:20:42: #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 17:20:42: #1 tags after filtering in treatment: 4887492 INFO @ Mon, 12 Aug 2019 17:20:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:20:42: #1 finished! INFO @ Mon, 12 Aug 2019 17:20:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:20:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:20:42: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:20:42: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:20:42: #1 total tags in treatment: 4887492 INFO @ Mon, 12 Aug 2019 17:20:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:20:42: #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 17:20:42: #1 tags after filtering in treatment: 4887492 INFO @ Mon, 12 Aug 2019 17:20:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:20:42: #1 finished! INFO @ Mon, 12 Aug 2019 17:20:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:20:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:20:42: #2 number of paired peaks: 391 WARNING @ Mon, 12 Aug 2019 17:20:42: Fewer paired peaks (391) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 391 pairs to build model! INFO @ Mon, 12 Aug 2019 17:20:42: start model_add_line... INFO @ Mon, 12 Aug 2019 17:20:42: start X-correlation... INFO @ Mon, 12 Aug 2019 17:20:42: end of X-cor INFO @ Mon, 12 Aug 2019 17:20:42: #2 finished! INFO @ Mon, 12 Aug 2019 17:20:42: #2 predicted fragment length is 77 bps INFO @ Mon, 12 Aug 2019 17:20:42: #2 alternative fragment length(s) may be 4,77 bps INFO @ Mon, 12 Aug 2019 17:20:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.20_model.r INFO @ Mon, 12 Aug 2019 17:20:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:20:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:20:42: #2 number of paired peaks: 391 WARNING @ Mon, 12 Aug 2019 17:20:42: Fewer paired peaks (391) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 391 pairs to build model! INFO @ Mon, 12 Aug 2019 17:20:42: start model_add_line... INFO @ Mon, 12 Aug 2019 17:20:43: start X-correlation... INFO @ Mon, 12 Aug 2019 17:20:43: end of X-cor INFO @ Mon, 12 Aug 2019 17:20:43: #2 finished! INFO @ Mon, 12 Aug 2019 17:20:43: #2 predicted fragment length is 77 bps INFO @ Mon, 12 Aug 2019 17:20:43: #2 alternative fragment length(s) may be 4,77 bps INFO @ Mon, 12 Aug 2019 17:20:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.05_model.r INFO @ Mon, 12 Aug 2019 17:20:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:20:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:20:43: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:20:43: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:20:43: #1 total tags in treatment: 4887492 INFO @ Mon, 12 Aug 2019 17:20:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:20:43: #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 17:20:43: #1 tags after filtering in treatment: 4887492 INFO @ Mon, 12 Aug 2019 17:20:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:20:43: #1 finished! INFO @ Mon, 12 Aug 2019 17:20:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:20:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:20:44: #2 number of paired peaks: 391 WARNING @ Mon, 12 Aug 2019 17:20:44: Fewer paired peaks (391) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 391 pairs to build model! INFO @ Mon, 12 Aug 2019 17:20:44: start model_add_line... INFO @ Mon, 12 Aug 2019 17:20:44: start X-correlation... INFO @ Mon, 12 Aug 2019 17:20:44: end of X-cor INFO @ Mon, 12 Aug 2019 17:20:44: #2 finished! INFO @ Mon, 12 Aug 2019 17:20:44: #2 predicted fragment length is 77 bps INFO @ Mon, 12 Aug 2019 17:20:44: #2 alternative fragment length(s) may be 4,77 bps INFO @ Mon, 12 Aug 2019 17:20:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.10_model.r INFO @ Mon, 12 Aug 2019 17:20:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:20:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:20:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:20:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:20:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:21:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:21:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:21:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.20_summits.bed INFO @ Mon, 12 Aug 2019 17:21:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (126 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:21:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:21:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:21:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.05_summits.bed INFO @ Mon, 12 Aug 2019 17:21:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1589 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:21:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:21:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:21:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065641/SRX065641.10_summits.bed INFO @ Mon, 12 Aug 2019 17:21:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (510 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。