Job ID = 2589921 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,605,956 reads read : 5,605,956 reads written : 5,605,956 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947565.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: 00:00:59 5605956 reads; of these: 5605956 (100.00%) were unpaired; of these: 449112 (8.01%) aligned 0 times 4354396 (77.67%) aligned exactly 1 time 802448 (14.31%) aligned >1 times 91.99% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 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] 1038145 / 5156844 = 0.2013 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 18:47:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.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 18:47:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:47:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:47:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.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 18:47:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:47:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:47:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.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 18:47:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:47:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:47:55: 1000000 INFO @ Mon, 12 Aug 2019 18:47:56: 1000000 INFO @ Mon, 12 Aug 2019 18:47:57: 1000000 INFO @ Mon, 12 Aug 2019 18:48:02: 2000000 INFO @ Mon, 12 Aug 2019 18:48:03: 2000000 INFO @ Mon, 12 Aug 2019 18:48:04: 2000000 INFO @ Mon, 12 Aug 2019 18:48:09: 3000000 INFO @ Mon, 12 Aug 2019 18:48:10: 3000000 INFO @ Mon, 12 Aug 2019 18:48:11: 3000000 INFO @ Mon, 12 Aug 2019 18:48:16: 4000000 INFO @ Mon, 12 Aug 2019 18:48:16: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:48:16: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:48:16: #1 total tags in treatment: 4118699 INFO @ Mon, 12 Aug 2019 18:48:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:48:16: #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 18:48:16: #1 tags after filtering in treatment: 4118699 INFO @ Mon, 12 Aug 2019 18:48:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:48:16: #1 finished! INFO @ Mon, 12 Aug 2019 18:48:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:48:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:48:17: 4000000 INFO @ Mon, 12 Aug 2019 18:48:17: #2 number of paired peaks: 874 WARNING @ Mon, 12 Aug 2019 18:48:17: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Mon, 12 Aug 2019 18:48:17: start model_add_line... INFO @ Mon, 12 Aug 2019 18:48:17: start X-correlation... INFO @ Mon, 12 Aug 2019 18:48:17: end of X-cor INFO @ Mon, 12 Aug 2019 18:48:17: #2 finished! INFO @ Mon, 12 Aug 2019 18:48:17: #2 predicted fragment length is 168 bps INFO @ Mon, 12 Aug 2019 18:48:17: #2 alternative fragment length(s) may be 168 bps INFO @ Mon, 12 Aug 2019 18:48:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.05_model.r INFO @ Mon, 12 Aug 2019 18:48:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:48:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:48:17: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:48:17: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:48:17: #1 total tags in treatment: 4118699 INFO @ Mon, 12 Aug 2019 18:48:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:48:17: #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 18:48:17: #1 tags after filtering in treatment: 4118699 INFO @ Mon, 12 Aug 2019 18:48:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:48:17: #1 finished! INFO @ Mon, 12 Aug 2019 18:48:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:48:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:48:18: 4000000 INFO @ Mon, 12 Aug 2019 18:48:18: #2 number of paired peaks: 874 WARNING @ Mon, 12 Aug 2019 18:48:18: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Mon, 12 Aug 2019 18:48:18: start model_add_line... INFO @ Mon, 12 Aug 2019 18:48:18: start X-correlation... INFO @ Mon, 12 Aug 2019 18:48:18: end of X-cor INFO @ Mon, 12 Aug 2019 18:48:18: #2 finished! INFO @ Mon, 12 Aug 2019 18:48:18: #2 predicted fragment length is 168 bps INFO @ Mon, 12 Aug 2019 18:48:18: #2 alternative fragment length(s) may be 168 bps INFO @ Mon, 12 Aug 2019 18:48:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.10_model.r INFO @ Mon, 12 Aug 2019 18:48:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:48:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:48:18: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:48:18: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:48:18: #1 total tags in treatment: 4118699 INFO @ Mon, 12 Aug 2019 18:48:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:48:18: #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 18:48:18: #1 tags after filtering in treatment: 4118699 INFO @ Mon, 12 Aug 2019 18:48:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:48:18: #1 finished! INFO @ Mon, 12 Aug 2019 18:48:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:48:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:48:19: #2 number of paired peaks: 874 WARNING @ Mon, 12 Aug 2019 18:48:19: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Mon, 12 Aug 2019 18:48:19: start model_add_line... INFO @ Mon, 12 Aug 2019 18:48:19: start X-correlation... INFO @ Mon, 12 Aug 2019 18:48:19: end of X-cor INFO @ Mon, 12 Aug 2019 18:48:19: #2 finished! INFO @ Mon, 12 Aug 2019 18:48:19: #2 predicted fragment length is 168 bps INFO @ Mon, 12 Aug 2019 18:48:19: #2 alternative fragment length(s) may be 168 bps INFO @ Mon, 12 Aug 2019 18:48:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.20_model.r INFO @ Mon, 12 Aug 2019 18:48:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:48:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:48:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:48:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:48:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:48:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:48:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:48:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.05_summits.bed INFO @ Mon, 12 Aug 2019 18:48:36: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3387 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:48:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:48:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:48:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.10_summits.bed INFO @ Mon, 12 Aug 2019 18:48:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2083 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:48:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:48:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:48:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331328/SRX331328.20_summits.bed INFO @ Mon, 12 Aug 2019 18:48:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (964 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。