Job ID = 2589645 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,741,029 reads read : 5,741,029 reads written : 5,741,029 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:52 5741029 reads; of these: 5741029 (100.00%) were unpaired; of these: 1110395 (19.34%) aligned 0 times 3949083 (68.79%) aligned exactly 1 time 681551 (11.87%) aligned >1 times 80.66% overall alignment rate Time searching: 00:00:53 Overall time: 00:00:53 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] 480108 / 4630634 = 0.1037 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 18:11:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.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 18:11:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:11:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:11:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.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 18:11:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:11:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:11:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.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 18:11:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:11:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:11:53: 1000000 INFO @ Mon, 12 Aug 2019 18:11:54: 1000000 INFO @ Mon, 12 Aug 2019 18:11:56: 1000000 INFO @ Mon, 12 Aug 2019 18:12:00: 2000000 INFO @ Mon, 12 Aug 2019 18:12:03: 2000000 INFO @ Mon, 12 Aug 2019 18:12:05: 2000000 INFO @ Mon, 12 Aug 2019 18:12:06: 3000000 INFO @ Mon, 12 Aug 2019 18:12:12: 3000000 INFO @ Mon, 12 Aug 2019 18:12:13: 4000000 INFO @ Mon, 12 Aug 2019 18:12:14: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:12:14: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:12:14: #1 total tags in treatment: 4150526 INFO @ Mon, 12 Aug 2019 18:12:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:12:14: #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 18:12:14: #1 tags after filtering in treatment: 4150526 INFO @ Mon, 12 Aug 2019 18:12:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:12:14: #1 finished! INFO @ Mon, 12 Aug 2019 18:12:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:12:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:12:15: #2 number of paired peaks: 924 WARNING @ Mon, 12 Aug 2019 18:12:15: Fewer paired peaks (924) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 924 pairs to build model! INFO @ Mon, 12 Aug 2019 18:12:15: start model_add_line... INFO @ Mon, 12 Aug 2019 18:12:15: start X-correlation... INFO @ Mon, 12 Aug 2019 18:12:15: end of X-cor INFO @ Mon, 12 Aug 2019 18:12:15: #2 finished! INFO @ Mon, 12 Aug 2019 18:12:15: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 18:12:15: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 12 Aug 2019 18:12:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.10_model.r INFO @ Mon, 12 Aug 2019 18:12:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:12:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:12:15: 3000000 INFO @ Mon, 12 Aug 2019 18:12:21: 4000000 INFO @ Mon, 12 Aug 2019 18:12:22: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:12:22: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:12:22: #1 total tags in treatment: 4150526 INFO @ Mon, 12 Aug 2019 18:12:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:12:22: #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 18:12:22: #1 tags after filtering in treatment: 4150526 INFO @ Mon, 12 Aug 2019 18:12:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:12:22: #1 finished! INFO @ Mon, 12 Aug 2019 18:12:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:12:23: #2 number of paired peaks: 924 WARNING @ Mon, 12 Aug 2019 18:12:23: Fewer paired peaks (924) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 924 pairs to build model! INFO @ Mon, 12 Aug 2019 18:12:23: start model_add_line... INFO @ Mon, 12 Aug 2019 18:12:23: start X-correlation... INFO @ Mon, 12 Aug 2019 18:12:23: end of X-cor INFO @ Mon, 12 Aug 2019 18:12:23: #2 finished! INFO @ Mon, 12 Aug 2019 18:12:23: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 18:12:23: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 12 Aug 2019 18:12:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.05_model.r INFO @ Mon, 12 Aug 2019 18:12:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:12:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:12:23: 4000000 INFO @ Mon, 12 Aug 2019 18:12:24: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:12:24: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:12:24: #1 total tags in treatment: 4150526 INFO @ Mon, 12 Aug 2019 18:12:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:12:24: #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 18:12:25: #1 tags after filtering in treatment: 4150526 INFO @ Mon, 12 Aug 2019 18:12:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:12:25: #1 finished! INFO @ Mon, 12 Aug 2019 18:12:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:12:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:12:25: #2 number of paired peaks: 924 WARNING @ Mon, 12 Aug 2019 18:12:25: Fewer paired peaks (924) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 924 pairs to build model! INFO @ Mon, 12 Aug 2019 18:12:25: start model_add_line... INFO @ Mon, 12 Aug 2019 18:12:25: start X-correlation... INFO @ Mon, 12 Aug 2019 18:12:25: end of X-cor INFO @ Mon, 12 Aug 2019 18:12:25: #2 finished! INFO @ Mon, 12 Aug 2019 18:12:25: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 18:12:25: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 12 Aug 2019 18:12:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.20_model.r INFO @ Mon, 12 Aug 2019 18:12:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:12:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:12:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:12:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:12:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:12:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.10_summits.bed INFO @ Mon, 12 Aug 2019 18:12:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1916 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:12:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:12:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:12:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:12:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:12:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.05_summits.bed INFO @ Mon, 12 Aug 2019 18:12:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3354 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:12:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:12:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:12:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277089/SRX277089.20_summits.bed INFO @ Mon, 12 Aug 2019 18:12:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (850 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。