Job ID = 2589809 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,507,231 reads read : 6,507,231 reads written : 6,507,231 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947440.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: 00:00:54 6507231 reads; of these: 6507231 (100.00%) were unpaired; of these: 2123239 (32.63%) aligned 0 times 3739123 (57.46%) aligned exactly 1 time 644869 (9.91%) aligned >1 times 67.37% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 485786 / 4383992 = 0.1108 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 18:32:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.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 18:32:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:32:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:32:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.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 18:32:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:32:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:32:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.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 18:32:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:32:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:32:22: 1000000 INFO @ Mon, 12 Aug 2019 18:32:24: 1000000 INFO @ Mon, 12 Aug 2019 18:32:26: 1000000 INFO @ Mon, 12 Aug 2019 18:32:30: 2000000 INFO @ Mon, 12 Aug 2019 18:32:32: 2000000 INFO @ Mon, 12 Aug 2019 18:32:35: 2000000 INFO @ Mon, 12 Aug 2019 18:32:38: 3000000 INFO @ Mon, 12 Aug 2019 18:32:40: 3000000 INFO @ Mon, 12 Aug 2019 18:32:45: 3000000 INFO @ Mon, 12 Aug 2019 18:32:45: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:32:45: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:32:45: #1 total tags in treatment: 3898206 INFO @ Mon, 12 Aug 2019 18:32:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:32:45: #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 18:32:45: #1 tags after filtering in treatment: 3898206 INFO @ Mon, 12 Aug 2019 18:32:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:32:45: #1 finished! INFO @ Mon, 12 Aug 2019 18:32:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:32:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:32:46: #2 number of paired peaks: 704 WARNING @ Mon, 12 Aug 2019 18:32:46: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Mon, 12 Aug 2019 18:32:46: start model_add_line... INFO @ Mon, 12 Aug 2019 18:32:46: start X-correlation... INFO @ Mon, 12 Aug 2019 18:32:46: end of X-cor INFO @ Mon, 12 Aug 2019 18:32:46: #2 finished! INFO @ Mon, 12 Aug 2019 18:32:46: #2 predicted fragment length is 160 bps INFO @ Mon, 12 Aug 2019 18:32:46: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 12 Aug 2019 18:32:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.05_model.r INFO @ Mon, 12 Aug 2019 18:32:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:32:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:32:46: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:32:46: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:32:46: #1 total tags in treatment: 3898206 INFO @ Mon, 12 Aug 2019 18:32:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:32:46: #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 18:32:46: #1 tags after filtering in treatment: 3898206 INFO @ Mon, 12 Aug 2019 18:32:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:32:46: #1 finished! INFO @ Mon, 12 Aug 2019 18:32:46: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:32:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:32:47: #2 number of paired peaks: 704 WARNING @ Mon, 12 Aug 2019 18:32:47: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Mon, 12 Aug 2019 18:32:47: start model_add_line... INFO @ Mon, 12 Aug 2019 18:32:47: start X-correlation... INFO @ Mon, 12 Aug 2019 18:32:47: end of X-cor INFO @ Mon, 12 Aug 2019 18:32:47: #2 finished! INFO @ Mon, 12 Aug 2019 18:32:47: #2 predicted fragment length is 160 bps INFO @ Mon, 12 Aug 2019 18:32:47: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 12 Aug 2019 18:32:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.10_model.r INFO @ Mon, 12 Aug 2019 18:32:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:32:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:32:52: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:32:52: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:32:52: #1 total tags in treatment: 3898206 INFO @ Mon, 12 Aug 2019 18:32:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:32:52: #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 18:32:53: #1 tags after filtering in treatment: 3898206 INFO @ Mon, 12 Aug 2019 18:32:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:32:53: #1 finished! INFO @ Mon, 12 Aug 2019 18:32:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:32:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:32:53: #2 number of paired peaks: 704 WARNING @ Mon, 12 Aug 2019 18:32:53: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Mon, 12 Aug 2019 18:32:53: start model_add_line... INFO @ Mon, 12 Aug 2019 18:32:53: start X-correlation... INFO @ Mon, 12 Aug 2019 18:32:53: end of X-cor INFO @ Mon, 12 Aug 2019 18:32:53: #2 finished! INFO @ Mon, 12 Aug 2019 18:32:53: #2 predicted fragment length is 160 bps INFO @ Mon, 12 Aug 2019 18:32:53: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 12 Aug 2019 18:32:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.20_model.r INFO @ Mon, 12 Aug 2019 18:32:53: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:32:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:32:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:32:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:33:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:33:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:33:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.05_summits.bed INFO @ Mon, 12 Aug 2019 18:33:04: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2607 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:33:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:33:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:33:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.10_summits.bed INFO @ Mon, 12 Aug 2019 18:33:05: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1282 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:33:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:33:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:33:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:33:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331208/SRX331208.20_summits.bed INFO @ Mon, 12 Aug 2019 18:33:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (473 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。