Job ID = 1292293 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,321,007 reads read : 4,321,007 reads written : 4,321,007 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:44 4321007 reads; of these: 4321007 (100.00%) were unpaired; of these: 741429 (17.16%) aligned 0 times 2948833 (68.24%) aligned exactly 1 time 630745 (14.60%) aligned >1 times 82.84% overall alignment rate Time searching: 00:00:44 Overall time: 00:00:44 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] 563863 / 3579578 = 0.1575 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 @ Sun, 02 Jun 2019 17:50:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.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 @ Sun, 02 Jun 2019 17:50:38: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:50:38: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:50:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.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 @ Sun, 02 Jun 2019 17:50:38: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:50:38: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:50:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.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 @ Sun, 02 Jun 2019 17:50:38: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:50:38: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:50:47: 1000000 INFO @ Sun, 02 Jun 2019 17:50:47: 1000000 INFO @ Sun, 02 Jun 2019 17:50:49: 1000000 INFO @ Sun, 02 Jun 2019 17:50:54: 2000000 INFO @ Sun, 02 Jun 2019 17:50:56: 2000000 INFO @ Sun, 02 Jun 2019 17:51:00: 2000000 INFO @ Sun, 02 Jun 2019 17:51:01: 3000000 INFO @ Sun, 02 Jun 2019 17:51:01: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:51:01: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:51:01: #1 total tags in treatment: 3015715 INFO @ Sun, 02 Jun 2019 17:51:01: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:51:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:51:02: #1 tags after filtering in treatment: 3015715 INFO @ Sun, 02 Jun 2019 17:51:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:51:02: #1 finished! INFO @ Sun, 02 Jun 2019 17:51:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:51:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:51:02: #2 number of paired peaks: 439 WARNING @ Sun, 02 Jun 2019 17:51:02: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Sun, 02 Jun 2019 17:51:02: start model_add_line... INFO @ Sun, 02 Jun 2019 17:51:02: start X-correlation... INFO @ Sun, 02 Jun 2019 17:51:02: end of X-cor INFO @ Sun, 02 Jun 2019 17:51:02: #2 finished! INFO @ Sun, 02 Jun 2019 17:51:02: #2 predicted fragment length is 95 bps INFO @ Sun, 02 Jun 2019 17:51:02: #2 alternative fragment length(s) may be 39,95,572 bps INFO @ Sun, 02 Jun 2019 17:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.10_model.r INFO @ Sun, 02 Jun 2019 17:51:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:51:04: 3000000 INFO @ Sun, 02 Jun 2019 17:51:04: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:51:04: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:51:04: #1 total tags in treatment: 3015715 INFO @ Sun, 02 Jun 2019 17:51:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:51:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:51:04: #1 tags after filtering in treatment: 3015715 INFO @ Sun, 02 Jun 2019 17:51:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:51:04: #1 finished! INFO @ Sun, 02 Jun 2019 17:51:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:51:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:51:05: #2 number of paired peaks: 439 WARNING @ Sun, 02 Jun 2019 17:51:05: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Sun, 02 Jun 2019 17:51:05: start model_add_line... INFO @ Sun, 02 Jun 2019 17:51:05: start X-correlation... INFO @ Sun, 02 Jun 2019 17:51:05: end of X-cor INFO @ Sun, 02 Jun 2019 17:51:05: #2 finished! INFO @ Sun, 02 Jun 2019 17:51:05: #2 predicted fragment length is 95 bps INFO @ Sun, 02 Jun 2019 17:51:05: #2 alternative fragment length(s) may be 39,95,572 bps INFO @ Sun, 02 Jun 2019 17:51:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.20_model.r INFO @ Sun, 02 Jun 2019 17:51:05: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:51:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:51:10: 3000000 INFO @ Sun, 02 Jun 2019 17:51:10: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:51:10: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:51:10: #1 total tags in treatment: 3015715 INFO @ Sun, 02 Jun 2019 17:51:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:51:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:51:10: #1 tags after filtering in treatment: 3015715 INFO @ Sun, 02 Jun 2019 17:51:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:51:10: #1 finished! INFO @ Sun, 02 Jun 2019 17:51:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:51:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:51:11: #2 number of paired peaks: 439 WARNING @ Sun, 02 Jun 2019 17:51:11: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Sun, 02 Jun 2019 17:51:11: start model_add_line... INFO @ Sun, 02 Jun 2019 17:51:11: start X-correlation... INFO @ Sun, 02 Jun 2019 17:51:11: end of X-cor INFO @ Sun, 02 Jun 2019 17:51:11: #2 finished! INFO @ Sun, 02 Jun 2019 17:51:11: #2 predicted fragment length is 95 bps INFO @ Sun, 02 Jun 2019 17:51:11: #2 alternative fragment length(s) may be 39,95,572 bps INFO @ Sun, 02 Jun 2019 17:51:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.05_model.r INFO @ Sun, 02 Jun 2019 17:51:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:51:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:51:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:51:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:51:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:51:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:51:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.10_summits.bed INFO @ Sun, 02 Jun 2019 17:51:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (322 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:51:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:51:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:51:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.20_summits.bed INFO @ Sun, 02 Jun 2019 17:51:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (128 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:51:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:51:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:51:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:51:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331320/SRX331320.05_summits.bed INFO @ Sun, 02 Jun 2019 17:51:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (581 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。