Job ID = 1292149 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,749,343 reads read : 2,749,343 reads written : 2,749,343 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: 00:00:32 2749343 reads; of these: 2749343 (100.00%) were unpaired; of these: 49231 (1.79%) aligned 0 times 2248665 (81.79%) aligned exactly 1 time 451447 (16.42%) aligned >1 times 98.21% overall alignment rate Time searching: 00:00:32 Overall time: 00:00:32 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] 157167 / 2700112 = 0.0582 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 17:33:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.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 17:33:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:33:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:33:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.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 17:33:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:33:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:33:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.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 17:33:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:33:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:33:36: 1000000 INFO @ Sun, 02 Jun 2019 17:33:37: 1000000 INFO @ Sun, 02 Jun 2019 17:33:37: 1000000 INFO @ Sun, 02 Jun 2019 17:33:47: 2000000 INFO @ Sun, 02 Jun 2019 17:33:48: 2000000 INFO @ Sun, 02 Jun 2019 17:33:48: 2000000 INFO @ Sun, 02 Jun 2019 17:33:53: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:33:53: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:33:53: #1 total tags in treatment: 2542945 INFO @ Sun, 02 Jun 2019 17:33:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:33:53: #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 17:33:53: #1 tags after filtering in treatment: 2542945 INFO @ Sun, 02 Jun 2019 17:33:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:33:53: #1 finished! INFO @ Sun, 02 Jun 2019 17:33:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:33:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:33:53: #2 number of paired peaks: 408 WARNING @ Sun, 02 Jun 2019 17:33:53: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Sun, 02 Jun 2019 17:33:53: start model_add_line... INFO @ Sun, 02 Jun 2019 17:33:53: start X-correlation... INFO @ Sun, 02 Jun 2019 17:33:53: end of X-cor INFO @ Sun, 02 Jun 2019 17:33:53: #2 finished! INFO @ Sun, 02 Jun 2019 17:33:53: #2 predicted fragment length is 32 bps INFO @ Sun, 02 Jun 2019 17:33:53: #2 alternative fragment length(s) may be 32,518,566 bps INFO @ Sun, 02 Jun 2019 17:33:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.10_model.r WARNING @ Sun, 02 Jun 2019 17:33:53: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:33:53: #2 You may need to consider one of the other alternative d(s): 32,518,566 WARNING @ Sun, 02 Jun 2019 17:33:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:33:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:33:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:33:53: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:33:53: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:33:53: #1 total tags in treatment: 2542945 INFO @ Sun, 02 Jun 2019 17:33:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:33:53: #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 17:33:53: #1 tags after filtering in treatment: 2542945 INFO @ Sun, 02 Jun 2019 17:33:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:33:53: #1 finished! INFO @ Sun, 02 Jun 2019 17:33:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:33:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:33:54: #2 number of paired peaks: 408 WARNING @ Sun, 02 Jun 2019 17:33:54: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Sun, 02 Jun 2019 17:33:54: start model_add_line... INFO @ Sun, 02 Jun 2019 17:33:54: start X-correlation... INFO @ Sun, 02 Jun 2019 17:33:54: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:33:54: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:33:54: #1 total tags in treatment: 2542945 INFO @ Sun, 02 Jun 2019 17:33:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:33:54: #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 17:33:54: end of X-cor INFO @ Sun, 02 Jun 2019 17:33:54: #2 finished! INFO @ Sun, 02 Jun 2019 17:33:54: #2 predicted fragment length is 32 bps INFO @ Sun, 02 Jun 2019 17:33:54: #2 alternative fragment length(s) may be 32,518,566 bps INFO @ Sun, 02 Jun 2019 17:33:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.20_model.r WARNING @ Sun, 02 Jun 2019 17:33:54: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:33:54: #2 You may need to consider one of the other alternative d(s): 32,518,566 WARNING @ Sun, 02 Jun 2019 17:33:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:33:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:33:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:33:54: #1 tags after filtering in treatment: 2542945 INFO @ Sun, 02 Jun 2019 17:33:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:33:54: #1 finished! INFO @ Sun, 02 Jun 2019 17:33:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:33:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:33:54: #2 number of paired peaks: 408 WARNING @ Sun, 02 Jun 2019 17:33:54: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Sun, 02 Jun 2019 17:33:54: start model_add_line... INFO @ Sun, 02 Jun 2019 17:33:54: start X-correlation... INFO @ Sun, 02 Jun 2019 17:33:54: end of X-cor INFO @ Sun, 02 Jun 2019 17:33:54: #2 finished! INFO @ Sun, 02 Jun 2019 17:33:54: #2 predicted fragment length is 32 bps INFO @ Sun, 02 Jun 2019 17:33:54: #2 alternative fragment length(s) may be 32,518,566 bps INFO @ Sun, 02 Jun 2019 17:33:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.05_model.r WARNING @ Sun, 02 Jun 2019 17:33:54: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:33:54: #2 You may need to consider one of the other alternative d(s): 32,518,566 WARNING @ Sun, 02 Jun 2019 17:33:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:33:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:33:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:34:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:34:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:34:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:34:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:34:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:34:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.10_summits.bed INFO @ Sun, 02 Jun 2019 17:34:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:34:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:34:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:34:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.20_summits.bed INFO @ Sun, 02 Jun 2019 17:34:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (49 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:34:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:34:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:34:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331187/SRX331187.05_summits.bed INFO @ Sun, 02 Jun 2019 17:34:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (279 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。