Job ID = 2589165 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,303,542 reads read : 3,303,542 reads written : 3,303,542 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107548.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: 00:00:20 3303542 reads; of these: 3303542 (100.00%) were unpaired; of these: 2878654 (87.14%) aligned 0 times 371204 (11.24%) aligned exactly 1 time 53684 (1.63%) aligned >1 times 12.86% overall alignment rate Time searching: 00:00:20 Overall time: 00:00:20 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] 7679 / 424888 = 0.0181 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 17:02:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.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 17:02:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:02:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:02:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.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 17:02:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:02:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:02:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.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 17:02:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:02:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:02:46: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:02:46: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:02:46: #1 total tags in treatment: 417209 INFO @ Mon, 12 Aug 2019 17:02:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:02:46: #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 17:02:46: #1 tags after filtering in treatment: 417209 INFO @ Mon, 12 Aug 2019 17:02:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:02:46: #1 finished! INFO @ Mon, 12 Aug 2019 17:02:46: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:02:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:02:46: #2 number of paired peaks: 183 WARNING @ Mon, 12 Aug 2019 17:02:46: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Mon, 12 Aug 2019 17:02:46: start model_add_line... INFO @ Mon, 12 Aug 2019 17:02:46: start X-correlation... INFO @ Mon, 12 Aug 2019 17:02:47: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:02:47: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:02:47: #1 total tags in treatment: 417209 INFO @ Mon, 12 Aug 2019 17:02:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:02:47: #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 17:02:47: end of X-cor INFO @ Mon, 12 Aug 2019 17:02:47: #2 finished! INFO @ Mon, 12 Aug 2019 17:02:47: #2 predicted fragment length is 39 bps INFO @ Mon, 12 Aug 2019 17:02:47: #2 alternative fragment length(s) may be 39,64,149,199,226,260,291,352,409,437,463,532,552,586 bps INFO @ Mon, 12 Aug 2019 17:02:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.05_model.r INFO @ Mon, 12 Aug 2019 17:02:47: #1 tags after filtering in treatment: 417209 INFO @ Mon, 12 Aug 2019 17:02:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:02:47: #1 finished! INFO @ Mon, 12 Aug 2019 17:02:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:02:47: #2 looking for paired plus/minus strand peaks... WARNING @ Mon, 12 Aug 2019 17:02:47: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:02:47: #2 You may need to consider one of the other alternative d(s): 39,64,149,199,226,260,291,352,409,437,463,532,552,586 WARNING @ Mon, 12 Aug 2019 17:02:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:02:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:02:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:02:47: #2 number of paired peaks: 183 WARNING @ Mon, 12 Aug 2019 17:02:47: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Mon, 12 Aug 2019 17:02:47: start model_add_line... INFO @ Mon, 12 Aug 2019 17:02:47: start X-correlation... INFO @ Mon, 12 Aug 2019 17:02:47: end of X-cor INFO @ Mon, 12 Aug 2019 17:02:47: #2 finished! INFO @ Mon, 12 Aug 2019 17:02:47: #2 predicted fragment length is 39 bps INFO @ Mon, 12 Aug 2019 17:02:47: #2 alternative fragment length(s) may be 39,64,149,199,226,260,291,352,409,437,463,532,552,586 bps INFO @ Mon, 12 Aug 2019 17:02:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.10_model.r WARNING @ Mon, 12 Aug 2019 17:02:47: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:02:47: #2 You may need to consider one of the other alternative d(s): 39,64,149,199,226,260,291,352,409,437,463,532,552,586 WARNING @ Mon, 12 Aug 2019 17:02:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:02:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:02:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:02:48: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:02:48: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:02:48: #1 total tags in treatment: 417209 INFO @ Mon, 12 Aug 2019 17:02:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:02:48: #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 17:02:48: #1 tags after filtering in treatment: 417209 INFO @ Mon, 12 Aug 2019 17:02:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:02:48: #1 finished! INFO @ Mon, 12 Aug 2019 17:02:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:02:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:02:48: #2 number of paired peaks: 183 WARNING @ Mon, 12 Aug 2019 17:02:48: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Mon, 12 Aug 2019 17:02:48: start model_add_line... INFO @ Mon, 12 Aug 2019 17:02:48: start X-correlation... INFO @ Mon, 12 Aug 2019 17:02:48: end of X-cor INFO @ Mon, 12 Aug 2019 17:02:48: #2 finished! INFO @ Mon, 12 Aug 2019 17:02:48: #2 predicted fragment length is 39 bps INFO @ Mon, 12 Aug 2019 17:02:48: #2 alternative fragment length(s) may be 39,64,149,199,226,260,291,352,409,437,463,532,552,586 bps INFO @ Mon, 12 Aug 2019 17:02:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.20_model.r WARNING @ Mon, 12 Aug 2019 17:02:48: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:02:48: #2 You may need to consider one of the other alternative d(s): 39,64,149,199,226,260,291,352,409,437,463,532,552,586 WARNING @ Mon, 12 Aug 2019 17:02:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:02:48: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:02:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:02:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:02:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:02:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:02:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:02:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.05_summits.bed INFO @ Mon, 12 Aug 2019 17:02:49: Done! INFO @ Mon, 12 Aug 2019 17:02:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:02:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:02:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.10_summits.bed INFO @ Mon, 12 Aug 2019 17:02:49: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (19 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 17:02:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:02:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:02:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:02:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043973/SRX043973.20_summits.bed INFO @ Mon, 12 Aug 2019 17:02:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。