Job ID = 2589153 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,980,441 reads read : 3,980,441 reads written : 3,980,441 spots read : 4,146,392 reads read : 4,146,392 reads written : 4,146,392 spots read : 4,161,350 reads read : 4,161,350 reads written : 4,161,350 spots read : 4,478,436 reads read : 4,478,436 reads written : 4,478,436 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107356.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107357.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107358.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107359.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: 00:01:16 16766619 reads; of these: 16766619 (100.00%) were unpaired; of these: 16031125 (95.61%) aligned 0 times 649179 (3.87%) aligned exactly 1 time 86315 (0.51%) aligned >1 times 4.39% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 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] 19590 / 735494 = 0.0266 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 17:05:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.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 17:05:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:05:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:05:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.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 17:05:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:05:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.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 17:05:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:05:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:05:33: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:05:33: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:05:33: #1 total tags in treatment: 715904 INFO @ Mon, 12 Aug 2019 17:05:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:05:33: #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 17:05:33: #1 tags after filtering in treatment: 715904 INFO @ Mon, 12 Aug 2019 17:05:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:05:33: #1 finished! INFO @ Mon, 12 Aug 2019 17:05:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:05:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:05:33: #2 number of paired peaks: 202 WARNING @ Mon, 12 Aug 2019 17:05:33: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Mon, 12 Aug 2019 17:05:33: start model_add_line... INFO @ Mon, 12 Aug 2019 17:05:33: start X-correlation... INFO @ Mon, 12 Aug 2019 17:05:33: end of X-cor INFO @ Mon, 12 Aug 2019 17:05:33: #2 finished! INFO @ Mon, 12 Aug 2019 17:05:33: #2 predicted fragment length is 40 bps INFO @ Mon, 12 Aug 2019 17:05:33: #2 alternative fragment length(s) may be 40,106,147,217,246,479,510,531 bps INFO @ Mon, 12 Aug 2019 17:05:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.05_model.r WARNING @ Mon, 12 Aug 2019 17:05:33: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:05:33: #2 You may need to consider one of the other alternative d(s): 40,106,147,217,246,479,510,531 WARNING @ Mon, 12 Aug 2019 17:05:33: #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 17:05:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:05:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:05:34: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:05:34: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:05:34: #1 total tags in treatment: 715904 INFO @ Mon, 12 Aug 2019 17:05:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:05:34: #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 17:05:34: #1 tags after filtering in treatment: 715904 INFO @ Mon, 12 Aug 2019 17:05:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:05:34: #1 finished! INFO @ Mon, 12 Aug 2019 17:05:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:05:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:05:34: #2 number of paired peaks: 202 WARNING @ Mon, 12 Aug 2019 17:05:34: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Mon, 12 Aug 2019 17:05:34: start model_add_line... INFO @ Mon, 12 Aug 2019 17:05:34: start X-correlation... INFO @ Mon, 12 Aug 2019 17:05:34: end of X-cor INFO @ Mon, 12 Aug 2019 17:05:34: #2 finished! INFO @ Mon, 12 Aug 2019 17:05:34: #2 predicted fragment length is 40 bps INFO @ Mon, 12 Aug 2019 17:05:34: #2 alternative fragment length(s) may be 40,106,147,217,246,479,510,531 bps INFO @ Mon, 12 Aug 2019 17:05:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.10_model.r INFO @ Mon, 12 Aug 2019 17:05:34: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:05:34: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:05:34: #1 total tags in treatment: 715904 INFO @ Mon, 12 Aug 2019 17:05:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:05:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) WARNING @ Mon, 12 Aug 2019 17:05:34: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:05:34: #2 You may need to consider one of the other alternative d(s): 40,106,147,217,246,479,510,531 WARNING @ Mon, 12 Aug 2019 17:05:34: #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 17:05:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:05:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:05:34: #1 tags after filtering in treatment: 715904 INFO @ Mon, 12 Aug 2019 17:05:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:05:34: #1 finished! INFO @ Mon, 12 Aug 2019 17:05:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:05:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:05:35: #2 number of paired peaks: 202 WARNING @ Mon, 12 Aug 2019 17:05:35: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Mon, 12 Aug 2019 17:05:35: start model_add_line... INFO @ Mon, 12 Aug 2019 17:05:35: start X-correlation... INFO @ Mon, 12 Aug 2019 17:05:35: end of X-cor INFO @ Mon, 12 Aug 2019 17:05:35: #2 finished! INFO @ Mon, 12 Aug 2019 17:05:35: #2 predicted fragment length is 40 bps INFO @ Mon, 12 Aug 2019 17:05:35: #2 alternative fragment length(s) may be 40,106,147,217,246,479,510,531 bps INFO @ Mon, 12 Aug 2019 17:05:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.20_model.r WARNING @ Mon, 12 Aug 2019 17:05:35: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:05:35: #2 You may need to consider one of the other alternative d(s): 40,106,147,217,246,479,510,531 WARNING @ Mon, 12 Aug 2019 17:05:35: #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 17:05:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:05:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:05:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:05:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:05:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:05:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.05_summits.bed INFO @ Mon, 12 Aug 2019 17:05:37: Done! INFO @ Mon, 12 Aug 2019 17:05:37: #3 Call peaks for each chromosome... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:05:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:05:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:05:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:05:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.10_summits.bed INFO @ Mon, 12 Aug 2019 17:05:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:05:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:05:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:05:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043881/SRX043881.20_summits.bed INFO @ Mon, 12 Aug 2019 17:05:38: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。