Job ID = 2589679 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,858,169 reads read : 4,858,169 reads written : 4,858,169 spots read : 4,544,721 reads read : 4,544,721 reads written : 4,544,721 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947279.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947280.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: 00:00:48 9402890 reads; of these: 9402890 (100.00%) were unpaired; of these: 8278015 (88.04%) aligned 0 times 934225 (9.94%) aligned exactly 1 time 190650 (2.03%) aligned >1 times 11.96% overall alignment rate Time searching: 00:00:48 Overall time: 00:00:48 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] 371456 / 1124875 = 0.3302 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 18:15:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.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 18:15:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:15:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:15:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.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 18:15:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:15:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.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 18:15:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:15:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:15:21: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:15:21: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:15:21: #1 total tags in treatment: 753419 INFO @ Mon, 12 Aug 2019 18:15:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:15:21: #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 18:15:21: #1 tags after filtering in treatment: 753419 INFO @ Mon, 12 Aug 2019 18:15:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:15:21: #1 finished! INFO @ Mon, 12 Aug 2019 18:15:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:15:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:15:21: #2 number of paired peaks: 446 WARNING @ Mon, 12 Aug 2019 18:15:21: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Mon, 12 Aug 2019 18:15:21: start model_add_line... INFO @ Mon, 12 Aug 2019 18:15:21: start X-correlation... INFO @ Mon, 12 Aug 2019 18:15:21: end of X-cor INFO @ Mon, 12 Aug 2019 18:15:21: #2 finished! INFO @ Mon, 12 Aug 2019 18:15:21: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 18:15:21: #2 alternative fragment length(s) may be 32,65,70,138,502,566,595 bps INFO @ Mon, 12 Aug 2019 18:15:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.05_model.r WARNING @ Mon, 12 Aug 2019 18:15:21: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:15:21: #2 You may need to consider one of the other alternative d(s): 32,65,70,138,502,566,595 WARNING @ Mon, 12 Aug 2019 18:15:21: #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 18:15:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:15:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:15:22: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:15:22: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:15:22: #1 total tags in treatment: 753419 INFO @ Mon, 12 Aug 2019 18:15:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:15:22: #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 18:15:22: #1 tags after filtering in treatment: 753419 INFO @ Mon, 12 Aug 2019 18:15:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:15:22: #1 finished! INFO @ Mon, 12 Aug 2019 18:15:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:15:22: #2 number of paired peaks: 446 WARNING @ Mon, 12 Aug 2019 18:15:22: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Mon, 12 Aug 2019 18:15:22: start model_add_line... INFO @ Mon, 12 Aug 2019 18:15:22: start X-correlation... INFO @ Mon, 12 Aug 2019 18:15:22: end of X-cor INFO @ Mon, 12 Aug 2019 18:15:22: #2 finished! INFO @ Mon, 12 Aug 2019 18:15:22: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 18:15:22: #2 alternative fragment length(s) may be 32,65,70,138,502,566,595 bps INFO @ Mon, 12 Aug 2019 18:15:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.10_model.r WARNING @ Mon, 12 Aug 2019 18:15:22: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:15:22: #2 You may need to consider one of the other alternative d(s): 32,65,70,138,502,566,595 WARNING @ Mon, 12 Aug 2019 18:15:22: #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 18:15:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:15:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:15:23: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:15:23: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:15:23: #1 total tags in treatment: 753419 INFO @ Mon, 12 Aug 2019 18:15:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:15:23: #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 18:15:23: #1 tags after filtering in treatment: 753419 INFO @ Mon, 12 Aug 2019 18:15:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:15:23: #1 finished! INFO @ Mon, 12 Aug 2019 18:15:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:15:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:15:23: #2 number of paired peaks: 446 WARNING @ Mon, 12 Aug 2019 18:15:23: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Mon, 12 Aug 2019 18:15:23: start model_add_line... INFO @ Mon, 12 Aug 2019 18:15:23: start X-correlation... INFO @ Mon, 12 Aug 2019 18:15:23: end of X-cor INFO @ Mon, 12 Aug 2019 18:15:23: #2 finished! INFO @ Mon, 12 Aug 2019 18:15:23: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 18:15:23: #2 alternative fragment length(s) may be 32,65,70,138,502,566,595 bps INFO @ Mon, 12 Aug 2019 18:15:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.20_model.r WARNING @ Mon, 12 Aug 2019 18:15:23: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:15:23: #2 You may need to consider one of the other alternative d(s): 32,65,70,138,502,566,595 WARNING @ Mon, 12 Aug 2019 18:15:23: #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 18:15:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:15:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:15:24: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:15:25: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:15:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:15:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:15:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.05_summits.bed INFO @ Mon, 12 Aug 2019 18:15:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:15:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:15:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:15:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:15:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.10_summits.bed INFO @ Mon, 12 Aug 2019 18:15:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (48 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 18:15:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:15:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:15:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331056/SRX331056.20_summits.bed INFO @ Mon, 12 Aug 2019 18:15:27: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。