Job ID = 2589528 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,535,812 reads read : 5,535,812 reads written : 5,535,812 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR701503.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: 00:00:49 5535812 reads; of these: 5535812 (100.00%) were unpaired; of these: 1788102 (32.30%) aligned 0 times 3140718 (56.73%) aligned exactly 1 time 606992 (10.96%) aligned >1 times 67.70% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 190724 / 3747710 = 0.0509 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 17:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.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 17:53:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.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 17:53:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.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 17:53:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:59: 1000000 INFO @ Mon, 12 Aug 2019 17:53:59: 1000000 INFO @ Mon, 12 Aug 2019 17:53:59: 1000000 INFO @ Mon, 12 Aug 2019 17:54:06: 2000000 INFO @ Mon, 12 Aug 2019 17:54:07: 2000000 INFO @ Mon, 12 Aug 2019 17:54:08: 2000000 INFO @ Mon, 12 Aug 2019 17:54:13: 3000000 INFO @ Mon, 12 Aug 2019 17:54:16: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:54:16: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:54:16: #1 total tags in treatment: 3556986 INFO @ Mon, 12 Aug 2019 17:54:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:16: #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 17:54:16: #1 tags after filtering in treatment: 3556986 INFO @ Mon, 12 Aug 2019 17:54:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:16: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:17: #2 number of paired peaks: 402 WARNING @ Mon, 12 Aug 2019 17:54:17: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:17: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:17: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:17: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:17: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:17: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 17:54:17: #2 alternative fragment length(s) may be 4,34,444,576 bps INFO @ Mon, 12 Aug 2019 17:54:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.20_model.r WARNING @ Mon, 12 Aug 2019 17:54:17: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:54:17: #2 You may need to consider one of the other alternative d(s): 4,34,444,576 WARNING @ Mon, 12 Aug 2019 17:54:17: #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 17:54:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:17: 3000000 INFO @ Mon, 12 Aug 2019 17:54:17: 3000000 INFO @ Mon, 12 Aug 2019 17:54:22: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:54:22: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:54:22: #1 total tags in treatment: 3556986 INFO @ Mon, 12 Aug 2019 17:54:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:22: #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 17:54:22: #1 tags after filtering in treatment: 3556986 INFO @ Mon, 12 Aug 2019 17:54:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:22: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:22: #2 number of paired peaks: 402 WARNING @ Mon, 12 Aug 2019 17:54:22: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:22: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:22: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:22: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:22: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:22: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 17:54:22: #2 alternative fragment length(s) may be 4,34,444,576 bps INFO @ Mon, 12 Aug 2019 17:54:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.05_model.r WARNING @ Mon, 12 Aug 2019 17:54:22: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:54:22: #2 You may need to consider one of the other alternative d(s): 4,34,444,576 WARNING @ Mon, 12 Aug 2019 17:54:22: #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 17:54:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:22: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:54:22: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:54:22: #1 total tags in treatment: 3556986 INFO @ Mon, 12 Aug 2019 17:54:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:22: #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 17:54:22: #1 tags after filtering in treatment: 3556986 INFO @ Mon, 12 Aug 2019 17:54:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:22: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:23: #2 number of paired peaks: 402 WARNING @ Mon, 12 Aug 2019 17:54:23: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:23: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:23: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:23: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:23: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:23: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 17:54:23: #2 alternative fragment length(s) may be 4,34,444,576 bps INFO @ Mon, 12 Aug 2019 17:54:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.10_model.r WARNING @ Mon, 12 Aug 2019 17:54:23: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:54:23: #2 You may need to consider one of the other alternative d(s): 4,34,444,576 WARNING @ Mon, 12 Aug 2019 17:54:23: #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 17:54:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.20_summits.bed INFO @ Mon, 12 Aug 2019 17:54:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (41 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:54:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.05_summits.bed INFO @ Mon, 12 Aug 2019 17:54:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (377 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:54:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233448/SRX233448.10_summits.bed INFO @ Mon, 12 Aug 2019 17:54:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (178 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。