Job ID = 1292983 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,732,212 reads read : 41,464,424 reads written : 20,732,212 reads 0-length : 20,732,212 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: 00:06:26 20732212 reads; of these: 20732212 (100.00%) were unpaired; of these: 3471593 (16.74%) aligned 0 times 14303200 (68.99%) aligned exactly 1 time 2957419 (14.26%) aligned >1 times 83.26% overall alignment rate Time searching: 00:06:26 Overall time: 00:06:26 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3674790 / 17260619 = 0.2129 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 21:35:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.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 21:35:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:35:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:35:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.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 21:35:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:35:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:35:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.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 21:35:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:35:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:35:55: 1000000 INFO @ Sun, 02 Jun 2019 21:35:56: 1000000 INFO @ Sun, 02 Jun 2019 21:35:56: 1000000 INFO @ Sun, 02 Jun 2019 21:36:02: 2000000 INFO @ Sun, 02 Jun 2019 21:36:04: 2000000 INFO @ Sun, 02 Jun 2019 21:36:04: 2000000 INFO @ Sun, 02 Jun 2019 21:36:09: 3000000 INFO @ Sun, 02 Jun 2019 21:36:11: 3000000 INFO @ Sun, 02 Jun 2019 21:36:11: 3000000 INFO @ Sun, 02 Jun 2019 21:36:15: 4000000 INFO @ Sun, 02 Jun 2019 21:36:18: 4000000 INFO @ Sun, 02 Jun 2019 21:36:18: 4000000 INFO @ Sun, 02 Jun 2019 21:36:22: 5000000 INFO @ Sun, 02 Jun 2019 21:36:25: 5000000 INFO @ Sun, 02 Jun 2019 21:36:25: 5000000 INFO @ Sun, 02 Jun 2019 21:36:29: 6000000 INFO @ Sun, 02 Jun 2019 21:36:33: 6000000 INFO @ Sun, 02 Jun 2019 21:36:33: 6000000 INFO @ Sun, 02 Jun 2019 21:36:35: 7000000 INFO @ Sun, 02 Jun 2019 21:36:40: 7000000 INFO @ Sun, 02 Jun 2019 21:36:40: 7000000 INFO @ Sun, 02 Jun 2019 21:36:42: 8000000 INFO @ Sun, 02 Jun 2019 21:36:47: 8000000 INFO @ Sun, 02 Jun 2019 21:36:47: 8000000 INFO @ Sun, 02 Jun 2019 21:36:49: 9000000 INFO @ Sun, 02 Jun 2019 21:36:54: 9000000 INFO @ Sun, 02 Jun 2019 21:36:54: 9000000 INFO @ Sun, 02 Jun 2019 21:36:55: 10000000 INFO @ Sun, 02 Jun 2019 21:37:01: 10000000 INFO @ Sun, 02 Jun 2019 21:37:01: 10000000 INFO @ Sun, 02 Jun 2019 21:37:02: 11000000 INFO @ Sun, 02 Jun 2019 21:37:08: 11000000 INFO @ Sun, 02 Jun 2019 21:37:08: 12000000 INFO @ Sun, 02 Jun 2019 21:37:08: 11000000 INFO @ Sun, 02 Jun 2019 21:37:15: 13000000 INFO @ Sun, 02 Jun 2019 21:37:15: 12000000 INFO @ Sun, 02 Jun 2019 21:37:15: 12000000 INFO @ Sun, 02 Jun 2019 21:37:19: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:37:19: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:37:19: #1 total tags in treatment: 13585829 INFO @ Sun, 02 Jun 2019 21:37:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:37:19: #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 21:37:19: #1 tags after filtering in treatment: 13585829 INFO @ Sun, 02 Jun 2019 21:37:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:37:19: #1 finished! INFO @ Sun, 02 Jun 2019 21:37:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:37:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:37:20: #2 number of paired peaks: 424 WARNING @ Sun, 02 Jun 2019 21:37:20: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sun, 02 Jun 2019 21:37:20: start model_add_line... INFO @ Sun, 02 Jun 2019 21:37:20: start X-correlation... INFO @ Sun, 02 Jun 2019 21:37:20: end of X-cor INFO @ Sun, 02 Jun 2019 21:37:20: #2 finished! INFO @ Sun, 02 Jun 2019 21:37:20: #2 predicted fragment length is 111 bps INFO @ Sun, 02 Jun 2019 21:37:20: #2 alternative fragment length(s) may be 111 bps INFO @ Sun, 02 Jun 2019 21:37:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.20_model.r WARNING @ Sun, 02 Jun 2019 21:37:20: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:37:20: #2 You may need to consider one of the other alternative d(s): 111 WARNING @ Sun, 02 Jun 2019 21:37:20: #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 21:37:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:37:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:37:22: 13000000 INFO @ Sun, 02 Jun 2019 21:37:22: 13000000 INFO @ Sun, 02 Jun 2019 21:37:26: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:37:26: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:37:26: #1 total tags in treatment: 13585829 INFO @ Sun, 02 Jun 2019 21:37:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:37:26: #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 21:37:27: #1 tags after filtering in treatment: 13585829 INFO @ Sun, 02 Jun 2019 21:37:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:37:27: #1 finished! INFO @ Sun, 02 Jun 2019 21:37:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:37:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:37:27: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:37:27: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:37:27: #1 total tags in treatment: 13585829 INFO @ Sun, 02 Jun 2019 21:37:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:37:27: #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 21:37:27: #1 tags after filtering in treatment: 13585829 INFO @ Sun, 02 Jun 2019 21:37:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:37:27: #1 finished! INFO @ Sun, 02 Jun 2019 21:37:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:37:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:37:28: #2 number of paired peaks: 424 WARNING @ Sun, 02 Jun 2019 21:37:28: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sun, 02 Jun 2019 21:37:28: start model_add_line... INFO @ Sun, 02 Jun 2019 21:37:28: start X-correlation... INFO @ Sun, 02 Jun 2019 21:37:28: end of X-cor INFO @ Sun, 02 Jun 2019 21:37:28: #2 finished! INFO @ Sun, 02 Jun 2019 21:37:28: #2 predicted fragment length is 111 bps INFO @ Sun, 02 Jun 2019 21:37:28: #2 alternative fragment length(s) may be 111 bps INFO @ Sun, 02 Jun 2019 21:37:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.05_model.r WARNING @ Sun, 02 Jun 2019 21:37:28: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:37:28: #2 You may need to consider one of the other alternative d(s): 111 WARNING @ Sun, 02 Jun 2019 21:37:28: #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 21:37:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:37:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:37:28: #2 number of paired peaks: 424 WARNING @ Sun, 02 Jun 2019 21:37:28: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sun, 02 Jun 2019 21:37:28: start model_add_line... INFO @ Sun, 02 Jun 2019 21:37:28: start X-correlation... INFO @ Sun, 02 Jun 2019 21:37:28: end of X-cor INFO @ Sun, 02 Jun 2019 21:37:28: #2 finished! INFO @ Sun, 02 Jun 2019 21:37:28: #2 predicted fragment length is 111 bps INFO @ Sun, 02 Jun 2019 21:37:28: #2 alternative fragment length(s) may be 111 bps INFO @ Sun, 02 Jun 2019 21:37:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.10_model.r WARNING @ Sun, 02 Jun 2019 21:37:28: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:37:28: #2 You may need to consider one of the other alternative d(s): 111 WARNING @ Sun, 02 Jun 2019 21:37:28: #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 21:37:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:37:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:37:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:38:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:38:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:38:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:38:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:38:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.20_summits.bed INFO @ Sun, 02 Jun 2019 21:38:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (555 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:38:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:38:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:38:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.05_summits.bed INFO @ Sun, 02 Jun 2019 21:38:21: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1737 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:38:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:38:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:38:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020760/SRX5020760.10_summits.bed INFO @ Sun, 02 Jun 2019 21:38:22: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1007 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。