Job ID = 4178401 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,378,315 reads read : 20,756,630 reads written : 10,378,315 reads 0-length : 10,378,315 rm: cannot remove ‘[DSE]RR*’: 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: 00:04:17 10378315 reads; of these: 10378315 (100.00%) were unpaired; of these: 856729 (8.25%) aligned 0 times 7817528 (75.33%) aligned exactly 1 time 1704058 (16.42%) aligned >1 times 91.75% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 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] 808566 / 9521586 = 0.0849 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:29:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.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 @ Thu, 05 Dec 2019 12:29:06: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:06: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:15: 1000000 INFO @ Thu, 05 Dec 2019 12:29:23: 2000000 INFO @ Thu, 05 Dec 2019 12:29:32: 3000000 INFO @ Thu, 05 Dec 2019 12:29:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.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 @ Thu, 05 Dec 2019 12:29:34: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:34: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:40: 4000000 INFO @ Thu, 05 Dec 2019 12:29:43: 1000000 INFO @ Thu, 05 Dec 2019 12:29:50: 5000000 INFO @ Thu, 05 Dec 2019 12:29:52: 2000000 INFO @ Thu, 05 Dec 2019 12:30:01: 6000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:30:03: 3000000 INFO @ Thu, 05 Dec 2019 12:30:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.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 @ Thu, 05 Dec 2019 12:30:05: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:30:05: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:30:10: 7000000 INFO @ Thu, 05 Dec 2019 12:30:12: 4000000 INFO @ Thu, 05 Dec 2019 12:30:14: 1000000 INFO @ Thu, 05 Dec 2019 12:30:19: 8000000 INFO @ Thu, 05 Dec 2019 12:30:21: 5000000 INFO @ Thu, 05 Dec 2019 12:30:23: 2000000 INFO @ Thu, 05 Dec 2019 12:30:25: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:30:25: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:30:25: #1 total tags in treatment: 8713020 INFO @ Thu, 05 Dec 2019 12:30:25: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:30:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:30:26: #1 tags after filtering in treatment: 8713020 INFO @ Thu, 05 Dec 2019 12:30:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:30:26: #1 finished! INFO @ Thu, 05 Dec 2019 12:30:26: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:30:26: #2 number of paired peaks: 337 WARNING @ Thu, 05 Dec 2019 12:30:26: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Thu, 05 Dec 2019 12:30:26: start model_add_line... INFO @ Thu, 05 Dec 2019 12:30:26: start X-correlation... INFO @ Thu, 05 Dec 2019 12:30:27: end of X-cor INFO @ Thu, 05 Dec 2019 12:30:27: #2 finished! INFO @ Thu, 05 Dec 2019 12:30:27: #2 predicted fragment length is 73 bps INFO @ Thu, 05 Dec 2019 12:30:27: #2 alternative fragment length(s) may be 4,73 bps INFO @ Thu, 05 Dec 2019 12:30:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.05_model.r WARNING @ Thu, 05 Dec 2019 12:30:27: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:30:27: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Thu, 05 Dec 2019 12:30:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:30:27: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:30:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:30:30: 6000000 INFO @ Thu, 05 Dec 2019 12:30:32: 3000000 INFO @ Thu, 05 Dec 2019 12:30:39: 7000000 INFO @ Thu, 05 Dec 2019 12:30:41: 4000000 INFO @ Thu, 05 Dec 2019 12:30:44: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:30:48: 8000000 INFO @ Thu, 05 Dec 2019 12:30:50: 5000000 INFO @ Thu, 05 Dec 2019 12:30:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:30:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:30:54: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:30:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.05_summits.bed INFO @ Thu, 05 Dec 2019 12:30:54: Done! INFO @ Thu, 05 Dec 2019 12:30:54: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:30:54: #1 total tags in treatment: 8713020 INFO @ Thu, 05 Dec 2019 12:30:54: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:30:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:30:54: #1 tags after filtering in treatment: 8713020 INFO @ Thu, 05 Dec 2019 12:30:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:30:54: #1 finished! INFO @ Thu, 05 Dec 2019 12:30:54: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:30:54: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1148 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:30:55: #2 number of paired peaks: 337 WARNING @ Thu, 05 Dec 2019 12:30:55: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Thu, 05 Dec 2019 12:30:55: start model_add_line... INFO @ Thu, 05 Dec 2019 12:30:55: start X-correlation... INFO @ Thu, 05 Dec 2019 12:30:55: end of X-cor INFO @ Thu, 05 Dec 2019 12:30:55: #2 finished! INFO @ Thu, 05 Dec 2019 12:30:55: #2 predicted fragment length is 73 bps INFO @ Thu, 05 Dec 2019 12:30:55: #2 alternative fragment length(s) may be 4,73 bps INFO @ Thu, 05 Dec 2019 12:30:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.10_model.r WARNING @ Thu, 05 Dec 2019 12:30:55: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:30:55: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Thu, 05 Dec 2019 12:30:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:30:55: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:30:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:30:58: 6000000 INFO @ Thu, 05 Dec 2019 12:31:07: 7000000 INFO @ Thu, 05 Dec 2019 12:31:12: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:31:16: 8000000 INFO @ Thu, 05 Dec 2019 12:31:22: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:31:22: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:31:22: #1 total tags in treatment: 8713020 INFO @ Thu, 05 Dec 2019 12:31:22: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:31:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:31:22: #1 tags after filtering in treatment: 8713020 INFO @ Thu, 05 Dec 2019 12:31:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:31:22: #1 finished! INFO @ Thu, 05 Dec 2019 12:31:22: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:31:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:31:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:31:23: #2 number of paired peaks: 337 WARNING @ Thu, 05 Dec 2019 12:31:23: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Thu, 05 Dec 2019 12:31:23: start model_add_line... INFO @ Thu, 05 Dec 2019 12:31:23: start X-correlation... INFO @ Thu, 05 Dec 2019 12:31:23: end of X-cor INFO @ Thu, 05 Dec 2019 12:31:23: #2 finished! INFO @ Thu, 05 Dec 2019 12:31:23: #2 predicted fragment length is 73 bps INFO @ Thu, 05 Dec 2019 12:31:23: #2 alternative fragment length(s) may be 4,73 bps INFO @ Thu, 05 Dec 2019 12:31:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.20_model.r WARNING @ Thu, 05 Dec 2019 12:31:25: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:31:25: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Thu, 05 Dec 2019 12:31:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:31:25: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:31:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:31:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:31:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.10_summits.bed INFO @ Thu, 05 Dec 2019 12:31:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (473 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:31:42: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:31:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:31:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:31:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5729149/SRX5729149.20_summits.bed INFO @ Thu, 05 Dec 2019 12:31:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (220 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。