Job ID = 2590023 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,639,516 reads read : 25,639,516 reads written : 25,639,516 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: 00:07:16 25639516 reads; of these: 25639516 (100.00%) were unpaired; of these: 2292736 (8.94%) aligned 0 times 18971603 (73.99%) aligned exactly 1 time 4375177 (17.06%) aligned >1 times 91.06% overall alignment rate Time searching: 00:07:16 Overall time: 00:07:16 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_sort_core] merging from 12 files... [bam_rmdupse_core] 8874491 / 23346780 = 0.3801 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 19:33:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.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 19:33:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:33:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:33:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.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 19:33:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:33:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:33:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.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 19:33:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:33:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:33:25: 1000000 INFO @ Mon, 12 Aug 2019 19:33:27: 1000000 INFO @ Mon, 12 Aug 2019 19:33:29: 1000000 INFO @ Mon, 12 Aug 2019 19:33:33: 2000000 INFO @ Mon, 12 Aug 2019 19:33:35: 2000000 INFO @ Mon, 12 Aug 2019 19:33:42: 2000000 INFO @ Mon, 12 Aug 2019 19:33:44: 3000000 INFO @ Mon, 12 Aug 2019 19:33:45: 3000000 INFO @ Mon, 12 Aug 2019 19:33:53: 4000000 INFO @ Mon, 12 Aug 2019 19:33:53: 3000000 INFO @ Mon, 12 Aug 2019 19:33:53: 4000000 INFO @ Mon, 12 Aug 2019 19:34:01: 5000000 INFO @ Mon, 12 Aug 2019 19:34:01: 5000000 INFO @ Mon, 12 Aug 2019 19:34:03: 4000000 INFO @ Mon, 12 Aug 2019 19:34:09: 6000000 INFO @ Mon, 12 Aug 2019 19:34:10: 6000000 INFO @ Mon, 12 Aug 2019 19:34:14: 5000000 INFO @ Mon, 12 Aug 2019 19:34:17: 7000000 INFO @ Mon, 12 Aug 2019 19:34:19: 7000000 INFO @ Mon, 12 Aug 2019 19:34:24: 6000000 INFO @ Mon, 12 Aug 2019 19:34:24: 8000000 INFO @ Mon, 12 Aug 2019 19:34:27: 8000000 INFO @ Mon, 12 Aug 2019 19:34:32: 9000000 INFO @ Mon, 12 Aug 2019 19:34:34: 7000000 INFO @ Mon, 12 Aug 2019 19:34:36: 9000000 INFO @ Mon, 12 Aug 2019 19:34:40: 10000000 INFO @ Mon, 12 Aug 2019 19:34:44: 10000000 INFO @ Mon, 12 Aug 2019 19:34:44: 8000000 INFO @ Mon, 12 Aug 2019 19:34:48: 11000000 INFO @ Mon, 12 Aug 2019 19:34:53: 11000000 INFO @ Mon, 12 Aug 2019 19:34:55: 9000000 INFO @ Mon, 12 Aug 2019 19:34:55: 12000000 INFO @ Mon, 12 Aug 2019 19:35:01: 12000000 INFO @ Mon, 12 Aug 2019 19:35:03: 13000000 INFO @ Mon, 12 Aug 2019 19:35:05: 10000000 INFO @ Mon, 12 Aug 2019 19:35:10: 13000000 INFO @ Mon, 12 Aug 2019 19:35:11: 14000000 INFO @ Mon, 12 Aug 2019 19:35:14: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:35:14: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:35:14: #1 total tags in treatment: 14472289 INFO @ Mon, 12 Aug 2019 19:35:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:35:14: #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 19:35:15: #1 tags after filtering in treatment: 14472289 INFO @ Mon, 12 Aug 2019 19:35:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:35:15: #1 finished! INFO @ Mon, 12 Aug 2019 19:35:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:35:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:35:15: 11000000 INFO @ Mon, 12 Aug 2019 19:35:16: #2 number of paired peaks: 464 WARNING @ Mon, 12 Aug 2019 19:35:16: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Mon, 12 Aug 2019 19:35:16: start model_add_line... INFO @ Mon, 12 Aug 2019 19:35:16: start X-correlation... INFO @ Mon, 12 Aug 2019 19:35:16: end of X-cor INFO @ Mon, 12 Aug 2019 19:35:16: #2 finished! INFO @ Mon, 12 Aug 2019 19:35:16: #2 predicted fragment length is 53 bps INFO @ Mon, 12 Aug 2019 19:35:16: #2 alternative fragment length(s) may be 3,53,567 bps INFO @ Mon, 12 Aug 2019 19:35:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.05_model.r WARNING @ Mon, 12 Aug 2019 19:35:16: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:35:16: #2 You may need to consider one of the other alternative d(s): 3,53,567 WARNING @ Mon, 12 Aug 2019 19:35:16: #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 19:35:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:35:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:35:18: 14000000 INFO @ Mon, 12 Aug 2019 19:35:22: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:35:22: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:35:22: #1 total tags in treatment: 14472289 INFO @ Mon, 12 Aug 2019 19:35:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:35:22: #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 19:35:22: #1 tags after filtering in treatment: 14472289 INFO @ Mon, 12 Aug 2019 19:35:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:35:22: #1 finished! INFO @ Mon, 12 Aug 2019 19:35:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:35:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:35:24: #2 number of paired peaks: 464 WARNING @ Mon, 12 Aug 2019 19:35:24: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Mon, 12 Aug 2019 19:35:24: start model_add_line... INFO @ Mon, 12 Aug 2019 19:35:24: start X-correlation... INFO @ Mon, 12 Aug 2019 19:35:24: end of X-cor INFO @ Mon, 12 Aug 2019 19:35:24: #2 finished! INFO @ Mon, 12 Aug 2019 19:35:24: #2 predicted fragment length is 53 bps INFO @ Mon, 12 Aug 2019 19:35:24: #2 alternative fragment length(s) may be 3,53,567 bps INFO @ Mon, 12 Aug 2019 19:35:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.10_model.r WARNING @ Mon, 12 Aug 2019 19:35:24: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:35:24: #2 You may need to consider one of the other alternative d(s): 3,53,567 WARNING @ Mon, 12 Aug 2019 19:35:24: #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 19:35:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:35:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:35:25: 12000000 INFO @ Mon, 12 Aug 2019 19:35:35: 13000000 INFO @ Mon, 12 Aug 2019 19:35:45: 14000000 INFO @ Mon, 12 Aug 2019 19:35:49: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:35:49: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:35:49: #1 total tags in treatment: 14472289 INFO @ Mon, 12 Aug 2019 19:35:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:35:49: #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 19:35:50: #1 tags after filtering in treatment: 14472289 INFO @ Mon, 12 Aug 2019 19:35:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:35:50: #1 finished! INFO @ Mon, 12 Aug 2019 19:35:50: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:35:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:35:51: #2 number of paired peaks: 464 WARNING @ Mon, 12 Aug 2019 19:35:51: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Mon, 12 Aug 2019 19:35:51: start model_add_line... INFO @ Mon, 12 Aug 2019 19:35:51: start X-correlation... INFO @ Mon, 12 Aug 2019 19:35:51: end of X-cor INFO @ Mon, 12 Aug 2019 19:35:51: #2 finished! INFO @ Mon, 12 Aug 2019 19:35:51: #2 predicted fragment length is 53 bps INFO @ Mon, 12 Aug 2019 19:35:51: #2 alternative fragment length(s) may be 3,53,567 bps INFO @ Mon, 12 Aug 2019 19:35:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.20_model.r WARNING @ Mon, 12 Aug 2019 19:35:51: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:35:51: #2 You may need to consider one of the other alternative d(s): 3,53,567 WARNING @ Mon, 12 Aug 2019 19:35:51: #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 19:35:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:35:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:35:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:36:00: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.05_summits.bed INFO @ Mon, 12 Aug 2019 19:36:10: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1740 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:36:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:36:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:36:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.10_summits.bed INFO @ Mon, 12 Aug 2019 19:36:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (888 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:36:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:36:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:36:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:36:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494867/SRX494867.20_summits.bed INFO @ Mon, 12 Aug 2019 19:36:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (327 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。