Job ID = 1291859 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,854,814 reads read : 18,854,814 reads written : 18,854,814 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: 00:04:05 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 289127 (1.53%) aligned 0 times 14953767 (79.31%) aligned exactly 1 time 3611920 (19.16%) aligned >1 times 98.47% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 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] 3521736 / 18565687 = 0.1897 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 16:57:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.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 16:57:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:57:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:57:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.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 16:57:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:57:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:57:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.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 16:57:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:57:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:57:47: 1000000 INFO @ Sun, 02 Jun 2019 16:57:48: 1000000 INFO @ Sun, 02 Jun 2019 16:57:48: 1000000 INFO @ Sun, 02 Jun 2019 16:57:54: 2000000 INFO @ Sun, 02 Jun 2019 16:57:55: 2000000 INFO @ Sun, 02 Jun 2019 16:57:55: 2000000 INFO @ Sun, 02 Jun 2019 16:58:00: 3000000 INFO @ Sun, 02 Jun 2019 16:58:02: 3000000 INFO @ Sun, 02 Jun 2019 16:58:02: 3000000 INFO @ Sun, 02 Jun 2019 16:58:06: 4000000 INFO @ Sun, 02 Jun 2019 16:58:09: 4000000 INFO @ Sun, 02 Jun 2019 16:58:09: 4000000 INFO @ Sun, 02 Jun 2019 16:58:12: 5000000 INFO @ Sun, 02 Jun 2019 16:58:16: 5000000 INFO @ Sun, 02 Jun 2019 16:58:16: 5000000 INFO @ Sun, 02 Jun 2019 16:58:19: 6000000 INFO @ Sun, 02 Jun 2019 16:58:22: 6000000 INFO @ Sun, 02 Jun 2019 16:58:23: 6000000 INFO @ Sun, 02 Jun 2019 16:58:25: 7000000 INFO @ Sun, 02 Jun 2019 16:58:29: 7000000 INFO @ Sun, 02 Jun 2019 16:58:30: 7000000 INFO @ Sun, 02 Jun 2019 16:58:31: 8000000 INFO @ Sun, 02 Jun 2019 16:58:35: 8000000 INFO @ Sun, 02 Jun 2019 16:58:37: 8000000 INFO @ Sun, 02 Jun 2019 16:58:37: 9000000 INFO @ Sun, 02 Jun 2019 16:58:42: 9000000 INFO @ Sun, 02 Jun 2019 16:58:44: 10000000 INFO @ Sun, 02 Jun 2019 16:58:44: 9000000 INFO @ Sun, 02 Jun 2019 16:58:49: 10000000 INFO @ Sun, 02 Jun 2019 16:58:50: 11000000 INFO @ Sun, 02 Jun 2019 16:58:51: 10000000 INFO @ Sun, 02 Jun 2019 16:58:55: 11000000 INFO @ Sun, 02 Jun 2019 16:58:56: 12000000 INFO @ Sun, 02 Jun 2019 16:58:58: 11000000 INFO @ Sun, 02 Jun 2019 16:59:02: 12000000 INFO @ Sun, 02 Jun 2019 16:59:02: 13000000 INFO @ Sun, 02 Jun 2019 16:59:05: 12000000 INFO @ Sun, 02 Jun 2019 16:59:08: 14000000 INFO @ Sun, 02 Jun 2019 16:59:09: 13000000 INFO @ Sun, 02 Jun 2019 16:59:12: 13000000 INFO @ Sun, 02 Jun 2019 16:59:14: 15000000 INFO @ Sun, 02 Jun 2019 16:59:15: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:59:15: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:59:15: #1 total tags in treatment: 15043951 INFO @ Sun, 02 Jun 2019 16:59:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:59:15: #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 16:59:15: 14000000 INFO @ Sun, 02 Jun 2019 16:59:15: #1 tags after filtering in treatment: 15043951 INFO @ Sun, 02 Jun 2019 16:59:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:59:15: #1 finished! INFO @ Sun, 02 Jun 2019 16:59:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:59:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:59:17: #2 number of paired peaks: 415 WARNING @ Sun, 02 Jun 2019 16:59:17: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Sun, 02 Jun 2019 16:59:17: start model_add_line... INFO @ Sun, 02 Jun 2019 16:59:17: start X-correlation... INFO @ Sun, 02 Jun 2019 16:59:17: end of X-cor INFO @ Sun, 02 Jun 2019 16:59:17: #2 finished! INFO @ Sun, 02 Jun 2019 16:59:17: #2 predicted fragment length is 56 bps INFO @ Sun, 02 Jun 2019 16:59:17: #2 alternative fragment length(s) may be 2,56 bps INFO @ Sun, 02 Jun 2019 16:59:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.05_model.r WARNING @ Sun, 02 Jun 2019 16:59:17: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:59:17: #2 You may need to consider one of the other alternative d(s): 2,56 WARNING @ Sun, 02 Jun 2019 16:59:17: #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 16:59:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:59:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:59:19: 14000000 INFO @ Sun, 02 Jun 2019 16:59:22: 15000000 INFO @ Sun, 02 Jun 2019 16:59:22: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:59:22: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:59:22: #1 total tags in treatment: 15043951 INFO @ Sun, 02 Jun 2019 16:59:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:59:22: #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 16:59:23: #1 tags after filtering in treatment: 15043951 INFO @ Sun, 02 Jun 2019 16:59:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:59:23: #1 finished! INFO @ Sun, 02 Jun 2019 16:59:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:59:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:59:24: #2 number of paired peaks: 415 WARNING @ Sun, 02 Jun 2019 16:59:24: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Sun, 02 Jun 2019 16:59:24: start model_add_line... INFO @ Sun, 02 Jun 2019 16:59:24: start X-correlation... INFO @ Sun, 02 Jun 2019 16:59:24: end of X-cor INFO @ Sun, 02 Jun 2019 16:59:24: #2 finished! INFO @ Sun, 02 Jun 2019 16:59:24: #2 predicted fragment length is 56 bps INFO @ Sun, 02 Jun 2019 16:59:24: #2 alternative fragment length(s) may be 2,56 bps INFO @ Sun, 02 Jun 2019 16:59:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.20_model.r WARNING @ Sun, 02 Jun 2019 16:59:24: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:59:24: #2 You may need to consider one of the other alternative d(s): 2,56 WARNING @ Sun, 02 Jun 2019 16:59:24: #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 16:59:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:59:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:59:25: 15000000 INFO @ Sun, 02 Jun 2019 16:59:26: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:59:26: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:59:26: #1 total tags in treatment: 15043951 INFO @ Sun, 02 Jun 2019 16:59:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:59:26: #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 16:59:26: #1 tags after filtering in treatment: 15043951 INFO @ Sun, 02 Jun 2019 16:59:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:59:26: #1 finished! INFO @ Sun, 02 Jun 2019 16:59:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:59:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:59:27: #2 number of paired peaks: 415 WARNING @ Sun, 02 Jun 2019 16:59:27: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Sun, 02 Jun 2019 16:59:27: start model_add_line... INFO @ Sun, 02 Jun 2019 16:59:27: start X-correlation... INFO @ Sun, 02 Jun 2019 16:59:27: end of X-cor INFO @ Sun, 02 Jun 2019 16:59:27: #2 finished! INFO @ Sun, 02 Jun 2019 16:59:27: #2 predicted fragment length is 56 bps INFO @ Sun, 02 Jun 2019 16:59:27: #2 alternative fragment length(s) may be 2,56 bps INFO @ Sun, 02 Jun 2019 16:59:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.10_model.r WARNING @ Sun, 02 Jun 2019 16:59:27: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:59:27: #2 You may need to consider one of the other alternative d(s): 2,56 WARNING @ Sun, 02 Jun 2019 16:59:27: #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 16:59:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:59:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:59:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:00:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:00:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:00:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:00:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:00:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.05_summits.bed INFO @ Sun, 02 Jun 2019 17:00:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5357 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:00:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:00:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:00:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.20_summits.bed INFO @ Sun, 02 Jun 2019 17:00:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (356 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:00:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:00:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:00:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257694/SRX257694.10_summits.bed INFO @ Sun, 02 Jun 2019 17:00:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1258 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。