Job ID = 1292866 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: 00:04:01 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 289136 (1.53%) aligned 0 times 14953728 (79.31%) aligned exactly 1 time 3611950 (19.16%) aligned >1 times 98.47% overall alignment rate Time searching: 00:04:01 Overall time: 00:04:01 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] 3522248 / 18565678 = 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 21:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.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 21:06:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:06:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.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 21:06:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:06:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.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 21:06:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:06:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:06:52: 1000000 INFO @ Sun, 02 Jun 2019 21:06:54: 1000000 INFO @ Sun, 02 Jun 2019 21:06:54: 1000000 INFO @ Sun, 02 Jun 2019 21:06:59: 2000000 INFO @ Sun, 02 Jun 2019 21:07:04: 2000000 INFO @ Sun, 02 Jun 2019 21:07:04: 2000000 INFO @ Sun, 02 Jun 2019 21:07:07: 3000000 INFO @ Sun, 02 Jun 2019 21:07:13: 3000000 INFO @ Sun, 02 Jun 2019 21:07:13: 3000000 INFO @ Sun, 02 Jun 2019 21:07:15: 4000000 INFO @ Sun, 02 Jun 2019 21:07:23: 4000000 INFO @ Sun, 02 Jun 2019 21:07:23: 4000000 INFO @ Sun, 02 Jun 2019 21:07:23: 5000000 INFO @ Sun, 02 Jun 2019 21:07:31: 6000000 INFO @ Sun, 02 Jun 2019 21:07:32: 5000000 INFO @ Sun, 02 Jun 2019 21:07:32: 5000000 INFO @ Sun, 02 Jun 2019 21:07:39: 7000000 INFO @ Sun, 02 Jun 2019 21:07:42: 6000000 INFO @ Sun, 02 Jun 2019 21:07:42: 6000000 INFO @ Sun, 02 Jun 2019 21:07:47: 8000000 INFO @ Sun, 02 Jun 2019 21:07:52: 7000000 INFO @ Sun, 02 Jun 2019 21:07:52: 7000000 INFO @ Sun, 02 Jun 2019 21:07:55: 9000000 INFO @ Sun, 02 Jun 2019 21:08:01: 8000000 INFO @ Sun, 02 Jun 2019 21:08:03: 8000000 INFO @ Sun, 02 Jun 2019 21:08:03: 10000000 INFO @ Sun, 02 Jun 2019 21:08:11: 11000000 INFO @ Sun, 02 Jun 2019 21:08:11: 9000000 INFO @ Sun, 02 Jun 2019 21:08:12: 9000000 INFO @ Sun, 02 Jun 2019 21:08:19: 12000000 INFO @ Sun, 02 Jun 2019 21:08:21: 10000000 INFO @ Sun, 02 Jun 2019 21:08:22: 10000000 INFO @ Sun, 02 Jun 2019 21:08:26: 13000000 INFO @ Sun, 02 Jun 2019 21:08:32: 11000000 INFO @ Sun, 02 Jun 2019 21:08:32: 11000000 INFO @ Sun, 02 Jun 2019 21:08:35: 14000000 INFO @ Sun, 02 Jun 2019 21:08:42: 12000000 INFO @ Sun, 02 Jun 2019 21:08:42: 15000000 INFO @ Sun, 02 Jun 2019 21:08:43: 12000000 INFO @ Sun, 02 Jun 2019 21:08:43: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:08:43: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:08:43: #1 total tags in treatment: 15043430 INFO @ Sun, 02 Jun 2019 21:08:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:08:43: #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 21:08:43: #1 tags after filtering in treatment: 15043430 INFO @ Sun, 02 Jun 2019 21:08:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:08:43: #1 finished! INFO @ Sun, 02 Jun 2019 21:08:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:08:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:08:45: #2 number of paired peaks: 426 WARNING @ Sun, 02 Jun 2019 21:08:45: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Sun, 02 Jun 2019 21:08:45: start model_add_line... INFO @ Sun, 02 Jun 2019 21:08:45: start X-correlation... INFO @ Sun, 02 Jun 2019 21:08:45: end of X-cor INFO @ Sun, 02 Jun 2019 21:08:45: #2 finished! INFO @ Sun, 02 Jun 2019 21:08:45: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 21:08:45: #2 alternative fragment length(s) may be 2,44,587 bps INFO @ Sun, 02 Jun 2019 21:08:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.20_model.r WARNING @ Sun, 02 Jun 2019 21:08:45: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:08:45: #2 You may need to consider one of the other alternative d(s): 2,44,587 WARNING @ Sun, 02 Jun 2019 21:08:45: #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 21:08:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:08:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:08:51: 13000000 INFO @ Sun, 02 Jun 2019 21:08:53: 13000000 INFO @ Sun, 02 Jun 2019 21:09:01: 14000000 INFO @ Sun, 02 Jun 2019 21:09:03: 14000000 INFO @ Sun, 02 Jun 2019 21:09:11: 15000000 INFO @ Sun, 02 Jun 2019 21:09:12: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:09:12: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:09:12: #1 total tags in treatment: 15043430 INFO @ Sun, 02 Jun 2019 21:09:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:09:12: #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 21:09:12: #1 tags after filtering in treatment: 15043430 INFO @ Sun, 02 Jun 2019 21:09:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:09:12: #1 finished! INFO @ Sun, 02 Jun 2019 21:09:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:09:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:09:13: 15000000 INFO @ Sun, 02 Jun 2019 21:09:13: #2 number of paired peaks: 426 WARNING @ Sun, 02 Jun 2019 21:09:13: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Sun, 02 Jun 2019 21:09:13: start model_add_line... INFO @ Sun, 02 Jun 2019 21:09:13: start X-correlation... INFO @ Sun, 02 Jun 2019 21:09:13: end of X-cor INFO @ Sun, 02 Jun 2019 21:09:13: #2 finished! INFO @ Sun, 02 Jun 2019 21:09:13: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 21:09:13: #2 alternative fragment length(s) may be 2,44,587 bps INFO @ Sun, 02 Jun 2019 21:09:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.05_model.r WARNING @ Sun, 02 Jun 2019 21:09:13: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:09:13: #2 You may need to consider one of the other alternative d(s): 2,44,587 WARNING @ Sun, 02 Jun 2019 21:09:13: #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 21:09:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:09:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:09:14: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:09:14: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:09:14: #1 total tags in treatment: 15043430 INFO @ Sun, 02 Jun 2019 21:09:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:09:14: #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 21:09:14: #1 tags after filtering in treatment: 15043430 INFO @ Sun, 02 Jun 2019 21:09:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:09:14: #1 finished! INFO @ Sun, 02 Jun 2019 21:09:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:09:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:09:15: #2 number of paired peaks: 426 WARNING @ Sun, 02 Jun 2019 21:09:15: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Sun, 02 Jun 2019 21:09:15: start model_add_line... INFO @ Sun, 02 Jun 2019 21:09:16: start X-correlation... INFO @ Sun, 02 Jun 2019 21:09:16: end of X-cor INFO @ Sun, 02 Jun 2019 21:09:16: #2 finished! INFO @ Sun, 02 Jun 2019 21:09:16: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 21:09:16: #2 alternative fragment length(s) may be 2,44,587 bps INFO @ Sun, 02 Jun 2019 21:09:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.10_model.r WARNING @ Sun, 02 Jun 2019 21:09:16: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:09:16: #2 You may need to consider one of the other alternative d(s): 2,44,587 WARNING @ Sun, 02 Jun 2019 21:09:16: #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 21:09:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:09:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:09:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:09:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:09:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:09:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.20_summits.bed INFO @ Sun, 02 Jun 2019 21:09:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (256 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:09:52: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:09:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:10:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:10:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:10:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.05_summits.bed INFO @ Sun, 02 Jun 2019 21:10:12: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3610 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:10:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:10:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:10:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495090/SRX495090.10_summits.bed INFO @ Sun, 02 Jun 2019 21:10:14: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (901 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。