Job ID = 1291871 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,914,368 reads read : 6,914,368 reads written : 6,914,368 spots read : 8,907,367 reads read : 8,907,367 reads written : 8,907,367 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: 00:03:57 15821735 reads; of these: 15821735 (100.00%) were unpaired; of these: 242014 (1.53%) aligned 0 times 12968712 (81.97%) aligned exactly 1 time 2611009 (16.50%) aligned >1 times 98.47% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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] 1382331 / 15579721 = 0.0887 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 17:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.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 17:05:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:05:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.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 17:05:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:05:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.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 17:05:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:05:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:05:11: 1000000 INFO @ Sun, 02 Jun 2019 17:05:14: 1000000 INFO @ Sun, 02 Jun 2019 17:05:14: 1000000 INFO @ Sun, 02 Jun 2019 17:05:19: 2000000 INFO @ Sun, 02 Jun 2019 17:05:24: 2000000 INFO @ Sun, 02 Jun 2019 17:05:24: 2000000 INFO @ Sun, 02 Jun 2019 17:05:26: 3000000 INFO @ Sun, 02 Jun 2019 17:05:33: 4000000 INFO @ Sun, 02 Jun 2019 17:05:34: 3000000 INFO @ Sun, 02 Jun 2019 17:05:34: 3000000 INFO @ Sun, 02 Jun 2019 17:05:40: 5000000 INFO @ Sun, 02 Jun 2019 17:05:43: 4000000 INFO @ Sun, 02 Jun 2019 17:05:44: 4000000 INFO @ Sun, 02 Jun 2019 17:05:48: 6000000 INFO @ Sun, 02 Jun 2019 17:05:53: 5000000 INFO @ Sun, 02 Jun 2019 17:05:53: 5000000 INFO @ Sun, 02 Jun 2019 17:05:55: 7000000 INFO @ Sun, 02 Jun 2019 17:06:02: 8000000 INFO @ Sun, 02 Jun 2019 17:06:03: 6000000 INFO @ Sun, 02 Jun 2019 17:06:03: 6000000 INFO @ Sun, 02 Jun 2019 17:06:09: 9000000 INFO @ Sun, 02 Jun 2019 17:06:12: 7000000 INFO @ Sun, 02 Jun 2019 17:06:13: 7000000 INFO @ Sun, 02 Jun 2019 17:06:17: 10000000 INFO @ Sun, 02 Jun 2019 17:06:21: 8000000 INFO @ Sun, 02 Jun 2019 17:06:22: 8000000 INFO @ Sun, 02 Jun 2019 17:06:24: 11000000 INFO @ Sun, 02 Jun 2019 17:06:30: 9000000 INFO @ Sun, 02 Jun 2019 17:06:31: 12000000 INFO @ Sun, 02 Jun 2019 17:06:31: 9000000 INFO @ Sun, 02 Jun 2019 17:06:38: 13000000 INFO @ Sun, 02 Jun 2019 17:06:39: 10000000 INFO @ Sun, 02 Jun 2019 17:06:41: 10000000 INFO @ Sun, 02 Jun 2019 17:06:45: 14000000 INFO @ Sun, 02 Jun 2019 17:06:47: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:06:47: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:06:47: #1 total tags in treatment: 14197390 INFO @ Sun, 02 Jun 2019 17:06:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:06:47: #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 17:06:47: #1 tags after filtering in treatment: 14197390 INFO @ Sun, 02 Jun 2019 17:06:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:06:47: #1 finished! INFO @ Sun, 02 Jun 2019 17:06:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:06:48: 11000000 INFO @ Sun, 02 Jun 2019 17:06:48: #2 number of paired peaks: 280 WARNING @ Sun, 02 Jun 2019 17:06:48: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Sun, 02 Jun 2019 17:06:48: start model_add_line... INFO @ Sun, 02 Jun 2019 17:06:49: start X-correlation... INFO @ Sun, 02 Jun 2019 17:06:49: end of X-cor INFO @ Sun, 02 Jun 2019 17:06:49: #2 finished! INFO @ Sun, 02 Jun 2019 17:06:49: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 17:06:49: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 02 Jun 2019 17:06:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.10_model.r WARNING @ Sun, 02 Jun 2019 17:06:49: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:06:49: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 02 Jun 2019 17:06:49: #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 17:06:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:06:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:06:50: 11000000 INFO @ Sun, 02 Jun 2019 17:06:58: 12000000 INFO @ Sun, 02 Jun 2019 17:06:59: 12000000 INFO @ Sun, 02 Jun 2019 17:07:07: 13000000 INFO @ Sun, 02 Jun 2019 17:07:08: 13000000 INFO @ Sun, 02 Jun 2019 17:07:16: 14000000 INFO @ Sun, 02 Jun 2019 17:07:17: 14000000 INFO @ Sun, 02 Jun 2019 17:07:18: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:07:18: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:07:18: #1 total tags in treatment: 14197390 INFO @ Sun, 02 Jun 2019 17:07:18: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:07:18: #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 17:07:18: #1 tags after filtering in treatment: 14197390 INFO @ Sun, 02 Jun 2019 17:07:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:07:18: #1 finished! INFO @ Sun, 02 Jun 2019 17:07:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:07:19: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:07:19: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:07:19: #1 total tags in treatment: 14197390 INFO @ Sun, 02 Jun 2019 17:07:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:07:19: #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 17:07:20: #1 tags after filtering in treatment: 14197390 INFO @ Sun, 02 Jun 2019 17:07:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:07:20: #1 finished! INFO @ Sun, 02 Jun 2019 17:07:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:07:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:07:20: #2 number of paired peaks: 280 WARNING @ Sun, 02 Jun 2019 17:07:20: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Sun, 02 Jun 2019 17:07:20: start model_add_line... INFO @ Sun, 02 Jun 2019 17:07:20: start X-correlation... INFO @ Sun, 02 Jun 2019 17:07:20: end of X-cor INFO @ Sun, 02 Jun 2019 17:07:20: #2 finished! INFO @ Sun, 02 Jun 2019 17:07:20: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 17:07:20: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 02 Jun 2019 17:07:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.05_model.r WARNING @ Sun, 02 Jun 2019 17:07:20: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:07:20: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 02 Jun 2019 17:07:20: #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 17:07:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:07:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:07:21: #2 number of paired peaks: 280 WARNING @ Sun, 02 Jun 2019 17:07:21: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Sun, 02 Jun 2019 17:07:21: start model_add_line... INFO @ Sun, 02 Jun 2019 17:07:21: start X-correlation... INFO @ Sun, 02 Jun 2019 17:07:21: end of X-cor INFO @ Sun, 02 Jun 2019 17:07:21: #2 finished! INFO @ Sun, 02 Jun 2019 17:07:21: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 17:07:21: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 02 Jun 2019 17:07:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.20_model.r WARNING @ Sun, 02 Jun 2019 17:07:21: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:07:21: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 02 Jun 2019 17:07:21: #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 17:07:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:07:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:07:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:07:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:07:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:07:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.10_summits.bed INFO @ Sun, 02 Jun 2019 17:07:42: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (464 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:07:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:07:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:08:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:08:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:08:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.05_summits.bed INFO @ Sun, 02 Jun 2019 17:08:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (695 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:08:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:08:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:08:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257706/SRX257706.20_summits.bed INFO @ Sun, 02 Jun 2019 17:08:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (185 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。