Job ID = 1292507 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,509,609 reads read : 21,509,609 reads written : 21,509,609 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: 00:04:30 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 256457 (1.19%) aligned 0 times 17820550 (82.85%) aligned exactly 1 time 3432602 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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] 3667435 / 21253152 = 0.1726 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 19:20:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.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 19:20:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:20:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:20:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.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 19:20:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:20:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:20:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.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 19:20:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:20:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:20:56: 1000000 INFO @ Sun, 02 Jun 2019 19:20:57: 1000000 INFO @ Sun, 02 Jun 2019 19:20:57: 1000000 INFO @ Sun, 02 Jun 2019 19:21:03: 2000000 INFO @ Sun, 02 Jun 2019 19:21:03: 2000000 INFO @ Sun, 02 Jun 2019 19:21:05: 2000000 INFO @ Sun, 02 Jun 2019 19:21:09: 3000000 INFO @ Sun, 02 Jun 2019 19:21:10: 3000000 INFO @ Sun, 02 Jun 2019 19:21:12: 3000000 INFO @ Sun, 02 Jun 2019 19:21:16: 4000000 INFO @ Sun, 02 Jun 2019 19:21:16: 4000000 INFO @ Sun, 02 Jun 2019 19:21:21: 4000000 INFO @ Sun, 02 Jun 2019 19:21:22: 5000000 INFO @ Sun, 02 Jun 2019 19:21:23: 5000000 INFO @ Sun, 02 Jun 2019 19:21:29: 6000000 INFO @ Sun, 02 Jun 2019 19:21:29: 6000000 INFO @ Sun, 02 Jun 2019 19:21:30: 5000000 INFO @ Sun, 02 Jun 2019 19:21:35: 7000000 INFO @ Sun, 02 Jun 2019 19:21:36: 7000000 INFO @ Sun, 02 Jun 2019 19:21:38: 6000000 INFO @ Sun, 02 Jun 2019 19:21:42: 8000000 INFO @ Sun, 02 Jun 2019 19:21:42: 8000000 INFO @ Sun, 02 Jun 2019 19:21:46: 7000000 INFO @ Sun, 02 Jun 2019 19:21:48: 9000000 INFO @ Sun, 02 Jun 2019 19:21:49: 9000000 INFO @ Sun, 02 Jun 2019 19:21:54: 8000000 INFO @ Sun, 02 Jun 2019 19:21:55: 10000000 INFO @ Sun, 02 Jun 2019 19:21:55: 10000000 INFO @ Sun, 02 Jun 2019 19:22:01: 11000000 INFO @ Sun, 02 Jun 2019 19:22:01: 11000000 INFO @ Sun, 02 Jun 2019 19:22:02: 9000000 INFO @ Sun, 02 Jun 2019 19:22:08: 12000000 INFO @ Sun, 02 Jun 2019 19:22:08: 12000000 INFO @ Sun, 02 Jun 2019 19:22:09: 10000000 INFO @ Sun, 02 Jun 2019 19:22:14: 13000000 INFO @ Sun, 02 Jun 2019 19:22:14: 13000000 INFO @ Sun, 02 Jun 2019 19:22:17: 11000000 INFO @ Sun, 02 Jun 2019 19:22:21: 14000000 INFO @ Sun, 02 Jun 2019 19:22:21: 14000000 INFO @ Sun, 02 Jun 2019 19:22:25: 12000000 INFO @ Sun, 02 Jun 2019 19:22:27: 15000000 INFO @ Sun, 02 Jun 2019 19:22:27: 15000000 INFO @ Sun, 02 Jun 2019 19:22:32: 13000000 INFO @ Sun, 02 Jun 2019 19:22:34: 16000000 INFO @ Sun, 02 Jun 2019 19:22:34: 16000000 INFO @ Sun, 02 Jun 2019 19:22:40: 17000000 INFO @ Sun, 02 Jun 2019 19:22:40: 14000000 INFO @ Sun, 02 Jun 2019 19:22:40: 17000000 INFO @ Sun, 02 Jun 2019 19:22:44: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:22:44: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:22:44: #1 total tags in treatment: 17585717 INFO @ Sun, 02 Jun 2019 19:22:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:22:44: #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 19:22:44: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:22:44: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:22:44: #1 total tags in treatment: 17585717 INFO @ Sun, 02 Jun 2019 19:22:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:22:44: #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 19:22:45: #1 tags after filtering in treatment: 17585717 INFO @ Sun, 02 Jun 2019 19:22:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:22:45: #1 finished! INFO @ Sun, 02 Jun 2019 19:22:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:22:45: #1 tags after filtering in treatment: 17585717 INFO @ Sun, 02 Jun 2019 19:22:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:22:45: #1 finished! INFO @ Sun, 02 Jun 2019 19:22:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:22:47: #2 number of paired peaks: 205 WARNING @ Sun, 02 Jun 2019 19:22:47: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Sun, 02 Jun 2019 19:22:47: start model_add_line... INFO @ Sun, 02 Jun 2019 19:22:47: #2 number of paired peaks: 205 WARNING @ Sun, 02 Jun 2019 19:22:47: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Sun, 02 Jun 2019 19:22:47: start model_add_line... INFO @ Sun, 02 Jun 2019 19:22:47: start X-correlation... INFO @ Sun, 02 Jun 2019 19:22:47: end of X-cor INFO @ Sun, 02 Jun 2019 19:22:47: #2 finished! INFO @ Sun, 02 Jun 2019 19:22:47: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:22:47: #2 alternative fragment length(s) may be 1,40 bps INFO @ Sun, 02 Jun 2019 19:22:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.05_model.r WARNING @ Sun, 02 Jun 2019 19:22:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:22:47: #2 You may need to consider one of the other alternative d(s): 1,40 WARNING @ Sun, 02 Jun 2019 19:22:47: #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 19:22:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:22:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:22:47: start X-correlation... INFO @ Sun, 02 Jun 2019 19:22:47: end of X-cor INFO @ Sun, 02 Jun 2019 19:22:47: #2 finished! INFO @ Sun, 02 Jun 2019 19:22:47: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:22:47: #2 alternative fragment length(s) may be 1,40 bps INFO @ Sun, 02 Jun 2019 19:22:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.10_model.r WARNING @ Sun, 02 Jun 2019 19:22:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:22:47: #2 You may need to consider one of the other alternative d(s): 1,40 WARNING @ Sun, 02 Jun 2019 19:22:47: #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 19:22:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:22:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:22:48: 15000000 INFO @ Sun, 02 Jun 2019 19:22:55: 16000000 INFO @ Sun, 02 Jun 2019 19:23:03: 17000000 INFO @ Sun, 02 Jun 2019 19:23:08: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:23:08: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:23:08: #1 total tags in treatment: 17585717 INFO @ Sun, 02 Jun 2019 19:23:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:23:08: #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 19:23:08: #1 tags after filtering in treatment: 17585717 INFO @ Sun, 02 Jun 2019 19:23:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:23:08: #1 finished! INFO @ Sun, 02 Jun 2019 19:23:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:23:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:23:10: #2 number of paired peaks: 205 WARNING @ Sun, 02 Jun 2019 19:23:10: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Sun, 02 Jun 2019 19:23:10: start model_add_line... INFO @ Sun, 02 Jun 2019 19:23:10: start X-correlation... INFO @ Sun, 02 Jun 2019 19:23:10: end of X-cor INFO @ Sun, 02 Jun 2019 19:23:10: #2 finished! INFO @ Sun, 02 Jun 2019 19:23:10: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:23:10: #2 alternative fragment length(s) may be 1,40 bps INFO @ Sun, 02 Jun 2019 19:23:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.20_model.r WARNING @ Sun, 02 Jun 2019 19:23:10: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:23:10: #2 You may need to consider one of the other alternative d(s): 1,40 WARNING @ Sun, 02 Jun 2019 19:23:10: #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 19:23:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:23:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:23:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:23:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:23:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:23:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:23:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.05_summits.bed INFO @ Sun, 02 Jun 2019 19:23:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:23:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:23:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:23:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.10_summits.bed INFO @ Sun, 02 Jun 2019 19:23:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:23:52: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:24:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:24:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:24:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466516/SRX466516.20_summits.bed INFO @ Sun, 02 Jun 2019 19:24:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。