Job ID = 1291768 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,558,615 reads read : 26,558,615 reads written : 26,558,615 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:21 26558615 reads; of these: 26558615 (100.00%) were unpaired; of these: 2298096 (8.65%) aligned 0 times 19971542 (75.20%) aligned exactly 1 time 4288977 (16.15%) aligned >1 times 91.35% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 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] 3743882 / 24260519 = 0.1543 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 16:49:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.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 16:49:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:49:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:49:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.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 16:49:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:49:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:49:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.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 16:49:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:49:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:49:59: 1000000 INFO @ Sun, 02 Jun 2019 16:49:59: 1000000 INFO @ Sun, 02 Jun 2019 16:49:59: 1000000 INFO @ Sun, 02 Jun 2019 16:50:09: 2000000 INFO @ Sun, 02 Jun 2019 16:50:09: 2000000 INFO @ Sun, 02 Jun 2019 16:50:09: 2000000 INFO @ Sun, 02 Jun 2019 16:50:19: 3000000 INFO @ Sun, 02 Jun 2019 16:50:20: 3000000 INFO @ Sun, 02 Jun 2019 16:50:20: 3000000 INFO @ Sun, 02 Jun 2019 16:50:30: 4000000 INFO @ Sun, 02 Jun 2019 16:50:31: 4000000 INFO @ Sun, 02 Jun 2019 16:50:31: 4000000 INFO @ Sun, 02 Jun 2019 16:50:41: 5000000 INFO @ Sun, 02 Jun 2019 16:50:41: 5000000 INFO @ Sun, 02 Jun 2019 16:50:42: 5000000 INFO @ Sun, 02 Jun 2019 16:50:51: 6000000 INFO @ Sun, 02 Jun 2019 16:50:52: 6000000 INFO @ Sun, 02 Jun 2019 16:50:53: 6000000 INFO @ Sun, 02 Jun 2019 16:51:01: 7000000 INFO @ Sun, 02 Jun 2019 16:51:03: 7000000 INFO @ Sun, 02 Jun 2019 16:51:03: 7000000 INFO @ Sun, 02 Jun 2019 16:51:12: 8000000 INFO @ Sun, 02 Jun 2019 16:51:13: 8000000 INFO @ Sun, 02 Jun 2019 16:51:14: 8000000 INFO @ Sun, 02 Jun 2019 16:51:23: 9000000 INFO @ Sun, 02 Jun 2019 16:51:24: 9000000 INFO @ Sun, 02 Jun 2019 16:51:25: 9000000 INFO @ Sun, 02 Jun 2019 16:51:34: 10000000 INFO @ Sun, 02 Jun 2019 16:51:36: 10000000 INFO @ Sun, 02 Jun 2019 16:51:37: 10000000 INFO @ Sun, 02 Jun 2019 16:51:45: 11000000 INFO @ Sun, 02 Jun 2019 16:51:47: 11000000 INFO @ Sun, 02 Jun 2019 16:51:48: 11000000 INFO @ Sun, 02 Jun 2019 16:51:56: 12000000 INFO @ Sun, 02 Jun 2019 16:51:58: 12000000 INFO @ Sun, 02 Jun 2019 16:51:59: 12000000 INFO @ Sun, 02 Jun 2019 16:52:06: 13000000 INFO @ Sun, 02 Jun 2019 16:52:09: 13000000 INFO @ Sun, 02 Jun 2019 16:52:10: 13000000 INFO @ Sun, 02 Jun 2019 16:52:16: 14000000 INFO @ Sun, 02 Jun 2019 16:52:19: 14000000 INFO @ Sun, 02 Jun 2019 16:52:21: 14000000 INFO @ Sun, 02 Jun 2019 16:52:27: 15000000 INFO @ Sun, 02 Jun 2019 16:52:30: 15000000 INFO @ Sun, 02 Jun 2019 16:52:31: 15000000 INFO @ Sun, 02 Jun 2019 16:52:37: 16000000 INFO @ Sun, 02 Jun 2019 16:52:42: 16000000 INFO @ Sun, 02 Jun 2019 16:52:43: 16000000 INFO @ Sun, 02 Jun 2019 16:52:48: 17000000 INFO @ Sun, 02 Jun 2019 16:52:52: 17000000 INFO @ Sun, 02 Jun 2019 16:52:54: 17000000 INFO @ Sun, 02 Jun 2019 16:52:59: 18000000 INFO @ Sun, 02 Jun 2019 16:53:03: 18000000 INFO @ Sun, 02 Jun 2019 16:53:05: 18000000 INFO @ Sun, 02 Jun 2019 16:53:10: 19000000 INFO @ Sun, 02 Jun 2019 16:53:14: 19000000 INFO @ Sun, 02 Jun 2019 16:53:17: 19000000 INFO @ Sun, 02 Jun 2019 16:53:21: 20000000 INFO @ Sun, 02 Jun 2019 16:53:25: 20000000 INFO @ Sun, 02 Jun 2019 16:53:27: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:53:27: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:53:27: #1 total tags in treatment: 20516637 INFO @ Sun, 02 Jun 2019 16:53:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:53:27: #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 16:53:27: #1 tags after filtering in treatment: 20516637 INFO @ Sun, 02 Jun 2019 16:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:53:27: #1 finished! INFO @ Sun, 02 Jun 2019 16:53:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:53:28: 20000000 INFO @ Sun, 02 Jun 2019 16:53:30: #2 number of paired peaks: 131 WARNING @ Sun, 02 Jun 2019 16:53:30: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Sun, 02 Jun 2019 16:53:30: start model_add_line... INFO @ Sun, 02 Jun 2019 16:53:30: start X-correlation... INFO @ Sun, 02 Jun 2019 16:53:30: end of X-cor INFO @ Sun, 02 Jun 2019 16:53:30: #2 finished! INFO @ Sun, 02 Jun 2019 16:53:30: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 16:53:30: #2 alternative fragment length(s) may be 2,31,88,488 bps INFO @ Sun, 02 Jun 2019 16:53:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.05_model.r WARNING @ Sun, 02 Jun 2019 16:53:30: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:53:30: #2 You may need to consider one of the other alternative d(s): 2,31,88,488 WARNING @ Sun, 02 Jun 2019 16:53:30: #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 16:53:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:53:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:53:31: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:53:31: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:53:31: #1 total tags in treatment: 20516637 INFO @ Sun, 02 Jun 2019 16:53:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:53:31: #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 16:53:32: #1 tags after filtering in treatment: 20516637 INFO @ Sun, 02 Jun 2019 16:53:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:53:32: #1 finished! INFO @ Sun, 02 Jun 2019 16:53:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:53:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:53:34: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:53:34: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:53:34: #1 total tags in treatment: 20516637 INFO @ Sun, 02 Jun 2019 16:53:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:53:34: #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 16:53:34: #2 number of paired peaks: 131 WARNING @ Sun, 02 Jun 2019 16:53:34: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Sun, 02 Jun 2019 16:53:34: start model_add_line... INFO @ Sun, 02 Jun 2019 16:53:35: start X-correlation... INFO @ Sun, 02 Jun 2019 16:53:35: end of X-cor INFO @ Sun, 02 Jun 2019 16:53:35: #2 finished! INFO @ Sun, 02 Jun 2019 16:53:35: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 16:53:35: #2 alternative fragment length(s) may be 2,31,88,488 bps INFO @ Sun, 02 Jun 2019 16:53:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.20_model.r WARNING @ Sun, 02 Jun 2019 16:53:35: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:53:35: #2 You may need to consider one of the other alternative d(s): 2,31,88,488 WARNING @ Sun, 02 Jun 2019 16:53:35: #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 16:53:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:53:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:53:35: #1 tags after filtering in treatment: 20516637 INFO @ Sun, 02 Jun 2019 16:53:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:53:35: #1 finished! INFO @ Sun, 02 Jun 2019 16:53:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:53:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:53:37: #2 number of paired peaks: 131 WARNING @ Sun, 02 Jun 2019 16:53:37: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Sun, 02 Jun 2019 16:53:37: start model_add_line... INFO @ Sun, 02 Jun 2019 16:53:37: start X-correlation... INFO @ Sun, 02 Jun 2019 16:53:37: end of X-cor INFO @ Sun, 02 Jun 2019 16:53:37: #2 finished! INFO @ Sun, 02 Jun 2019 16:53:37: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 16:53:37: #2 alternative fragment length(s) may be 2,31,88,488 bps INFO @ Sun, 02 Jun 2019 16:53:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.10_model.r WARNING @ Sun, 02 Jun 2019 16:53:37: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:53:37: #2 You may need to consider one of the other alternative d(s): 2,31,88,488 WARNING @ Sun, 02 Jun 2019 16:53:37: #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 16:53:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:53:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:54:32: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:54:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:54:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:54:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:54:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:54:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.05_summits.bed INFO @ Sun, 02 Jun 2019 16:54:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:55:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:55:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:55:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.20_summits.bed INFO @ Sun, 02 Jun 2019 16:55:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:55:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:55:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:55:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX245917/SRX245917.10_summits.bed INFO @ Sun, 02 Jun 2019 16:55:07: 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。