Job ID = 2590227 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,203,719 reads read : 60,407,438 reads written : 30,203,719 reads 0-length : 30,203,719 rm: cannot remove ‘[DSE]RR*’: 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: 00:06:34 30203719 reads; of these: 30203719 (100.00%) were unpaired; of these: 4769481 (15.79%) aligned 0 times 21201379 (70.19%) aligned exactly 1 time 4232859 (14.01%) aligned >1 times 84.21% overall alignment rate Time searching: 00:06:34 Overall time: 00:06:34 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 12 files... [bam_rmdupse_core] 9557551 / 25434238 = 0.3758 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 @ Mon, 12 Aug 2019 20:30:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.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 @ Mon, 12 Aug 2019 20:30:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:30:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:30:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.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 @ Mon, 12 Aug 2019 20:30:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:30:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:30:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.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 @ Mon, 12 Aug 2019 20:30:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:30:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:30:50: 1000000 INFO @ Mon, 12 Aug 2019 20:30:50: 1000000 INFO @ Mon, 12 Aug 2019 20:30:52: 1000000 INFO @ Mon, 12 Aug 2019 20:30:58: 2000000 INFO @ Mon, 12 Aug 2019 20:30:58: 2000000 INFO @ Mon, 12 Aug 2019 20:31:00: 2000000 INFO @ Mon, 12 Aug 2019 20:31:05: 3000000 INFO @ Mon, 12 Aug 2019 20:31:05: 3000000 INFO @ Mon, 12 Aug 2019 20:31:08: 3000000 INFO @ Mon, 12 Aug 2019 20:31:12: 4000000 INFO @ Mon, 12 Aug 2019 20:31:12: 4000000 INFO @ Mon, 12 Aug 2019 20:31:16: 4000000 INFO @ Mon, 12 Aug 2019 20:31:19: 5000000 INFO @ Mon, 12 Aug 2019 20:31:19: 5000000 INFO @ Mon, 12 Aug 2019 20:31:23: 5000000 INFO @ Mon, 12 Aug 2019 20:31:26: 6000000 INFO @ Mon, 12 Aug 2019 20:31:26: 6000000 INFO @ Mon, 12 Aug 2019 20:31:31: 6000000 INFO @ Mon, 12 Aug 2019 20:31:33: 7000000 INFO @ Mon, 12 Aug 2019 20:31:33: 7000000 INFO @ Mon, 12 Aug 2019 20:31:39: 7000000 INFO @ Mon, 12 Aug 2019 20:31:41: 8000000 INFO @ Mon, 12 Aug 2019 20:31:41: 8000000 INFO @ Mon, 12 Aug 2019 20:31:47: 8000000 INFO @ Mon, 12 Aug 2019 20:31:48: 9000000 INFO @ Mon, 12 Aug 2019 20:31:48: 9000000 INFO @ Mon, 12 Aug 2019 20:31:55: 9000000 INFO @ Mon, 12 Aug 2019 20:31:55: 10000000 INFO @ Mon, 12 Aug 2019 20:31:55: 10000000 INFO @ Mon, 12 Aug 2019 20:32:02: 11000000 INFO @ Mon, 12 Aug 2019 20:32:02: 11000000 INFO @ Mon, 12 Aug 2019 20:32:03: 10000000 INFO @ Mon, 12 Aug 2019 20:32:09: 12000000 INFO @ Mon, 12 Aug 2019 20:32:09: 12000000 INFO @ Mon, 12 Aug 2019 20:32:10: 11000000 INFO @ Mon, 12 Aug 2019 20:32:17: 13000000 INFO @ Mon, 12 Aug 2019 20:32:17: 13000000 INFO @ Mon, 12 Aug 2019 20:32:18: 12000000 INFO @ Mon, 12 Aug 2019 20:32:24: 14000000 INFO @ Mon, 12 Aug 2019 20:32:24: 14000000 INFO @ Mon, 12 Aug 2019 20:32:26: 13000000 INFO @ Mon, 12 Aug 2019 20:32:32: 15000000 INFO @ Mon, 12 Aug 2019 20:32:32: 15000000 INFO @ Mon, 12 Aug 2019 20:32:34: 14000000 INFO @ Mon, 12 Aug 2019 20:32:38: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:32:38: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:32:38: #1 total tags in treatment: 15876687 INFO @ Mon, 12 Aug 2019 20:32:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:32:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:32:38: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:32:38: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:32:38: #1 total tags in treatment: 15876687 INFO @ Mon, 12 Aug 2019 20:32:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:32:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:32:38: #1 tags after filtering in treatment: 15876687 INFO @ Mon, 12 Aug 2019 20:32:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:32:38: #1 finished! INFO @ Mon, 12 Aug 2019 20:32:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:32:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:32:39: #1 tags after filtering in treatment: 15876687 INFO @ Mon, 12 Aug 2019 20:32:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:32:39: #1 finished! INFO @ Mon, 12 Aug 2019 20:32:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:32:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:32:40: #2 number of paired peaks: 353 WARNING @ Mon, 12 Aug 2019 20:32:40: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Mon, 12 Aug 2019 20:32:40: start model_add_line... INFO @ Mon, 12 Aug 2019 20:32:40: start X-correlation... INFO @ Mon, 12 Aug 2019 20:32:40: end of X-cor INFO @ Mon, 12 Aug 2019 20:32:40: #2 finished! INFO @ Mon, 12 Aug 2019 20:32:40: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:32:40: #2 alternative fragment length(s) may be 1,32 bps INFO @ Mon, 12 Aug 2019 20:32:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.10_model.r WARNING @ Mon, 12 Aug 2019 20:32:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:32:40: #2 You may need to consider one of the other alternative d(s): 1,32 WARNING @ Mon, 12 Aug 2019 20:32:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:32:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:32:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:32:40: #2 number of paired peaks: 353 WARNING @ Mon, 12 Aug 2019 20:32:40: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Mon, 12 Aug 2019 20:32:40: start model_add_line... INFO @ Mon, 12 Aug 2019 20:32:40: start X-correlation... INFO @ Mon, 12 Aug 2019 20:32:40: end of X-cor INFO @ Mon, 12 Aug 2019 20:32:40: #2 finished! INFO @ Mon, 12 Aug 2019 20:32:40: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:32:40: #2 alternative fragment length(s) may be 1,32 bps INFO @ Mon, 12 Aug 2019 20:32:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.05_model.r WARNING @ Mon, 12 Aug 2019 20:32:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:32:40: #2 You may need to consider one of the other alternative d(s): 1,32 WARNING @ Mon, 12 Aug 2019 20:32:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:32:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:32:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:32:41: 15000000 INFO @ Mon, 12 Aug 2019 20:32:48: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:32:48: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:32:48: #1 total tags in treatment: 15876687 INFO @ Mon, 12 Aug 2019 20:32:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:32:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:32:48: #1 tags after filtering in treatment: 15876687 INFO @ Mon, 12 Aug 2019 20:32:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:32:48: #1 finished! INFO @ Mon, 12 Aug 2019 20:32:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:32:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:32:50: #2 number of paired peaks: 353 WARNING @ Mon, 12 Aug 2019 20:32:50: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Mon, 12 Aug 2019 20:32:50: start model_add_line... INFO @ Mon, 12 Aug 2019 20:32:50: start X-correlation... INFO @ Mon, 12 Aug 2019 20:32:50: end of X-cor INFO @ Mon, 12 Aug 2019 20:32:50: #2 finished! INFO @ Mon, 12 Aug 2019 20:32:50: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:32:50: #2 alternative fragment length(s) may be 1,32 bps INFO @ Mon, 12 Aug 2019 20:32:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.20_model.r WARNING @ Mon, 12 Aug 2019 20:32:50: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:32:50: #2 You may need to consider one of the other alternative d(s): 1,32 WARNING @ Mon, 12 Aug 2019 20:32:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:32:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:32:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:33:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:33:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:33:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:33:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:33:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:33:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.10_summits.bed INFO @ Mon, 12 Aug 2019 20:33:34: Done! INFO @ Mon, 12 Aug 2019 20:33:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:33:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:33:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.05_summits.bed INFO @ Mon, 12 Aug 2019 20:33:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:33:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:33:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:33:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5709768/SRX5709768.20_summits.bed INFO @ Mon, 12 Aug 2019 20:33:44: Done! pass1 - making usageList (0 chroms): 2 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。