Job ID = 1293145 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,585,176 reads read : 30,585,176 reads written : 30,585,176 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: 00:07:01 30585176 reads; of these: 30585176 (100.00%) were unpaired; of these: 2495094 (8.16%) aligned 0 times 24366330 (79.67%) aligned exactly 1 time 3723752 (12.18%) aligned >1 times 91.84% overall alignment rate Time searching: 00:07:01 Overall time: 00:07:01 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 12 files... [bam_rmdupse_core] 6002385 / 28090082 = 0.2137 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 22:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.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 22:29:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:29:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.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 22:29:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:29:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.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 22:29:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:29:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:29:11: 1000000 INFO @ Sun, 02 Jun 2019 22:29:11: 1000000 INFO @ Sun, 02 Jun 2019 22:29:11: 1000000 INFO @ Sun, 02 Jun 2019 22:29:20: 2000000 INFO @ Sun, 02 Jun 2019 22:29:20: 2000000 INFO @ Sun, 02 Jun 2019 22:29:20: 2000000 INFO @ Sun, 02 Jun 2019 22:29:28: 3000000 INFO @ Sun, 02 Jun 2019 22:29:28: 3000000 INFO @ Sun, 02 Jun 2019 22:29:29: 3000000 INFO @ Sun, 02 Jun 2019 22:29:36: 4000000 INFO @ Sun, 02 Jun 2019 22:29:37: 4000000 INFO @ Sun, 02 Jun 2019 22:29:38: 4000000 INFO @ Sun, 02 Jun 2019 22:29:44: 5000000 INFO @ Sun, 02 Jun 2019 22:29:45: 5000000 INFO @ Sun, 02 Jun 2019 22:29:46: 5000000 INFO @ Sun, 02 Jun 2019 22:29:52: 6000000 INFO @ Sun, 02 Jun 2019 22:29:54: 6000000 INFO @ Sun, 02 Jun 2019 22:29:54: 6000000 INFO @ Sun, 02 Jun 2019 22:30:00: 7000000 INFO @ Sun, 02 Jun 2019 22:30:02: 7000000 INFO @ Sun, 02 Jun 2019 22:30:02: 7000000 INFO @ Sun, 02 Jun 2019 22:30:09: 8000000 INFO @ Sun, 02 Jun 2019 22:30:10: 8000000 INFO @ Sun, 02 Jun 2019 22:30:11: 8000000 INFO @ Sun, 02 Jun 2019 22:30:16: 9000000 INFO @ Sun, 02 Jun 2019 22:30:18: 9000000 INFO @ Sun, 02 Jun 2019 22:30:19: 9000000 INFO @ Sun, 02 Jun 2019 22:30:24: 10000000 INFO @ Sun, 02 Jun 2019 22:30:26: 10000000 INFO @ Sun, 02 Jun 2019 22:30:27: 10000000 INFO @ Sun, 02 Jun 2019 22:30:32: 11000000 INFO @ Sun, 02 Jun 2019 22:30:34: 11000000 INFO @ Sun, 02 Jun 2019 22:30:35: 11000000 INFO @ Sun, 02 Jun 2019 22:30:40: 12000000 INFO @ Sun, 02 Jun 2019 22:30:42: 12000000 INFO @ Sun, 02 Jun 2019 22:30:44: 12000000 INFO @ Sun, 02 Jun 2019 22:30:47: 13000000 INFO @ Sun, 02 Jun 2019 22:30:49: 13000000 INFO @ Sun, 02 Jun 2019 22:30:52: 13000000 INFO @ Sun, 02 Jun 2019 22:30:54: 14000000 INFO @ Sun, 02 Jun 2019 22:30:56: 14000000 INFO @ Sun, 02 Jun 2019 22:31:00: 14000000 INFO @ Sun, 02 Jun 2019 22:31:02: 15000000 INFO @ Sun, 02 Jun 2019 22:31:03: 15000000 INFO @ Sun, 02 Jun 2019 22:31:08: 15000000 INFO @ Sun, 02 Jun 2019 22:31:10: 16000000 INFO @ Sun, 02 Jun 2019 22:31:11: 16000000 INFO @ Sun, 02 Jun 2019 22:31:16: 16000000 INFO @ Sun, 02 Jun 2019 22:31:17: 17000000 INFO @ Sun, 02 Jun 2019 22:31:18: 17000000 INFO @ Sun, 02 Jun 2019 22:31:24: 17000000 INFO @ Sun, 02 Jun 2019 22:31:25: 18000000 INFO @ Sun, 02 Jun 2019 22:31:25: 18000000 INFO @ Sun, 02 Jun 2019 22:31:32: 18000000 INFO @ Sun, 02 Jun 2019 22:31:32: 19000000 INFO @ Sun, 02 Jun 2019 22:31:32: 19000000 INFO @ Sun, 02 Jun 2019 22:31:40: 20000000 INFO @ Sun, 02 Jun 2019 22:31:40: 19000000 INFO @ Sun, 02 Jun 2019 22:31:40: 20000000 INFO @ Sun, 02 Jun 2019 22:31:47: 21000000 INFO @ Sun, 02 Jun 2019 22:31:47: 21000000 INFO @ Sun, 02 Jun 2019 22:31:48: 20000000 INFO @ Sun, 02 Jun 2019 22:31:54: 22000000 INFO @ Sun, 02 Jun 2019 22:31:54: 22000000 INFO @ Sun, 02 Jun 2019 22:31:55: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:31:55: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:31:55: #1 total tags in treatment: 22087697 INFO @ Sun, 02 Jun 2019 22:31:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:31:55: #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 22:31:55: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:31:55: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:31:55: #1 total tags in treatment: 22087697 INFO @ Sun, 02 Jun 2019 22:31:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:31:55: #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 22:31:55: #1 tags after filtering in treatment: 22087697 INFO @ Sun, 02 Jun 2019 22:31:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:31:55: #1 finished! INFO @ Sun, 02 Jun 2019 22:31:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:31:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:31:56: #1 tags after filtering in treatment: 22087697 INFO @ Sun, 02 Jun 2019 22:31:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:31:56: #1 finished! INFO @ Sun, 02 Jun 2019 22:31:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:31:56: 21000000 INFO @ Sun, 02 Jun 2019 22:31:57: #2 number of paired peaks: 165 WARNING @ Sun, 02 Jun 2019 22:31:57: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sun, 02 Jun 2019 22:31:57: start model_add_line... INFO @ Sun, 02 Jun 2019 22:31:57: #2 number of paired peaks: 165 WARNING @ Sun, 02 Jun 2019 22:31:57: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sun, 02 Jun 2019 22:31:57: start model_add_line... INFO @ Sun, 02 Jun 2019 22:31:57: start X-correlation... INFO @ Sun, 02 Jun 2019 22:31:57: end of X-cor INFO @ Sun, 02 Jun 2019 22:31:57: #2 finished! INFO @ Sun, 02 Jun 2019 22:31:57: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:31:57: #2 alternative fragment length(s) may be 1,35,51,576,597 bps INFO @ Sun, 02 Jun 2019 22:31:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.05_model.r WARNING @ Sun, 02 Jun 2019 22:31:57: #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 22:31:57: #2 You may need to consider one of the other alternative d(s): 1,35,51,576,597 WARNING @ Sun, 02 Jun 2019 22:31:57: #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 22:31:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:31:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:31:58: start X-correlation... INFO @ Sun, 02 Jun 2019 22:31:58: end of X-cor INFO @ Sun, 02 Jun 2019 22:31:58: #2 finished! INFO @ Sun, 02 Jun 2019 22:31:58: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:31:58: #2 alternative fragment length(s) may be 1,35,51,576,597 bps INFO @ Sun, 02 Jun 2019 22:31:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.10_model.r WARNING @ Sun, 02 Jun 2019 22:31:58: #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 22:31:58: #2 You may need to consider one of the other alternative d(s): 1,35,51,576,597 WARNING @ Sun, 02 Jun 2019 22:31:58: #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 22:31:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:31:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:32:03: 22000000 INFO @ Sun, 02 Jun 2019 22:32:04: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:32:04: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:32:04: #1 total tags in treatment: 22087697 INFO @ Sun, 02 Jun 2019 22:32:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:32:04: #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 22:32:05: #1 tags after filtering in treatment: 22087697 INFO @ Sun, 02 Jun 2019 22:32:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:32:05: #1 finished! INFO @ Sun, 02 Jun 2019 22:32:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:32:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:32:07: #2 number of paired peaks: 165 WARNING @ Sun, 02 Jun 2019 22:32:07: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sun, 02 Jun 2019 22:32:07: start model_add_line... INFO @ Sun, 02 Jun 2019 22:32:07: start X-correlation... INFO @ Sun, 02 Jun 2019 22:32:07: end of X-cor INFO @ Sun, 02 Jun 2019 22:32:07: #2 finished! INFO @ Sun, 02 Jun 2019 22:32:07: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:32:07: #2 alternative fragment length(s) may be 1,35,51,576,597 bps INFO @ Sun, 02 Jun 2019 22:32:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.20_model.r WARNING @ Sun, 02 Jun 2019 22:32:07: #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 22:32:07: #2 You may need to consider one of the other alternative d(s): 1,35,51,576,597 WARNING @ Sun, 02 Jun 2019 22:32:07: #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 22:32:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:32:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:32:43: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:32:43: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:32:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:33:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:33:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:33:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.05_summits.bed INFO @ Sun, 02 Jun 2019 22:33:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:33:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:33:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:33:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.10_summits.bed INFO @ Sun, 02 Jun 2019 22:33:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:33:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:33:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:33:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402714/SRX5402714.20_summits.bed INFO @ Sun, 02 Jun 2019 22:33:11: 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。