Job ID = 1292321 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,231,749 reads read : 33,231,749 reads written : 33,231,749 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: 00:07:57 33231749 reads; of these: 33231749 (100.00%) were unpaired; of these: 359438 (1.08%) aligned 0 times 27444412 (82.58%) aligned exactly 1 time 5427899 (16.33%) aligned >1 times 98.92% overall alignment rate Time searching: 00:07:57 Overall time: 00:07:57 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 12 files... [bam_rmdupse_core] 7402654 / 32872311 = 0.2252 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 18:08:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.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 18:08:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:08:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:08:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.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 18:08:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:08:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:08:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.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 18:08:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:08:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:08:30: 1000000 INFO @ Sun, 02 Jun 2019 18:08:31: 1000000 INFO @ Sun, 02 Jun 2019 18:08:31: 1000000 INFO @ Sun, 02 Jun 2019 18:08:36: 2000000 INFO @ Sun, 02 Jun 2019 18:08:39: 2000000 INFO @ Sun, 02 Jun 2019 18:08:39: 2000000 INFO @ Sun, 02 Jun 2019 18:08:43: 3000000 INFO @ Sun, 02 Jun 2019 18:08:47: 3000000 INFO @ Sun, 02 Jun 2019 18:08:47: 3000000 INFO @ Sun, 02 Jun 2019 18:08:50: 4000000 INFO @ Sun, 02 Jun 2019 18:08:55: 4000000 INFO @ Sun, 02 Jun 2019 18:08:56: 4000000 INFO @ Sun, 02 Jun 2019 18:08:57: 5000000 INFO @ Sun, 02 Jun 2019 18:09:03: 6000000 INFO @ Sun, 02 Jun 2019 18:09:03: 5000000 INFO @ Sun, 02 Jun 2019 18:09:04: 5000000 INFO @ Sun, 02 Jun 2019 18:09:10: 7000000 INFO @ Sun, 02 Jun 2019 18:09:11: 6000000 INFO @ Sun, 02 Jun 2019 18:09:12: 6000000 INFO @ Sun, 02 Jun 2019 18:09:17: 8000000 INFO @ Sun, 02 Jun 2019 18:09:19: 7000000 INFO @ Sun, 02 Jun 2019 18:09:20: 7000000 INFO @ Sun, 02 Jun 2019 18:09:24: 9000000 INFO @ Sun, 02 Jun 2019 18:09:27: 8000000 INFO @ Sun, 02 Jun 2019 18:09:28: 8000000 INFO @ Sun, 02 Jun 2019 18:09:30: 10000000 INFO @ Sun, 02 Jun 2019 18:09:35: 9000000 INFO @ Sun, 02 Jun 2019 18:09:36: 9000000 INFO @ Sun, 02 Jun 2019 18:09:37: 11000000 INFO @ Sun, 02 Jun 2019 18:09:43: 10000000 INFO @ Sun, 02 Jun 2019 18:09:44: 12000000 INFO @ Sun, 02 Jun 2019 18:09:44: 10000000 INFO @ Sun, 02 Jun 2019 18:09:50: 13000000 INFO @ Sun, 02 Jun 2019 18:09:51: 11000000 INFO @ Sun, 02 Jun 2019 18:09:52: 11000000 INFO @ Sun, 02 Jun 2019 18:09:57: 14000000 INFO @ Sun, 02 Jun 2019 18:09:58: 12000000 INFO @ Sun, 02 Jun 2019 18:10:00: 12000000 INFO @ Sun, 02 Jun 2019 18:10:04: 15000000 INFO @ Sun, 02 Jun 2019 18:10:06: 13000000 INFO @ Sun, 02 Jun 2019 18:10:08: 13000000 INFO @ Sun, 02 Jun 2019 18:10:10: 16000000 INFO @ Sun, 02 Jun 2019 18:10:14: 14000000 INFO @ Sun, 02 Jun 2019 18:10:16: 14000000 INFO @ Sun, 02 Jun 2019 18:10:17: 17000000 INFO @ Sun, 02 Jun 2019 18:10:21: 15000000 INFO @ Sun, 02 Jun 2019 18:10:24: 18000000 INFO @ Sun, 02 Jun 2019 18:10:24: 15000000 INFO @ Sun, 02 Jun 2019 18:10:29: 16000000 INFO @ Sun, 02 Jun 2019 18:10:30: 19000000 INFO @ Sun, 02 Jun 2019 18:10:32: 16000000 INFO @ Sun, 02 Jun 2019 18:10:37: 17000000 INFO @ Sun, 02 Jun 2019 18:10:37: 20000000 INFO @ Sun, 02 Jun 2019 18:10:40: 17000000 INFO @ Sun, 02 Jun 2019 18:10:44: 21000000 INFO @ Sun, 02 Jun 2019 18:10:44: 18000000 INFO @ Sun, 02 Jun 2019 18:10:48: 18000000 INFO @ Sun, 02 Jun 2019 18:10:50: 22000000 INFO @ Sun, 02 Jun 2019 18:10:52: 19000000 INFO @ Sun, 02 Jun 2019 18:10:56: 19000000 INFO @ Sun, 02 Jun 2019 18:10:57: 23000000 INFO @ Sun, 02 Jun 2019 18:11:00: 20000000 INFO @ Sun, 02 Jun 2019 18:11:04: 24000000 INFO @ Sun, 02 Jun 2019 18:11:04: 20000000 INFO @ Sun, 02 Jun 2019 18:11:07: 21000000 INFO @ Sun, 02 Jun 2019 18:11:10: 25000000 INFO @ Sun, 02 Jun 2019 18:11:12: 21000000 INFO @ Sun, 02 Jun 2019 18:11:14: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 18:11:14: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 18:11:14: #1 total tags in treatment: 25469657 INFO @ Sun, 02 Jun 2019 18:11:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:11:14: #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 18:11:14: #1 tags after filtering in treatment: 25469657 INFO @ Sun, 02 Jun 2019 18:11:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:11:14: #1 finished! INFO @ Sun, 02 Jun 2019 18:11:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:11:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:11:15: 22000000 INFO @ Sun, 02 Jun 2019 18:11:16: #2 number of paired peaks: 154 WARNING @ Sun, 02 Jun 2019 18:11:16: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Sun, 02 Jun 2019 18:11:16: start model_add_line... INFO @ Sun, 02 Jun 2019 18:11:16: start X-correlation... INFO @ Sun, 02 Jun 2019 18:11:16: end of X-cor INFO @ Sun, 02 Jun 2019 18:11:16: #2 finished! INFO @ Sun, 02 Jun 2019 18:11:16: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:11:16: #2 alternative fragment length(s) may be 1,34,325,445,465,496,530 bps INFO @ Sun, 02 Jun 2019 18:11:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.20_model.r WARNING @ Sun, 02 Jun 2019 18:11:16: #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 18:11:16: #2 You may need to consider one of the other alternative d(s): 1,34,325,445,465,496,530 WARNING @ Sun, 02 Jun 2019 18:11:16: #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 18:11:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:11:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:11:20: 22000000 INFO @ Sun, 02 Jun 2019 18:11:23: 23000000 INFO @ Sun, 02 Jun 2019 18:11:28: 23000000 INFO @ Sun, 02 Jun 2019 18:11:30: 24000000 INFO @ Sun, 02 Jun 2019 18:11:35: 24000000 INFO @ Sun, 02 Jun 2019 18:11:38: 25000000 INFO @ Sun, 02 Jun 2019 18:11:42: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 18:11:42: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 18:11:42: #1 total tags in treatment: 25469657 INFO @ Sun, 02 Jun 2019 18:11:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:11:42: #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 18:11:42: #1 tags after filtering in treatment: 25469657 INFO @ Sun, 02 Jun 2019 18:11:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:11:42: #1 finished! INFO @ Sun, 02 Jun 2019 18:11:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:11:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:11:43: 25000000 INFO @ Sun, 02 Jun 2019 18:11:44: #2 number of paired peaks: 154 WARNING @ Sun, 02 Jun 2019 18:11:44: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Sun, 02 Jun 2019 18:11:44: start model_add_line... INFO @ Sun, 02 Jun 2019 18:11:45: start X-correlation... INFO @ Sun, 02 Jun 2019 18:11:45: end of X-cor INFO @ Sun, 02 Jun 2019 18:11:45: #2 finished! INFO @ Sun, 02 Jun 2019 18:11:45: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:11:45: #2 alternative fragment length(s) may be 1,34,325,445,465,496,530 bps INFO @ Sun, 02 Jun 2019 18:11:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.10_model.r WARNING @ Sun, 02 Jun 2019 18:11:45: #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 18:11:45: #2 You may need to consider one of the other alternative d(s): 1,34,325,445,465,496,530 WARNING @ Sun, 02 Jun 2019 18:11:45: #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 18:11:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:11:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:11:47: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 18:11:47: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 18:11:47: #1 total tags in treatment: 25469657 INFO @ Sun, 02 Jun 2019 18:11:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:11:47: #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 18:11:48: #1 tags after filtering in treatment: 25469657 INFO @ Sun, 02 Jun 2019 18:11:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:11:48: #1 finished! INFO @ Sun, 02 Jun 2019 18:11:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:11:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:11:50: #2 number of paired peaks: 154 WARNING @ Sun, 02 Jun 2019 18:11:50: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Sun, 02 Jun 2019 18:11:50: start model_add_line... INFO @ Sun, 02 Jun 2019 18:11:50: start X-correlation... INFO @ Sun, 02 Jun 2019 18:11:50: end of X-cor INFO @ Sun, 02 Jun 2019 18:11:50: #2 finished! INFO @ Sun, 02 Jun 2019 18:11:50: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:11:50: #2 alternative fragment length(s) may be 1,34,325,445,465,496,530 bps INFO @ Sun, 02 Jun 2019 18:11:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.05_model.r WARNING @ Sun, 02 Jun 2019 18:11:50: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:11:50: #2 You may need to consider one of the other alternative d(s): 1,34,325,445,465,496,530 WARNING @ Sun, 02 Jun 2019 18:11:50: #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 18:11:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:12:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:12:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:12:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:12:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.20_summits.bed INFO @ Sun, 02 Jun 2019 18:12:31: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:12:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:12:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:12:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:12:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:12:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.10_summits.bed INFO @ Sun, 02 Jun 2019 18:12:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:13:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:13:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:13:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331345/SRX331345.05_summits.bed INFO @ Sun, 02 Jun 2019 18:13:05: 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。