Job ID = 1291858 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,952,107 reads read : 20,952,107 reads written : 20,952,107 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: 00:04:52 20952107 reads; of these: 20952107 (100.00%) were unpaired; of these: 616213 (2.94%) aligned 0 times 16788221 (80.13%) aligned exactly 1 time 3547673 (16.93%) aligned >1 times 97.06% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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] 2047750 / 20335894 = 0.1007 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 16:55:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.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 16:55:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:55:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:55:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.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 16:55:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:55:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:55:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.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 16:55:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:55:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:55:52: 1000000 INFO @ Sun, 02 Jun 2019 16:55:53: 1000000 INFO @ Sun, 02 Jun 2019 16:55:54: 1000000 INFO @ Sun, 02 Jun 2019 16:56:00: 2000000 INFO @ Sun, 02 Jun 2019 16:56:01: 2000000 INFO @ Sun, 02 Jun 2019 16:56:04: 2000000 INFO @ Sun, 02 Jun 2019 16:56:07: 3000000 INFO @ Sun, 02 Jun 2019 16:56:10: 3000000 INFO @ Sun, 02 Jun 2019 16:56:14: 3000000 INFO @ Sun, 02 Jun 2019 16:56:15: 4000000 INFO @ Sun, 02 Jun 2019 16:56:19: 4000000 INFO @ Sun, 02 Jun 2019 16:56:23: 5000000 INFO @ Sun, 02 Jun 2019 16:56:24: 4000000 INFO @ Sun, 02 Jun 2019 16:56:29: 5000000 INFO @ Sun, 02 Jun 2019 16:56:31: 6000000 INFO @ Sun, 02 Jun 2019 16:56:33: 5000000 INFO @ Sun, 02 Jun 2019 16:56:38: 6000000 INFO @ Sun, 02 Jun 2019 16:56:38: 7000000 INFO @ Sun, 02 Jun 2019 16:56:43: 6000000 INFO @ Sun, 02 Jun 2019 16:56:46: 8000000 INFO @ Sun, 02 Jun 2019 16:56:46: 7000000 INFO @ Sun, 02 Jun 2019 16:56:53: 7000000 INFO @ Sun, 02 Jun 2019 16:56:53: 9000000 INFO @ Sun, 02 Jun 2019 16:56:54: 8000000 INFO @ Sun, 02 Jun 2019 16:57:01: 10000000 INFO @ Sun, 02 Jun 2019 16:57:02: 8000000 INFO @ Sun, 02 Jun 2019 16:57:02: 9000000 INFO @ Sun, 02 Jun 2019 16:57:09: 11000000 INFO @ Sun, 02 Jun 2019 16:57:11: 10000000 INFO @ Sun, 02 Jun 2019 16:57:12: 9000000 INFO @ Sun, 02 Jun 2019 16:57:16: 12000000 INFO @ Sun, 02 Jun 2019 16:57:19: 11000000 INFO @ Sun, 02 Jun 2019 16:57:21: 10000000 INFO @ Sun, 02 Jun 2019 16:57:24: 13000000 INFO @ Sun, 02 Jun 2019 16:57:28: 12000000 INFO @ Sun, 02 Jun 2019 16:57:31: 11000000 INFO @ Sun, 02 Jun 2019 16:57:31: 14000000 INFO @ Sun, 02 Jun 2019 16:57:36: 13000000 INFO @ Sun, 02 Jun 2019 16:57:39: 15000000 INFO @ Sun, 02 Jun 2019 16:57:40: 12000000 INFO @ Sun, 02 Jun 2019 16:57:44: 14000000 INFO @ Sun, 02 Jun 2019 16:57:46: 16000000 INFO @ Sun, 02 Jun 2019 16:57:50: 13000000 INFO @ Sun, 02 Jun 2019 16:57:52: 15000000 INFO @ Sun, 02 Jun 2019 16:57:54: 17000000 INFO @ Sun, 02 Jun 2019 16:57:59: 14000000 INFO @ Sun, 02 Jun 2019 16:58:01: 16000000 INFO @ Sun, 02 Jun 2019 16:58:02: 18000000 INFO @ Sun, 02 Jun 2019 16:58:04: #1 tag size is determined as 35 bps INFO @ Sun, 02 Jun 2019 16:58:04: #1 tag size = 35 INFO @ Sun, 02 Jun 2019 16:58:04: #1 total tags in treatment: 18288144 INFO @ Sun, 02 Jun 2019 16:58:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:58:04: #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 16:58:05: #1 tags after filtering in treatment: 18288144 INFO @ Sun, 02 Jun 2019 16:58:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:58:05: #1 finished! INFO @ Sun, 02 Jun 2019 16:58:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:58:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:58:06: #2 number of paired peaks: 230 WARNING @ Sun, 02 Jun 2019 16:58:06: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Sun, 02 Jun 2019 16:58:06: start model_add_line... INFO @ Sun, 02 Jun 2019 16:58:06: start X-correlation... INFO @ Sun, 02 Jun 2019 16:58:06: end of X-cor INFO @ Sun, 02 Jun 2019 16:58:06: #2 finished! INFO @ Sun, 02 Jun 2019 16:58:06: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:58:06: #2 alternative fragment length(s) may be 1,31,562,593 bps INFO @ Sun, 02 Jun 2019 16:58:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.10_model.r WARNING @ Sun, 02 Jun 2019 16:58:06: #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 16:58:06: #2 You may need to consider one of the other alternative d(s): 1,31,562,593 WARNING @ Sun, 02 Jun 2019 16:58:06: #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 16:58:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:58:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:58:09: 15000000 INFO @ Sun, 02 Jun 2019 16:58:09: 17000000 INFO @ Sun, 02 Jun 2019 16:58:17: 18000000 INFO @ Sun, 02 Jun 2019 16:58:18: 16000000 INFO @ Sun, 02 Jun 2019 16:58:19: #1 tag size is determined as 35 bps INFO @ Sun, 02 Jun 2019 16:58:19: #1 tag size = 35 INFO @ Sun, 02 Jun 2019 16:58:19: #1 total tags in treatment: 18288144 INFO @ Sun, 02 Jun 2019 16:58:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:58:19: #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 16:58:20: #1 tags after filtering in treatment: 18288144 INFO @ Sun, 02 Jun 2019 16:58:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:58:20: #1 finished! INFO @ Sun, 02 Jun 2019 16:58:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:58:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:58:21: #2 number of paired peaks: 230 WARNING @ Sun, 02 Jun 2019 16:58:21: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Sun, 02 Jun 2019 16:58:21: start model_add_line... INFO @ Sun, 02 Jun 2019 16:58:22: start X-correlation... INFO @ Sun, 02 Jun 2019 16:58:22: end of X-cor INFO @ Sun, 02 Jun 2019 16:58:22: #2 finished! INFO @ Sun, 02 Jun 2019 16:58:22: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:58:22: #2 alternative fragment length(s) may be 1,31,562,593 bps INFO @ Sun, 02 Jun 2019 16:58:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.05_model.r WARNING @ Sun, 02 Jun 2019 16:58:22: #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 16:58:22: #2 You may need to consider one of the other alternative d(s): 1,31,562,593 WARNING @ Sun, 02 Jun 2019 16:58:22: #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 16:58:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:58:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:58:28: 17000000 INFO @ Sun, 02 Jun 2019 16:58:37: 18000000 INFO @ Sun, 02 Jun 2019 16:58:40: #1 tag size is determined as 35 bps INFO @ Sun, 02 Jun 2019 16:58:40: #1 tag size = 35 INFO @ Sun, 02 Jun 2019 16:58:40: #1 total tags in treatment: 18288144 INFO @ Sun, 02 Jun 2019 16:58:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:58:40: #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 16:58:40: #1 tags after filtering in treatment: 18288144 INFO @ Sun, 02 Jun 2019 16:58:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:58:40: #1 finished! INFO @ Sun, 02 Jun 2019 16:58:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:58:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:58:42: #2 number of paired peaks: 230 WARNING @ Sun, 02 Jun 2019 16:58:42: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Sun, 02 Jun 2019 16:58:42: start model_add_line... INFO @ Sun, 02 Jun 2019 16:58:42: start X-correlation... INFO @ Sun, 02 Jun 2019 16:58:42: end of X-cor INFO @ Sun, 02 Jun 2019 16:58:42: #2 finished! INFO @ Sun, 02 Jun 2019 16:58:42: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:58:42: #2 alternative fragment length(s) may be 1,31,562,593 bps INFO @ Sun, 02 Jun 2019 16:58:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.20_model.r WARNING @ Sun, 02 Jun 2019 16:58:42: #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 16:58:42: #2 You may need to consider one of the other alternative d(s): 1,31,562,593 WARNING @ Sun, 02 Jun 2019 16:58:42: #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 16:58:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:58:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:58:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:59:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:59:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:59:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:59:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.10_summits.bed INFO @ Sun, 02 Jun 2019 16:59:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:59:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:59:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:59:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.05_summits.bed INFO @ Sun, 02 Jun 2019 16:59:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:59:28: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:59:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257693/SRX257693.20_summits.bed INFO @ Sun, 02 Jun 2019 16:59:48: 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。