Job ID = 1292359 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,925,633 reads read : 30,925,633 reads written : 30,925,633 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:01 30925633 reads; of these: 30925633 (100.00%) were unpaired; of these: 10862444 (35.12%) aligned 0 times 16576447 (53.60%) aligned exactly 1 time 3486742 (11.27%) aligned >1 times 64.88% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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] 2309460 / 20063189 = 0.1151 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 18:27:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.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 18:27:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:27:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:27:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.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 18:27:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:27:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:27:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.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 18:27:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:27:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:27:58: 1000000 INFO @ Sun, 02 Jun 2019 18:27:58: 1000000 INFO @ Sun, 02 Jun 2019 18:27:58: 1000000 INFO @ Sun, 02 Jun 2019 18:28:05: 2000000 INFO @ Sun, 02 Jun 2019 18:28:05: 2000000 INFO @ Sun, 02 Jun 2019 18:28:06: 2000000 INFO @ Sun, 02 Jun 2019 18:28:11: 3000000 INFO @ Sun, 02 Jun 2019 18:28:11: 3000000 INFO @ Sun, 02 Jun 2019 18:28:13: 3000000 INFO @ Sun, 02 Jun 2019 18:28:18: 4000000 INFO @ Sun, 02 Jun 2019 18:28:18: 4000000 INFO @ Sun, 02 Jun 2019 18:28:20: 4000000 INFO @ Sun, 02 Jun 2019 18:28:24: 5000000 INFO @ Sun, 02 Jun 2019 18:28:25: 5000000 INFO @ Sun, 02 Jun 2019 18:28:27: 5000000 INFO @ Sun, 02 Jun 2019 18:28:31: 6000000 INFO @ Sun, 02 Jun 2019 18:28:31: 6000000 INFO @ Sun, 02 Jun 2019 18:28:34: 6000000 INFO @ Sun, 02 Jun 2019 18:28:37: 7000000 INFO @ Sun, 02 Jun 2019 18:28:38: 7000000 INFO @ Sun, 02 Jun 2019 18:28:41: 7000000 INFO @ Sun, 02 Jun 2019 18:28:44: 8000000 INFO @ Sun, 02 Jun 2019 18:28:45: 8000000 INFO @ Sun, 02 Jun 2019 18:28:48: 8000000 INFO @ Sun, 02 Jun 2019 18:28:50: 9000000 INFO @ Sun, 02 Jun 2019 18:28:51: 9000000 INFO @ Sun, 02 Jun 2019 18:28:55: 9000000 INFO @ Sun, 02 Jun 2019 18:28:57: 10000000 INFO @ Sun, 02 Jun 2019 18:28:58: 10000000 INFO @ Sun, 02 Jun 2019 18:29:02: 10000000 INFO @ Sun, 02 Jun 2019 18:29:03: 11000000 INFO @ Sun, 02 Jun 2019 18:29:04: 11000000 INFO @ Sun, 02 Jun 2019 18:29:09: 11000000 INFO @ Sun, 02 Jun 2019 18:29:09: 12000000 INFO @ Sun, 02 Jun 2019 18:29:11: 12000000 INFO @ Sun, 02 Jun 2019 18:29:16: 13000000 INFO @ Sun, 02 Jun 2019 18:29:16: 12000000 INFO @ Sun, 02 Jun 2019 18:29:18: 13000000 INFO @ Sun, 02 Jun 2019 18:29:22: 14000000 INFO @ Sun, 02 Jun 2019 18:29:23: 13000000 INFO @ Sun, 02 Jun 2019 18:29:24: 14000000 INFO @ Sun, 02 Jun 2019 18:29:29: 15000000 INFO @ Sun, 02 Jun 2019 18:29:30: 14000000 INFO @ Sun, 02 Jun 2019 18:29:31: 15000000 INFO @ Sun, 02 Jun 2019 18:29:35: 16000000 INFO @ Sun, 02 Jun 2019 18:29:37: 15000000 INFO @ Sun, 02 Jun 2019 18:29:37: 16000000 INFO @ Sun, 02 Jun 2019 18:29:42: 17000000 INFO @ Sun, 02 Jun 2019 18:29:44: 17000000 INFO @ Sun, 02 Jun 2019 18:29:44: 16000000 INFO @ Sun, 02 Jun 2019 18:29:47: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 18:29:47: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 18:29:47: #1 total tags in treatment: 17753729 INFO @ Sun, 02 Jun 2019 18:29:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:29:47: #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 18:29:47: #1 tags after filtering in treatment: 17753729 INFO @ Sun, 02 Jun 2019 18:29:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:29:47: #1 finished! INFO @ Sun, 02 Jun 2019 18:29:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:29:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:29:49: #2 number of paired peaks: 230 WARNING @ Sun, 02 Jun 2019 18:29:49: 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 18:29:49: start model_add_line... INFO @ Sun, 02 Jun 2019 18:29:49: start X-correlation... INFO @ Sun, 02 Jun 2019 18:29:49: end of X-cor INFO @ Sun, 02 Jun 2019 18:29:49: #2 finished! INFO @ Sun, 02 Jun 2019 18:29:49: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:29:49: #2 alternative fragment length(s) may be 1,22,520,551,577,593,597 bps INFO @ Sun, 02 Jun 2019 18:29:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.05_model.r WARNING @ Sun, 02 Jun 2019 18:29:49: #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 18:29:49: #2 You may need to consider one of the other alternative d(s): 1,22,520,551,577,593,597 WARNING @ Sun, 02 Jun 2019 18:29:49: #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 18:29:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:29:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:29:49: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 18:29:49: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 18:29:49: #1 total tags in treatment: 17753729 INFO @ Sun, 02 Jun 2019 18:29:49: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:29:49: #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 18:29:50: #1 tags after filtering in treatment: 17753729 INFO @ Sun, 02 Jun 2019 18:29:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:29:50: #1 finished! INFO @ Sun, 02 Jun 2019 18:29:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:29:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:29:51: 17000000 INFO @ Sun, 02 Jun 2019 18:29:51: #2 number of paired peaks: 230 WARNING @ Sun, 02 Jun 2019 18:29:51: 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 18:29:51: start model_add_line... INFO @ Sun, 02 Jun 2019 18:29:51: start X-correlation... INFO @ Sun, 02 Jun 2019 18:29:51: end of X-cor INFO @ Sun, 02 Jun 2019 18:29:51: #2 finished! INFO @ Sun, 02 Jun 2019 18:29:51: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:29:51: #2 alternative fragment length(s) may be 1,22,520,551,577,593,597 bps INFO @ Sun, 02 Jun 2019 18:29:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.20_model.r WARNING @ Sun, 02 Jun 2019 18:29:51: #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 18:29:51: #2 You may need to consider one of the other alternative d(s): 1,22,520,551,577,593,597 WARNING @ Sun, 02 Jun 2019 18:29:51: #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 18:29:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:29:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:29:57: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 18:29:57: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 18:29:57: #1 total tags in treatment: 17753729 INFO @ Sun, 02 Jun 2019 18:29:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:29:57: #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 18:29:57: #1 tags after filtering in treatment: 17753729 INFO @ Sun, 02 Jun 2019 18:29:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:29:57: #1 finished! INFO @ Sun, 02 Jun 2019 18:29:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:29:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:29:58: #2 number of paired peaks: 230 WARNING @ Sun, 02 Jun 2019 18:29:58: 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 18:29:58: start model_add_line... INFO @ Sun, 02 Jun 2019 18:29:59: start X-correlation... INFO @ Sun, 02 Jun 2019 18:29:59: end of X-cor INFO @ Sun, 02 Jun 2019 18:29:59: #2 finished! INFO @ Sun, 02 Jun 2019 18:29:59: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:29:59: #2 alternative fragment length(s) may be 1,22,520,551,577,593,597 bps INFO @ Sun, 02 Jun 2019 18:29:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.10_model.r WARNING @ Sun, 02 Jun 2019 18:29:59: #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 18:29:59: #2 You may need to consider one of the other alternative d(s): 1,22,520,551,577,593,597 WARNING @ Sun, 02 Jun 2019 18:29:59: #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 18:29:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:29:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:30:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:30:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:30:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:30:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:30:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:30:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.05_summits.bed INFO @ Sun, 02 Jun 2019 18:30:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:30:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:30:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:30:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.20_summits.bed INFO @ Sun, 02 Jun 2019 18:30:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:30:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:30:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:30:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373274/SRX373274.10_summits.bed INFO @ Sun, 02 Jun 2019 18:30:57: 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。