Job ID = 2590156 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,434,363 reads read : 24,434,363 reads written : 24,434,363 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: 00:06:18 24434363 reads; of these: 24434363 (100.00%) were unpaired; of these: 3205470 (13.12%) aligned 0 times 17392767 (71.18%) aligned exactly 1 time 3836126 (15.70%) aligned >1 times 86.88% overall alignment rate Time searching: 00:06:18 Overall time: 00:06:18 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] 2473747 / 21228893 = 0.1165 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 20:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.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 20:10:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:10:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:10:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.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 20:10:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:10:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:10:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.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 20:10:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:10:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:10:27: 1000000 INFO @ Mon, 12 Aug 2019 20:10:28: 1000000 INFO @ Mon, 12 Aug 2019 20:10:30: 1000000 INFO @ Mon, 12 Aug 2019 20:10:35: 2000000 INFO @ Mon, 12 Aug 2019 20:10:36: 2000000 INFO @ Mon, 12 Aug 2019 20:10:37: 2000000 INFO @ Mon, 12 Aug 2019 20:10:43: 3000000 INFO @ Mon, 12 Aug 2019 20:10:44: 3000000 INFO @ Mon, 12 Aug 2019 20:10:45: 3000000 INFO @ Mon, 12 Aug 2019 20:10:50: 4000000 INFO @ Mon, 12 Aug 2019 20:10:51: 4000000 INFO @ Mon, 12 Aug 2019 20:10:53: 4000000 INFO @ Mon, 12 Aug 2019 20:10:58: 5000000 INFO @ Mon, 12 Aug 2019 20:10:59: 5000000 INFO @ Mon, 12 Aug 2019 20:11:01: 5000000 INFO @ Mon, 12 Aug 2019 20:11:05: 6000000 INFO @ Mon, 12 Aug 2019 20:11:06: 6000000 INFO @ Mon, 12 Aug 2019 20:11:08: 6000000 INFO @ Mon, 12 Aug 2019 20:11:12: 7000000 INFO @ Mon, 12 Aug 2019 20:11:14: 7000000 INFO @ Mon, 12 Aug 2019 20:11:15: 7000000 INFO @ Mon, 12 Aug 2019 20:11:20: 8000000 INFO @ Mon, 12 Aug 2019 20:11:21: 8000000 INFO @ Mon, 12 Aug 2019 20:11:23: 8000000 INFO @ Mon, 12 Aug 2019 20:11:27: 9000000 INFO @ Mon, 12 Aug 2019 20:11:29: 9000000 INFO @ Mon, 12 Aug 2019 20:11:30: 9000000 INFO @ Mon, 12 Aug 2019 20:11:35: 10000000 INFO @ Mon, 12 Aug 2019 20:11:36: 10000000 INFO @ Mon, 12 Aug 2019 20:11:38: 10000000 INFO @ Mon, 12 Aug 2019 20:11:42: 11000000 INFO @ Mon, 12 Aug 2019 20:11:44: 11000000 INFO @ Mon, 12 Aug 2019 20:11:45: 11000000 INFO @ Mon, 12 Aug 2019 20:11:49: 12000000 INFO @ Mon, 12 Aug 2019 20:11:51: 12000000 INFO @ Mon, 12 Aug 2019 20:11:53: 12000000 INFO @ Mon, 12 Aug 2019 20:11:57: 13000000 INFO @ Mon, 12 Aug 2019 20:11:58: 13000000 INFO @ Mon, 12 Aug 2019 20:12:00: 13000000 INFO @ Mon, 12 Aug 2019 20:12:04: 14000000 INFO @ Mon, 12 Aug 2019 20:12:06: 14000000 INFO @ Mon, 12 Aug 2019 20:12:07: 14000000 INFO @ Mon, 12 Aug 2019 20:12:11: 15000000 INFO @ Mon, 12 Aug 2019 20:12:13: 15000000 INFO @ Mon, 12 Aug 2019 20:12:15: 15000000 INFO @ Mon, 12 Aug 2019 20:12:19: 16000000 INFO @ Mon, 12 Aug 2019 20:12:21: 16000000 INFO @ Mon, 12 Aug 2019 20:12:22: 16000000 INFO @ Mon, 12 Aug 2019 20:12:26: 17000000 INFO @ Mon, 12 Aug 2019 20:12:29: 17000000 INFO @ Mon, 12 Aug 2019 20:12:30: 17000000 INFO @ Mon, 12 Aug 2019 20:12:35: 18000000 INFO @ Mon, 12 Aug 2019 20:12:36: 18000000 INFO @ Mon, 12 Aug 2019 20:12:39: 18000000 INFO @ Mon, 12 Aug 2019 20:12:43: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:12:43: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:12:43: #1 total tags in treatment: 18755146 INFO @ Mon, 12 Aug 2019 20:12:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:12:43: #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 20:12:44: #1 tags after filtering in treatment: 18755146 INFO @ Mon, 12 Aug 2019 20:12:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:12:44: #1 finished! INFO @ Mon, 12 Aug 2019 20:12:44: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:12:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:12:44: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:12:44: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:12:44: #1 total tags in treatment: 18755146 INFO @ Mon, 12 Aug 2019 20:12:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:12:44: #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 20:12:45: #1 tags after filtering in treatment: 18755146 INFO @ Mon, 12 Aug 2019 20:12:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:12:45: #1 finished! INFO @ Mon, 12 Aug 2019 20:12:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:12:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:12:45: #2 number of paired peaks: 247 WARNING @ Mon, 12 Aug 2019 20:12:45: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Mon, 12 Aug 2019 20:12:45: start model_add_line... INFO @ Mon, 12 Aug 2019 20:12:45: start X-correlation... INFO @ Mon, 12 Aug 2019 20:12:45: end of X-cor INFO @ Mon, 12 Aug 2019 20:12:45: #2 finished! INFO @ Mon, 12 Aug 2019 20:12:45: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 20:12:45: #2 alternative fragment length(s) may be 1,45,509 bps INFO @ Mon, 12 Aug 2019 20:12:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.10_model.r WARNING @ Mon, 12 Aug 2019 20:12:45: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:12:45: #2 You may need to consider one of the other alternative d(s): 1,45,509 WARNING @ Mon, 12 Aug 2019 20:12:45: #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 20:12:45: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:12:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:12:46: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:12:46: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:12:46: #1 total tags in treatment: 18755146 INFO @ Mon, 12 Aug 2019 20:12:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:12:46: #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 20:12:46: #1 tags after filtering in treatment: 18755146 INFO @ Mon, 12 Aug 2019 20:12:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:12:46: #1 finished! INFO @ Mon, 12 Aug 2019 20:12:46: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:12:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:12:46: #2 number of paired peaks: 247 WARNING @ Mon, 12 Aug 2019 20:12:46: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Mon, 12 Aug 2019 20:12:46: start model_add_line... INFO @ Mon, 12 Aug 2019 20:12:47: start X-correlation... INFO @ Mon, 12 Aug 2019 20:12:47: end of X-cor INFO @ Mon, 12 Aug 2019 20:12:47: #2 finished! INFO @ Mon, 12 Aug 2019 20:12:47: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 20:12:47: #2 alternative fragment length(s) may be 1,45,509 bps INFO @ Mon, 12 Aug 2019 20:12:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.05_model.r WARNING @ Mon, 12 Aug 2019 20:12:47: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:12:47: #2 You may need to consider one of the other alternative d(s): 1,45,509 WARNING @ Mon, 12 Aug 2019 20:12:47: #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 20:12:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:12:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:12:48: #2 number of paired peaks: 247 WARNING @ Mon, 12 Aug 2019 20:12:48: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Mon, 12 Aug 2019 20:12:48: start model_add_line... INFO @ Mon, 12 Aug 2019 20:12:48: start X-correlation... INFO @ Mon, 12 Aug 2019 20:12:48: end of X-cor INFO @ Mon, 12 Aug 2019 20:12:48: #2 finished! INFO @ Mon, 12 Aug 2019 20:12:48: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 20:12:48: #2 alternative fragment length(s) may be 1,45,509 bps INFO @ Mon, 12 Aug 2019 20:12:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.20_model.r WARNING @ Mon, 12 Aug 2019 20:12:48: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:12:48: #2 You may need to consider one of the other alternative d(s): 1,45,509 WARNING @ Mon, 12 Aug 2019 20:12:48: #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 20:12:48: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:12:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:13:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:13:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:13:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:13:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:13:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:13:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.10_summits.bed INFO @ Mon, 12 Aug 2019 20:13:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (474 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:13:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:13:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:13:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.20_summits.bed INFO @ Mon, 12 Aug 2019 20:13:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (175 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:13:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:13:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:13:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495026/SRX495026.05_summits.bed INFO @ Mon, 12 Aug 2019 20:13:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (832 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。