Job ID = 4303051 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,141,045 reads read : 19,141,045 reads written : 19,141,045 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1265812.sra.cache’: 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: 00:03:19 19141045 reads; of these: 19141045 (100.00%) were unpaired; of these: 248358 (1.30%) aligned 0 times 15163934 (79.22%) aligned exactly 1 time 3728753 (19.48%) aligned >1 times 98.70% overall alignment rate Time searching: 00:03:19 Overall time: 00:03:19 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] 2763225 / 18892687 = 0.1463 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:44:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.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 @ Thu, 12 Dec 2019 00:44:09: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:44:09: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:44:14: 1000000 INFO @ Thu, 12 Dec 2019 00:44:20: 2000000 INFO @ Thu, 12 Dec 2019 00:44:26: 3000000 INFO @ Thu, 12 Dec 2019 00:44:32: 4000000 INFO @ Thu, 12 Dec 2019 00:44:37: 5000000 INFO @ Thu, 12 Dec 2019 00:44:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.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 @ Thu, 12 Dec 2019 00:44:38: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:44:38: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:44:44: 6000000 INFO @ Thu, 12 Dec 2019 00:44:44: 1000000 INFO @ Thu, 12 Dec 2019 00:44:50: 7000000 INFO @ Thu, 12 Dec 2019 00:44:51: 2000000 INFO @ Thu, 12 Dec 2019 00:44:56: 8000000 INFO @ Thu, 12 Dec 2019 00:44:57: 3000000 INFO @ Thu, 12 Dec 2019 00:45:02: 9000000 INFO @ Thu, 12 Dec 2019 00:45:04: 4000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:45:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.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 @ Thu, 12 Dec 2019 00:45:08: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:45:08: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:45:09: 10000000 INFO @ Thu, 12 Dec 2019 00:45:10: 5000000 INFO @ Thu, 12 Dec 2019 00:45:14: 1000000 INFO @ Thu, 12 Dec 2019 00:45:15: 11000000 INFO @ Thu, 12 Dec 2019 00:45:16: 6000000 INFO @ Thu, 12 Dec 2019 00:45:20: 2000000 INFO @ Thu, 12 Dec 2019 00:45:21: 12000000 INFO @ Thu, 12 Dec 2019 00:45:22: 7000000 INFO @ Thu, 12 Dec 2019 00:45:26: 3000000 INFO @ Thu, 12 Dec 2019 00:45:27: 13000000 INFO @ Thu, 12 Dec 2019 00:45:28: 8000000 INFO @ Thu, 12 Dec 2019 00:45:32: 4000000 INFO @ Thu, 12 Dec 2019 00:45:33: 14000000 INFO @ Thu, 12 Dec 2019 00:45:34: 9000000 INFO @ Thu, 12 Dec 2019 00:45:38: 5000000 INFO @ Thu, 12 Dec 2019 00:45:39: 15000000 INFO @ Thu, 12 Dec 2019 00:45:40: 10000000 INFO @ Thu, 12 Dec 2019 00:45:44: 6000000 INFO @ Thu, 12 Dec 2019 00:45:45: 16000000 INFO @ Thu, 12 Dec 2019 00:45:46: 11000000 INFO @ Thu, 12 Dec 2019 00:45:46: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:45:46: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:45:46: #1 total tags in treatment: 16129462 INFO @ Thu, 12 Dec 2019 00:45:46: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:45:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:45:46: #1 tags after filtering in treatment: 16129462 INFO @ Thu, 12 Dec 2019 00:45:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:45:46: #1 finished! INFO @ Thu, 12 Dec 2019 00:45:46: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:45:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:45:47: #2 number of paired peaks: 270 WARNING @ Thu, 12 Dec 2019 00:45:47: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Thu, 12 Dec 2019 00:45:47: start model_add_line... INFO @ Thu, 12 Dec 2019 00:45:48: start X-correlation... INFO @ Thu, 12 Dec 2019 00:45:48: end of X-cor INFO @ Thu, 12 Dec 2019 00:45:48: #2 finished! INFO @ Thu, 12 Dec 2019 00:45:48: #2 predicted fragment length is 41 bps INFO @ Thu, 12 Dec 2019 00:45:48: #2 alternative fragment length(s) may be 2,41,584 bps INFO @ Thu, 12 Dec 2019 00:45:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.05_model.r WARNING @ Thu, 12 Dec 2019 00:45:48: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:45:48: #2 You may need to consider one of the other alternative d(s): 2,41,584 WARNING @ Thu, 12 Dec 2019 00:45:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:45:48: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:45:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:45:50: 7000000 INFO @ Thu, 12 Dec 2019 00:45:52: 12000000 INFO @ Thu, 12 Dec 2019 00:45:55: 8000000 INFO @ Thu, 12 Dec 2019 00:45:57: 13000000 INFO @ Thu, 12 Dec 2019 00:46:01: 9000000 INFO @ Thu, 12 Dec 2019 00:46:03: 14000000 INFO @ Thu, 12 Dec 2019 00:46:07: 10000000 INFO @ Thu, 12 Dec 2019 00:46:09: 15000000 INFO @ Thu, 12 Dec 2019 00:46:12: 11000000 INFO @ Thu, 12 Dec 2019 00:46:15: 16000000 INFO @ Thu, 12 Dec 2019 00:46:15: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:46:16: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:46:16: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:46:16: #1 total tags in treatment: 16129462 INFO @ Thu, 12 Dec 2019 00:46:16: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:46:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:46:16: #1 tags after filtering in treatment: 16129462 INFO @ Thu, 12 Dec 2019 00:46:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:46:16: #1 finished! INFO @ Thu, 12 Dec 2019 00:46:16: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:46:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:46:17: #2 number of paired peaks: 270 WARNING @ Thu, 12 Dec 2019 00:46:17: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Thu, 12 Dec 2019 00:46:17: start model_add_line... INFO @ Thu, 12 Dec 2019 00:46:17: start X-correlation... INFO @ Thu, 12 Dec 2019 00:46:17: end of X-cor INFO @ Thu, 12 Dec 2019 00:46:17: #2 finished! INFO @ Thu, 12 Dec 2019 00:46:17: #2 predicted fragment length is 41 bps INFO @ Thu, 12 Dec 2019 00:46:17: #2 alternative fragment length(s) may be 2,41,584 bps INFO @ Thu, 12 Dec 2019 00:46:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.10_model.r WARNING @ Thu, 12 Dec 2019 00:46:17: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:46:17: #2 You may need to consider one of the other alternative d(s): 2,41,584 WARNING @ Thu, 12 Dec 2019 00:46:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:46:17: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:46:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:46:18: 12000000 INFO @ Thu, 12 Dec 2019 00:46:23: 13000000 INFO @ Thu, 12 Dec 2019 00:46:29: 14000000 INFO @ Thu, 12 Dec 2019 00:46:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:46:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:46:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.05_summits.bed INFO @ Thu, 12 Dec 2019 00:46:31: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (12203 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:46:34: 15000000 INFO @ Thu, 12 Dec 2019 00:46:40: 16000000 INFO @ Thu, 12 Dec 2019 00:46:41: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:46:41: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:46:41: #1 total tags in treatment: 16129462 INFO @ Thu, 12 Dec 2019 00:46:41: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:46:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:46:41: #1 tags after filtering in treatment: 16129462 INFO @ Thu, 12 Dec 2019 00:46:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:46:41: #1 finished! INFO @ Thu, 12 Dec 2019 00:46:41: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:46:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:46:42: #2 number of paired peaks: 270 WARNING @ Thu, 12 Dec 2019 00:46:42: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Thu, 12 Dec 2019 00:46:42: start model_add_line... INFO @ Thu, 12 Dec 2019 00:46:42: start X-correlation... INFO @ Thu, 12 Dec 2019 00:46:42: end of X-cor INFO @ Thu, 12 Dec 2019 00:46:42: #2 finished! INFO @ Thu, 12 Dec 2019 00:46:42: #2 predicted fragment length is 41 bps INFO @ Thu, 12 Dec 2019 00:46:42: #2 alternative fragment length(s) may be 2,41,584 bps INFO @ Thu, 12 Dec 2019 00:46:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.20_model.r WARNING @ Thu, 12 Dec 2019 00:46:42: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:46:42: #2 You may need to consider one of the other alternative d(s): 2,41,584 WARNING @ Thu, 12 Dec 2019 00:46:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:46:42: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:46:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:46:44: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:46:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:46:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:46:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.10_summits.bed INFO @ Thu, 12 Dec 2019 00:46:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2104 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:47:09: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:47:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:47:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:47:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529208/SRX529208.20_summits.bed INFO @ Thu, 12 Dec 2019 00:47:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (201 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。