Job ID = 1291784 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,807,102 reads read : 35,614,204 reads written : 17,807,102 reads 0-length : 17,807,102 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: 00:06:45 17807102 reads; of these: 17807102 (100.00%) were unpaired; of these: 1007909 (5.66%) aligned 0 times 14568453 (81.81%) aligned exactly 1 time 2230740 (12.53%) aligned >1 times 94.34% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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] 3116369 / 16799193 = 0.1855 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 16:46:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.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 16:46:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:46:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:46:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.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 16:46:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:46:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:46:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.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 16:46:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:46:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:46:52: 1000000 INFO @ Sun, 02 Jun 2019 16:46:54: 1000000 INFO @ Sun, 02 Jun 2019 16:46:54: 1000000 INFO @ Sun, 02 Jun 2019 16:47:01: 2000000 INFO @ Sun, 02 Jun 2019 16:47:04: 2000000 INFO @ Sun, 02 Jun 2019 16:47:04: 2000000 INFO @ Sun, 02 Jun 2019 16:47:10: 3000000 INFO @ Sun, 02 Jun 2019 16:47:14: 3000000 INFO @ Sun, 02 Jun 2019 16:47:15: 3000000 INFO @ Sun, 02 Jun 2019 16:47:18: 4000000 INFO @ Sun, 02 Jun 2019 16:47:23: 4000000 INFO @ Sun, 02 Jun 2019 16:47:25: 4000000 INFO @ Sun, 02 Jun 2019 16:47:27: 5000000 INFO @ Sun, 02 Jun 2019 16:47:33: 5000000 INFO @ Sun, 02 Jun 2019 16:47:35: 5000000 INFO @ Sun, 02 Jun 2019 16:47:35: 6000000 INFO @ Sun, 02 Jun 2019 16:47:42: 6000000 INFO @ Sun, 02 Jun 2019 16:47:44: 7000000 INFO @ Sun, 02 Jun 2019 16:47:45: 6000000 INFO @ Sun, 02 Jun 2019 16:47:52: 7000000 INFO @ Sun, 02 Jun 2019 16:47:52: 8000000 INFO @ Sun, 02 Jun 2019 16:47:55: 7000000 INFO @ Sun, 02 Jun 2019 16:48:01: 9000000 INFO @ Sun, 02 Jun 2019 16:48:02: 8000000 INFO @ Sun, 02 Jun 2019 16:48:05: 8000000 INFO @ Sun, 02 Jun 2019 16:48:09: 10000000 INFO @ Sun, 02 Jun 2019 16:48:11: 9000000 INFO @ Sun, 02 Jun 2019 16:48:15: 9000000 INFO @ Sun, 02 Jun 2019 16:48:18: 11000000 INFO @ Sun, 02 Jun 2019 16:48:21: 10000000 INFO @ Sun, 02 Jun 2019 16:48:25: 10000000 INFO @ Sun, 02 Jun 2019 16:48:26: 12000000 INFO @ Sun, 02 Jun 2019 16:48:30: 11000000 INFO @ Sun, 02 Jun 2019 16:48:35: 11000000 INFO @ Sun, 02 Jun 2019 16:48:35: 13000000 INFO @ Sun, 02 Jun 2019 16:48:40: 12000000 INFO @ Sun, 02 Jun 2019 16:48:40: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:48:40: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:48:40: #1 total tags in treatment: 13682824 INFO @ Sun, 02 Jun 2019 16:48:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:48:40: #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 16:48:41: #1 tags after filtering in treatment: 13682824 INFO @ Sun, 02 Jun 2019 16:48:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:48:41: #1 finished! INFO @ Sun, 02 Jun 2019 16:48:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:48:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:48:42: #2 number of paired peaks: 296 WARNING @ Sun, 02 Jun 2019 16:48:42: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Sun, 02 Jun 2019 16:48:42: start model_add_line... INFO @ Sun, 02 Jun 2019 16:48:42: start X-correlation... INFO @ Sun, 02 Jun 2019 16:48:42: end of X-cor INFO @ Sun, 02 Jun 2019 16:48:42: #2 finished! INFO @ Sun, 02 Jun 2019 16:48:42: #2 predicted fragment length is 140 bps INFO @ Sun, 02 Jun 2019 16:48:42: #2 alternative fragment length(s) may be 4,140,150 bps INFO @ Sun, 02 Jun 2019 16:48:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.20_model.r WARNING @ Sun, 02 Jun 2019 16:48:42: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:48:42: #2 You may need to consider one of the other alternative d(s): 4,140,150 WARNING @ Sun, 02 Jun 2019 16:48:42: #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 16:48:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:48:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:48:45: 12000000 INFO @ Sun, 02 Jun 2019 16:48:49: 13000000 INFO @ Sun, 02 Jun 2019 16:48:54: 13000000 INFO @ Sun, 02 Jun 2019 16:48:56: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:48:56: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:48:56: #1 total tags in treatment: 13682824 INFO @ Sun, 02 Jun 2019 16:48:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:48:56: #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 16:48:56: #1 tags after filtering in treatment: 13682824 INFO @ Sun, 02 Jun 2019 16:48:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:48:56: #1 finished! INFO @ Sun, 02 Jun 2019 16:48:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:48:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:48:57: #2 number of paired peaks: 296 WARNING @ Sun, 02 Jun 2019 16:48:57: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Sun, 02 Jun 2019 16:48:57: start model_add_line... INFO @ Sun, 02 Jun 2019 16:48:57: start X-correlation... INFO @ Sun, 02 Jun 2019 16:48:57: end of X-cor INFO @ Sun, 02 Jun 2019 16:48:57: #2 finished! INFO @ Sun, 02 Jun 2019 16:48:57: #2 predicted fragment length is 140 bps INFO @ Sun, 02 Jun 2019 16:48:57: #2 alternative fragment length(s) may be 4,140,150 bps INFO @ Sun, 02 Jun 2019 16:48:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.05_model.r WARNING @ Sun, 02 Jun 2019 16:48:57: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:48:57: #2 You may need to consider one of the other alternative d(s): 4,140,150 WARNING @ Sun, 02 Jun 2019 16:48:57: #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 16:48:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:48:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:49:01: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:49:01: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:49:01: #1 total tags in treatment: 13682824 INFO @ Sun, 02 Jun 2019 16:49:01: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:49:01: #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 16:49:01: #1 tags after filtering in treatment: 13682824 INFO @ Sun, 02 Jun 2019 16:49:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:49:01: #1 finished! INFO @ Sun, 02 Jun 2019 16:49:01: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:49:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:49:02: #2 number of paired peaks: 296 WARNING @ Sun, 02 Jun 2019 16:49:02: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Sun, 02 Jun 2019 16:49:02: start model_add_line... INFO @ Sun, 02 Jun 2019 16:49:02: start X-correlation... INFO @ Sun, 02 Jun 2019 16:49:02: end of X-cor INFO @ Sun, 02 Jun 2019 16:49:02: #2 finished! INFO @ Sun, 02 Jun 2019 16:49:02: #2 predicted fragment length is 140 bps INFO @ Sun, 02 Jun 2019 16:49:02: #2 alternative fragment length(s) may be 4,140,150 bps INFO @ Sun, 02 Jun 2019 16:49:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.10_model.r WARNING @ Sun, 02 Jun 2019 16:49:02: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:49:02: #2 You may need to consider one of the other alternative d(s): 4,140,150 WARNING @ Sun, 02 Jun 2019 16:49:02: #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 16:49:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:49:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:49:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:49:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:49:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:49:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:49:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.20_summits.bed INFO @ Sun, 02 Jun 2019 16:49:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (340 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:49:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:49:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:49:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:49:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.05_summits.bed INFO @ Sun, 02 Jun 2019 16:49:53: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5741 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:49:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:49:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:49:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543054/SRX2543054.10_summits.bed INFO @ Sun, 02 Jun 2019 16:49:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1847 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。