Job ID = 1291684 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,651,868 reads read : 21,651,868 reads written : 21,651,868 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: 00:05:17 21651868 reads; of these: 21651868 (100.00%) were unpaired; of these: 1074343 (4.96%) aligned 0 times 17784929 (82.14%) aligned exactly 1 time 2792596 (12.90%) aligned >1 times 95.04% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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] 2333358 / 20577525 = 0.1134 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 16:27:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.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 16:27:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:27:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:27:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.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 16:27:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.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 16:27:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:27:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:27:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:27:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:27:20: 1000000 INFO @ Sun, 02 Jun 2019 16:27:21: 1000000 INFO @ Sun, 02 Jun 2019 16:27:21: 1000000 INFO @ Sun, 02 Jun 2019 16:27:28: 2000000 INFO @ Sun, 02 Jun 2019 16:27:30: 2000000 INFO @ Sun, 02 Jun 2019 16:27:30: 2000000 INFO @ Sun, 02 Jun 2019 16:27:36: 3000000 INFO @ Sun, 02 Jun 2019 16:27:39: 3000000 INFO @ Sun, 02 Jun 2019 16:27:39: 3000000 INFO @ Sun, 02 Jun 2019 16:27:44: 4000000 INFO @ Sun, 02 Jun 2019 16:27:48: 4000000 INFO @ Sun, 02 Jun 2019 16:27:48: 4000000 INFO @ Sun, 02 Jun 2019 16:27:53: 5000000 INFO @ Sun, 02 Jun 2019 16:27:56: 5000000 INFO @ Sun, 02 Jun 2019 16:27:58: 5000000 INFO @ Sun, 02 Jun 2019 16:28:02: 6000000 INFO @ Sun, 02 Jun 2019 16:28:05: 6000000 INFO @ Sun, 02 Jun 2019 16:28:07: 6000000 INFO @ Sun, 02 Jun 2019 16:28:12: 7000000 INFO @ Sun, 02 Jun 2019 16:28:13: 7000000 INFO @ Sun, 02 Jun 2019 16:28:16: 7000000 INFO @ Sun, 02 Jun 2019 16:28:21: 8000000 INFO @ Sun, 02 Jun 2019 16:28:21: 8000000 INFO @ Sun, 02 Jun 2019 16:28:25: 8000000 INFO @ Sun, 02 Jun 2019 16:28:29: 9000000 INFO @ Sun, 02 Jun 2019 16:28:30: 9000000 INFO @ Sun, 02 Jun 2019 16:28:34: 9000000 INFO @ Sun, 02 Jun 2019 16:28:37: 10000000 INFO @ Sun, 02 Jun 2019 16:28:39: 10000000 INFO @ Sun, 02 Jun 2019 16:28:43: 10000000 INFO @ Sun, 02 Jun 2019 16:28:45: 11000000 INFO @ Sun, 02 Jun 2019 16:28:48: 11000000 INFO @ Sun, 02 Jun 2019 16:28:52: 12000000 INFO @ Sun, 02 Jun 2019 16:28:52: 11000000 INFO @ Sun, 02 Jun 2019 16:28:57: 12000000 INFO @ Sun, 02 Jun 2019 16:29:00: 13000000 INFO @ Sun, 02 Jun 2019 16:29:02: 12000000 INFO @ Sun, 02 Jun 2019 16:29:06: 13000000 INFO @ Sun, 02 Jun 2019 16:29:08: 14000000 INFO @ Sun, 02 Jun 2019 16:29:10: 13000000 INFO @ Sun, 02 Jun 2019 16:29:15: 14000000 INFO @ Sun, 02 Jun 2019 16:29:16: 15000000 INFO @ Sun, 02 Jun 2019 16:29:20: 14000000 INFO @ Sun, 02 Jun 2019 16:29:24: 16000000 INFO @ Sun, 02 Jun 2019 16:29:24: 15000000 INFO @ Sun, 02 Jun 2019 16:29:29: 15000000 INFO @ Sun, 02 Jun 2019 16:29:32: 17000000 INFO @ Sun, 02 Jun 2019 16:29:33: 16000000 INFO @ Sun, 02 Jun 2019 16:29:38: 16000000 INFO @ Sun, 02 Jun 2019 16:29:40: 18000000 INFO @ Sun, 02 Jun 2019 16:29:42: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:29:42: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:29:42: #1 total tags in treatment: 18244167 INFO @ Sun, 02 Jun 2019 16:29:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:29:42: #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 16:29:42: #1 tags after filtering in treatment: 18244167 INFO @ Sun, 02 Jun 2019 16:29:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:29:42: #1 finished! INFO @ Sun, 02 Jun 2019 16:29:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:29:42: 17000000 INFO @ Sun, 02 Jun 2019 16:29:44: #2 number of paired peaks: 188 WARNING @ Sun, 02 Jun 2019 16:29:44: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Sun, 02 Jun 2019 16:29:44: start model_add_line... INFO @ Sun, 02 Jun 2019 16:29:44: start X-correlation... INFO @ Sun, 02 Jun 2019 16:29:44: end of X-cor INFO @ Sun, 02 Jun 2019 16:29:44: #2 finished! INFO @ Sun, 02 Jun 2019 16:29:44: #2 predicted fragment length is 63 bps INFO @ Sun, 02 Jun 2019 16:29:44: #2 alternative fragment length(s) may be 2,63 bps INFO @ Sun, 02 Jun 2019 16:29:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.20_model.r WARNING @ Sun, 02 Jun 2019 16:29:44: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:29:44: #2 You may need to consider one of the other alternative d(s): 2,63 WARNING @ Sun, 02 Jun 2019 16:29:44: #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 16:29:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:29:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:29:46: 17000000 INFO @ Sun, 02 Jun 2019 16:29:51: 18000000 INFO @ Sun, 02 Jun 2019 16:29:53: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:29:53: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:29:53: #1 total tags in treatment: 18244167 INFO @ Sun, 02 Jun 2019 16:29:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:29:53: #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 16:29:54: #1 tags after filtering in treatment: 18244167 INFO @ Sun, 02 Jun 2019 16:29:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:29:54: #1 finished! INFO @ Sun, 02 Jun 2019 16:29:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:29:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:29:55: 18000000 INFO @ Sun, 02 Jun 2019 16:29:55: #2 number of paired peaks: 188 WARNING @ Sun, 02 Jun 2019 16:29:55: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Sun, 02 Jun 2019 16:29:55: start model_add_line... INFO @ Sun, 02 Jun 2019 16:29:55: start X-correlation... INFO @ Sun, 02 Jun 2019 16:29:55: end of X-cor INFO @ Sun, 02 Jun 2019 16:29:55: #2 finished! INFO @ Sun, 02 Jun 2019 16:29:55: #2 predicted fragment length is 63 bps INFO @ Sun, 02 Jun 2019 16:29:55: #2 alternative fragment length(s) may be 2,63 bps INFO @ Sun, 02 Jun 2019 16:29:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.05_model.r WARNING @ Sun, 02 Jun 2019 16:29:55: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:29:55: #2 You may need to consider one of the other alternative d(s): 2,63 WARNING @ Sun, 02 Jun 2019 16:29:55: #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 16:29:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:29:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:29:57: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:29:57: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:29:57: #1 total tags in treatment: 18244167 INFO @ Sun, 02 Jun 2019 16:29:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:29:57: #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 16:29:57: #1 tags after filtering in treatment: 18244167 INFO @ Sun, 02 Jun 2019 16:29:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:29:57: #1 finished! INFO @ Sun, 02 Jun 2019 16:29:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:29:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:29:59: #2 number of paired peaks: 188 WARNING @ Sun, 02 Jun 2019 16:29:59: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Sun, 02 Jun 2019 16:29:59: start model_add_line... INFO @ Sun, 02 Jun 2019 16:29:59: start X-correlation... INFO @ Sun, 02 Jun 2019 16:29:59: end of X-cor INFO @ Sun, 02 Jun 2019 16:29:59: #2 finished! INFO @ Sun, 02 Jun 2019 16:29:59: #2 predicted fragment length is 63 bps INFO @ Sun, 02 Jun 2019 16:29:59: #2 alternative fragment length(s) may be 2,63 bps INFO @ Sun, 02 Jun 2019 16:29:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.10_model.r WARNING @ Sun, 02 Jun 2019 16:29:59: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:29:59: #2 You may need to consider one of the other alternative d(s): 2,63 WARNING @ Sun, 02 Jun 2019 16:29:59: #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 16:29:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:29:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:30:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:30:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:30:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:30:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:30:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:30:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.20_summits.bed INFO @ Sun, 02 Jun 2019 16:30:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:30:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:30:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:30:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.05_summits.bed INFO @ Sun, 02 Jun 2019 16:30:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1109 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:31:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:31:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:31:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216753/SRX216753.10_summits.bed INFO @ Sun, 02 Jun 2019 16:31:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (525 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。