Job ID = 1292770 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,621,140 reads read : 22,621,140 reads written : 22,621,140 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: 00:04:57 22621140 reads; of these: 22621140 (100.00%) were unpaired; of these: 262496 (1.16%) aligned 0 times 18791105 (83.07%) aligned exactly 1 time 3567539 (15.77%) aligned >1 times 98.84% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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] 3355087 / 22358644 = 0.1501 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 20:45:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.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 20:45:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:45:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:45:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.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 20:45:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:45:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:45:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.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 20:45:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:45:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:45:11: 1000000 INFO @ Sun, 02 Jun 2019 20:45:11: 1000000 INFO @ Sun, 02 Jun 2019 20:45:12: 1000000 INFO @ Sun, 02 Jun 2019 20:45:17: 2000000 INFO @ Sun, 02 Jun 2019 20:45:19: 2000000 INFO @ Sun, 02 Jun 2019 20:45:20: 2000000 INFO @ Sun, 02 Jun 2019 20:45:24: 3000000 INFO @ Sun, 02 Jun 2019 20:45:26: 3000000 INFO @ Sun, 02 Jun 2019 20:45:28: 3000000 INFO @ Sun, 02 Jun 2019 20:45:31: 4000000 INFO @ Sun, 02 Jun 2019 20:45:33: 4000000 INFO @ Sun, 02 Jun 2019 20:45:36: 4000000 INFO @ Sun, 02 Jun 2019 20:45:38: 5000000 INFO @ Sun, 02 Jun 2019 20:45:41: 5000000 INFO @ Sun, 02 Jun 2019 20:45:43: 5000000 INFO @ Sun, 02 Jun 2019 20:45:44: 6000000 INFO @ Sun, 02 Jun 2019 20:45:48: 6000000 INFO @ Sun, 02 Jun 2019 20:45:51: 6000000 INFO @ Sun, 02 Jun 2019 20:45:51: 7000000 INFO @ Sun, 02 Jun 2019 20:45:56: 7000000 INFO @ Sun, 02 Jun 2019 20:45:58: 8000000 INFO @ Sun, 02 Jun 2019 20:45:59: 7000000 INFO @ Sun, 02 Jun 2019 20:46:03: 8000000 INFO @ Sun, 02 Jun 2019 20:46:05: 9000000 INFO @ Sun, 02 Jun 2019 20:46:06: 8000000 INFO @ Sun, 02 Jun 2019 20:46:10: 9000000 INFO @ Sun, 02 Jun 2019 20:46:11: 10000000 INFO @ Sun, 02 Jun 2019 20:46:14: 9000000 INFO @ Sun, 02 Jun 2019 20:46:18: 10000000 INFO @ Sun, 02 Jun 2019 20:46:18: 11000000 INFO @ Sun, 02 Jun 2019 20:46:22: 10000000 INFO @ Sun, 02 Jun 2019 20:46:25: 11000000 INFO @ Sun, 02 Jun 2019 20:46:25: 12000000 INFO @ Sun, 02 Jun 2019 20:46:29: 11000000 INFO @ Sun, 02 Jun 2019 20:46:32: 13000000 INFO @ Sun, 02 Jun 2019 20:46:32: 12000000 INFO @ Sun, 02 Jun 2019 20:46:37: 12000000 INFO @ Sun, 02 Jun 2019 20:46:39: 14000000 INFO @ Sun, 02 Jun 2019 20:46:40: 13000000 INFO @ Sun, 02 Jun 2019 20:46:45: 13000000 INFO @ Sun, 02 Jun 2019 20:46:45: 15000000 INFO @ Sun, 02 Jun 2019 20:46:47: 14000000 INFO @ Sun, 02 Jun 2019 20:46:52: 14000000 INFO @ Sun, 02 Jun 2019 20:46:53: 16000000 INFO @ Sun, 02 Jun 2019 20:46:54: 15000000 INFO @ Sun, 02 Jun 2019 20:47:00: 15000000 INFO @ Sun, 02 Jun 2019 20:47:00: 17000000 INFO @ Sun, 02 Jun 2019 20:47:01: 16000000 INFO @ Sun, 02 Jun 2019 20:47:07: 18000000 INFO @ Sun, 02 Jun 2019 20:47:07: 16000000 INFO @ Sun, 02 Jun 2019 20:47:08: 17000000 INFO @ Sun, 02 Jun 2019 20:47:14: 19000000 INFO @ Sun, 02 Jun 2019 20:47:14: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:47:14: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:47:14: #1 total tags in treatment: 19003557 INFO @ Sun, 02 Jun 2019 20:47:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:47:14: #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 20:47:14: #1 tags after filtering in treatment: 19003557 INFO @ Sun, 02 Jun 2019 20:47:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:47:14: #1 finished! INFO @ Sun, 02 Jun 2019 20:47:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:47:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:47:15: 17000000 INFO @ Sun, 02 Jun 2019 20:47:15: 18000000 INFO @ Sun, 02 Jun 2019 20:47:16: #2 number of paired peaks: 226 WARNING @ Sun, 02 Jun 2019 20:47:16: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Sun, 02 Jun 2019 20:47:16: start model_add_line... INFO @ Sun, 02 Jun 2019 20:47:16: start X-correlation... INFO @ Sun, 02 Jun 2019 20:47:16: end of X-cor INFO @ Sun, 02 Jun 2019 20:47:16: #2 finished! INFO @ Sun, 02 Jun 2019 20:47:16: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 20:47:16: #2 alternative fragment length(s) may be 1,39,579 bps INFO @ Sun, 02 Jun 2019 20:47:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.05_model.r WARNING @ Sun, 02 Jun 2019 20:47:16: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:47:16: #2 You may need to consider one of the other alternative d(s): 1,39,579 WARNING @ Sun, 02 Jun 2019 20:47:16: #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 20:47:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:47:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:47:22: 19000000 INFO @ Sun, 02 Jun 2019 20:47:22: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:47:22: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:47:22: #1 total tags in treatment: 19003557 INFO @ Sun, 02 Jun 2019 20:47:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:47:22: #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 20:47:22: 18000000 INFO @ Sun, 02 Jun 2019 20:47:23: #1 tags after filtering in treatment: 19003557 INFO @ Sun, 02 Jun 2019 20:47:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:47:23: #1 finished! INFO @ Sun, 02 Jun 2019 20:47:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:47:24: #2 number of paired peaks: 226 WARNING @ Sun, 02 Jun 2019 20:47:24: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Sun, 02 Jun 2019 20:47:24: start model_add_line... INFO @ Sun, 02 Jun 2019 20:47:25: start X-correlation... INFO @ Sun, 02 Jun 2019 20:47:25: end of X-cor INFO @ Sun, 02 Jun 2019 20:47:25: #2 finished! INFO @ Sun, 02 Jun 2019 20:47:25: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 20:47:25: #2 alternative fragment length(s) may be 1,39,579 bps INFO @ Sun, 02 Jun 2019 20:47:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.20_model.r WARNING @ Sun, 02 Jun 2019 20:47:25: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:47:25: #2 You may need to consider one of the other alternative d(s): 1,39,579 WARNING @ Sun, 02 Jun 2019 20:47:25: #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 20:47:25: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:47:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:47:30: 19000000 INFO @ Sun, 02 Jun 2019 20:47:30: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:47:30: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:47:30: #1 total tags in treatment: 19003557 INFO @ Sun, 02 Jun 2019 20:47:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:47:30: #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 20:47:30: #1 tags after filtering in treatment: 19003557 INFO @ Sun, 02 Jun 2019 20:47:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:47:30: #1 finished! INFO @ Sun, 02 Jun 2019 20:47:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:47:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:47:32: #2 number of paired peaks: 226 WARNING @ Sun, 02 Jun 2019 20:47:32: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Sun, 02 Jun 2019 20:47:32: start model_add_line... INFO @ Sun, 02 Jun 2019 20:47:32: start X-correlation... INFO @ Sun, 02 Jun 2019 20:47:32: end of X-cor INFO @ Sun, 02 Jun 2019 20:47:32: #2 finished! INFO @ Sun, 02 Jun 2019 20:47:32: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 20:47:32: #2 alternative fragment length(s) may be 1,39,579 bps INFO @ Sun, 02 Jun 2019 20:47:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.10_model.r WARNING @ Sun, 02 Jun 2019 20:47:32: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:47:32: #2 You may need to consider one of the other alternative d(s): 1,39,579 WARNING @ Sun, 02 Jun 2019 20:47:32: #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 20:47:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:47:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:48:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:48:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:48:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:48:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:48:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:48:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.05_summits.bed INFO @ Sun, 02 Jun 2019 20:48:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (726 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:48:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:48:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:48:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.20_summits.bed INFO @ Sun, 02 Jun 2019 20:48:34: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (116 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:48:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:48:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:48:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494994/SRX494994.10_summits.bed INFO @ Sun, 02 Jun 2019 20:48:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (373 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。