Job ID = 1293178 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,950,235 reads read : 29,950,235 reads written : 29,950,235 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: 00:09:42 29950235 reads; of these: 29950235 (100.00%) were unpaired; of these: 2471104 (8.25%) aligned 0 times 15502961 (51.76%) aligned exactly 1 time 11976170 (39.99%) aligned >1 times 91.75% overall alignment rate Time searching: 00:09:42 Overall time: 00:09:42 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] 13245537 / 27479131 = 0.4820 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 22:40:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.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 22:40:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:40:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:40:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.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 22:40:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:40:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:40:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.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 22:40:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:40:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:40:59: 1000000 INFO @ Sun, 02 Jun 2019 22:40:59: 1000000 INFO @ Sun, 02 Jun 2019 22:41:00: 1000000 INFO @ Sun, 02 Jun 2019 22:41:06: 2000000 INFO @ Sun, 02 Jun 2019 22:41:07: 2000000 INFO @ Sun, 02 Jun 2019 22:41:08: 2000000 INFO @ Sun, 02 Jun 2019 22:41:14: 3000000 INFO @ Sun, 02 Jun 2019 22:41:15: 3000000 INFO @ Sun, 02 Jun 2019 22:41:17: 3000000 INFO @ Sun, 02 Jun 2019 22:41:22: 4000000 INFO @ Sun, 02 Jun 2019 22:41:24: 4000000 INFO @ Sun, 02 Jun 2019 22:41:25: 4000000 INFO @ Sun, 02 Jun 2019 22:41:30: 5000000 INFO @ Sun, 02 Jun 2019 22:41:32: 5000000 INFO @ Sun, 02 Jun 2019 22:41:33: 5000000 INFO @ Sun, 02 Jun 2019 22:41:37: 6000000 INFO @ Sun, 02 Jun 2019 22:41:39: 6000000 INFO @ Sun, 02 Jun 2019 22:41:41: 6000000 INFO @ Sun, 02 Jun 2019 22:41:44: 7000000 INFO @ Sun, 02 Jun 2019 22:41:47: 7000000 INFO @ Sun, 02 Jun 2019 22:41:49: 7000000 INFO @ Sun, 02 Jun 2019 22:41:52: 8000000 INFO @ Sun, 02 Jun 2019 22:41:54: 8000000 INFO @ Sun, 02 Jun 2019 22:41:57: 8000000 INFO @ Sun, 02 Jun 2019 22:41:59: 9000000 INFO @ Sun, 02 Jun 2019 22:42:02: 9000000 INFO @ Sun, 02 Jun 2019 22:42:06: 9000000 INFO @ Sun, 02 Jun 2019 22:42:07: 10000000 INFO @ Sun, 02 Jun 2019 22:42:09: 10000000 INFO @ Sun, 02 Jun 2019 22:42:14: 10000000 INFO @ Sun, 02 Jun 2019 22:42:14: 11000000 INFO @ Sun, 02 Jun 2019 22:42:17: 11000000 INFO @ Sun, 02 Jun 2019 22:42:21: 12000000 INFO @ Sun, 02 Jun 2019 22:42:22: 11000000 INFO @ Sun, 02 Jun 2019 22:42:24: 12000000 INFO @ Sun, 02 Jun 2019 22:42:29: 13000000 INFO @ Sun, 02 Jun 2019 22:42:31: 12000000 INFO @ Sun, 02 Jun 2019 22:42:32: 13000000 INFO @ Sun, 02 Jun 2019 22:42:37: 14000000 INFO @ Sun, 02 Jun 2019 22:42:39: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:42:39: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:42:39: #1 total tags in treatment: 14233594 INFO @ Sun, 02 Jun 2019 22:42:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:42:39: #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 22:42:39: #1 tags after filtering in treatment: 14233594 INFO @ Sun, 02 Jun 2019 22:42:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:42:39: #1 finished! INFO @ Sun, 02 Jun 2019 22:42:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:42:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:42:39: 14000000 INFO @ Sun, 02 Jun 2019 22:42:40: 13000000 INFO @ Sun, 02 Jun 2019 22:42:41: #2 number of paired peaks: 3040 INFO @ Sun, 02 Jun 2019 22:42:41: start model_add_line... INFO @ Sun, 02 Jun 2019 22:42:41: start X-correlation... INFO @ Sun, 02 Jun 2019 22:42:41: end of X-cor INFO @ Sun, 02 Jun 2019 22:42:41: #2 finished! INFO @ Sun, 02 Jun 2019 22:42:41: #2 predicted fragment length is 98 bps INFO @ Sun, 02 Jun 2019 22:42:41: #2 alternative fragment length(s) may be 4,98 bps INFO @ Sun, 02 Jun 2019 22:42:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.05_model.r WARNING @ Sun, 02 Jun 2019 22:42:41: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:42:41: #2 You may need to consider one of the other alternative d(s): 4,98 WARNING @ Sun, 02 Jun 2019 22:42:41: #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 22:42:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:42:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:42:42: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:42:42: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:42:42: #1 total tags in treatment: 14233594 INFO @ Sun, 02 Jun 2019 22:42:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:42:42: #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 22:42:42: #1 tags after filtering in treatment: 14233594 INFO @ Sun, 02 Jun 2019 22:42:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:42:42: #1 finished! INFO @ Sun, 02 Jun 2019 22:42:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:42:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:42:43: #2 number of paired peaks: 3040 INFO @ Sun, 02 Jun 2019 22:42:43: start model_add_line... INFO @ Sun, 02 Jun 2019 22:42:44: start X-correlation... INFO @ Sun, 02 Jun 2019 22:42:44: end of X-cor INFO @ Sun, 02 Jun 2019 22:42:44: #2 finished! INFO @ Sun, 02 Jun 2019 22:42:44: #2 predicted fragment length is 98 bps INFO @ Sun, 02 Jun 2019 22:42:44: #2 alternative fragment length(s) may be 4,98 bps INFO @ Sun, 02 Jun 2019 22:42:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.20_model.r WARNING @ Sun, 02 Jun 2019 22:42:44: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:42:44: #2 You may need to consider one of the other alternative d(s): 4,98 WARNING @ Sun, 02 Jun 2019 22:42:44: #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 22:42:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:42:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:42:48: 14000000 INFO @ Sun, 02 Jun 2019 22:42:50: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:42:50: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:42:50: #1 total tags in treatment: 14233594 INFO @ Sun, 02 Jun 2019 22:42:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:42:50: #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 22:42:50: #1 tags after filtering in treatment: 14233594 INFO @ Sun, 02 Jun 2019 22:42:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:42:50: #1 finished! INFO @ Sun, 02 Jun 2019 22:42:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:42:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:42:52: #2 number of paired peaks: 3040 INFO @ Sun, 02 Jun 2019 22:42:52: start model_add_line... INFO @ Sun, 02 Jun 2019 22:42:52: start X-correlation... INFO @ Sun, 02 Jun 2019 22:42:52: end of X-cor INFO @ Sun, 02 Jun 2019 22:42:52: #2 finished! INFO @ Sun, 02 Jun 2019 22:42:52: #2 predicted fragment length is 98 bps INFO @ Sun, 02 Jun 2019 22:42:52: #2 alternative fragment length(s) may be 4,98 bps INFO @ Sun, 02 Jun 2019 22:42:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.10_model.r WARNING @ Sun, 02 Jun 2019 22:42:52: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:42:52: #2 You may need to consider one of the other alternative d(s): 4,98 WARNING @ Sun, 02 Jun 2019 22:42:52: #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 22:42:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:42:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:43:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:43:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:43:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:43:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:43:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:43:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.05_summits.bed INFO @ Sun, 02 Jun 2019 22:43:41: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8888 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:43:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:43:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:43:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.20_summits.bed INFO @ Sun, 02 Jun 2019 22:43:43: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2847 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:43:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:43:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:43:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402740/SRX5402740.10_summits.bed INFO @ Sun, 02 Jun 2019 22:43:51: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (5982 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。