Job ID = 1293092 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,496,409 reads read : 50,992,818 reads written : 25,496,409 reads 0-length : 25,496,409 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: 00:06:29 25496409 reads; of these: 25496409 (100.00%) were unpaired; of these: 1158994 (4.55%) aligned 0 times 20217653 (79.30%) aligned exactly 1 time 4119762 (16.16%) aligned >1 times 95.45% overall alignment rate Time searching: 00:06:29 Overall time: 00:06:29 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] 6117296 / 24337415 = 0.2514 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 22:01:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.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 22:01:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:01:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:01:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.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 22:01:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:01:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:01:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.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 22:01:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:01:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:01:36: 1000000 INFO @ Sun, 02 Jun 2019 22:01:36: 1000000 INFO @ Sun, 02 Jun 2019 22:01:37: 1000000 INFO @ Sun, 02 Jun 2019 22:01:45: 2000000 INFO @ Sun, 02 Jun 2019 22:01:46: 2000000 INFO @ Sun, 02 Jun 2019 22:01:47: 2000000 INFO @ Sun, 02 Jun 2019 22:01:54: 3000000 INFO @ Sun, 02 Jun 2019 22:01:55: 3000000 INFO @ Sun, 02 Jun 2019 22:01:57: 3000000 INFO @ Sun, 02 Jun 2019 22:02:03: 4000000 INFO @ Sun, 02 Jun 2019 22:02:04: 4000000 INFO @ Sun, 02 Jun 2019 22:02:07: 4000000 INFO @ Sun, 02 Jun 2019 22:02:13: 5000000 INFO @ Sun, 02 Jun 2019 22:02:14: 5000000 INFO @ Sun, 02 Jun 2019 22:02:18: 5000000 INFO @ Sun, 02 Jun 2019 22:02:22: 6000000 INFO @ Sun, 02 Jun 2019 22:02:23: 6000000 INFO @ Sun, 02 Jun 2019 22:02:28: 6000000 INFO @ Sun, 02 Jun 2019 22:02:31: 7000000 INFO @ Sun, 02 Jun 2019 22:02:33: 7000000 INFO @ Sun, 02 Jun 2019 22:02:38: 7000000 INFO @ Sun, 02 Jun 2019 22:02:41: 8000000 INFO @ Sun, 02 Jun 2019 22:02:43: 8000000 INFO @ Sun, 02 Jun 2019 22:02:49: 8000000 INFO @ Sun, 02 Jun 2019 22:02:51: 9000000 INFO @ Sun, 02 Jun 2019 22:02:52: 9000000 INFO @ Sun, 02 Jun 2019 22:03:00: 9000000 INFO @ Sun, 02 Jun 2019 22:03:00: 10000000 INFO @ Sun, 02 Jun 2019 22:03:02: 10000000 INFO @ Sun, 02 Jun 2019 22:03:09: 11000000 INFO @ Sun, 02 Jun 2019 22:03:10: 10000000 INFO @ Sun, 02 Jun 2019 22:03:11: 11000000 INFO @ Sun, 02 Jun 2019 22:03:18: 12000000 INFO @ Sun, 02 Jun 2019 22:03:20: 11000000 INFO @ Sun, 02 Jun 2019 22:03:21: 12000000 INFO @ Sun, 02 Jun 2019 22:03:28: 13000000 INFO @ Sun, 02 Jun 2019 22:03:30: 12000000 INFO @ Sun, 02 Jun 2019 22:03:30: 13000000 INFO @ Sun, 02 Jun 2019 22:03:37: 14000000 INFO @ Sun, 02 Jun 2019 22:03:40: 13000000 INFO @ Sun, 02 Jun 2019 22:03:41: 14000000 INFO @ Sun, 02 Jun 2019 22:03:46: 15000000 INFO @ Sun, 02 Jun 2019 22:03:50: 15000000 INFO @ Sun, 02 Jun 2019 22:03:51: 14000000 INFO @ Sun, 02 Jun 2019 22:03:55: 16000000 INFO @ Sun, 02 Jun 2019 22:04:00: 16000000 INFO @ Sun, 02 Jun 2019 22:04:02: 15000000 INFO @ Sun, 02 Jun 2019 22:04:04: 17000000 INFO @ Sun, 02 Jun 2019 22:04:09: 17000000 INFO @ Sun, 02 Jun 2019 22:04:12: 16000000 INFO @ Sun, 02 Jun 2019 22:04:13: 18000000 INFO @ Sun, 02 Jun 2019 22:04:15: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:04:15: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:04:15: #1 total tags in treatment: 18220119 INFO @ Sun, 02 Jun 2019 22:04:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:15: #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 22:04:16: #1 tags after filtering in treatment: 18220119 INFO @ Sun, 02 Jun 2019 22:04:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:16: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:17: #2 number of paired peaks: 158 WARNING @ Sun, 02 Jun 2019 22:04:17: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sun, 02 Jun 2019 22:04:17: start model_add_line... INFO @ Sun, 02 Jun 2019 22:04:17: start X-correlation... INFO @ Sun, 02 Jun 2019 22:04:17: end of X-cor INFO @ Sun, 02 Jun 2019 22:04:17: #2 finished! INFO @ Sun, 02 Jun 2019 22:04:17: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 22:04:17: #2 alternative fragment length(s) may be 1,50,568 bps INFO @ Sun, 02 Jun 2019 22:04:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.10_model.r WARNING @ Sun, 02 Jun 2019 22:04:17: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:04:17: #2 You may need to consider one of the other alternative d(s): 1,50,568 WARNING @ Sun, 02 Jun 2019 22:04:17: #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 22:04:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:04:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:04:18: 18000000 INFO @ Sun, 02 Jun 2019 22:04:20: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:04:20: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:04:20: #1 total tags in treatment: 18220119 INFO @ Sun, 02 Jun 2019 22:04:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:20: #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 22:04:20: #1 tags after filtering in treatment: 18220119 INFO @ Sun, 02 Jun 2019 22:04:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:20: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:22: 17000000 INFO @ Sun, 02 Jun 2019 22:04:22: #2 number of paired peaks: 158 WARNING @ Sun, 02 Jun 2019 22:04:22: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sun, 02 Jun 2019 22:04:22: start model_add_line... INFO @ Sun, 02 Jun 2019 22:04:22: start X-correlation... INFO @ Sun, 02 Jun 2019 22:04:22: end of X-cor INFO @ Sun, 02 Jun 2019 22:04:22: #2 finished! INFO @ Sun, 02 Jun 2019 22:04:22: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 22:04:22: #2 alternative fragment length(s) may be 1,50,568 bps INFO @ Sun, 02 Jun 2019 22:04:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.20_model.r WARNING @ Sun, 02 Jun 2019 22:04:22: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:04:22: #2 You may need to consider one of the other alternative d(s): 1,50,568 WARNING @ Sun, 02 Jun 2019 22:04:22: #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 22:04:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:04:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:04:32: 18000000 INFO @ Sun, 02 Jun 2019 22:04:34: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:04:34: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:04:34: #1 total tags in treatment: 18220119 INFO @ Sun, 02 Jun 2019 22:04:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:34: #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 22:04:34: #1 tags after filtering in treatment: 18220119 INFO @ Sun, 02 Jun 2019 22:04:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:34: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:36: #2 number of paired peaks: 158 WARNING @ Sun, 02 Jun 2019 22:04:36: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sun, 02 Jun 2019 22:04:36: start model_add_line... INFO @ Sun, 02 Jun 2019 22:04:36: start X-correlation... INFO @ Sun, 02 Jun 2019 22:04:36: end of X-cor INFO @ Sun, 02 Jun 2019 22:04:36: #2 finished! INFO @ Sun, 02 Jun 2019 22:04:36: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 22:04:36: #2 alternative fragment length(s) may be 1,50,568 bps INFO @ Sun, 02 Jun 2019 22:04:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.05_model.r WARNING @ Sun, 02 Jun 2019 22:04:36: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:04:36: #2 You may need to consider one of the other alternative d(s): 1,50,568 WARNING @ Sun, 02 Jun 2019 22:04:36: #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 22:04:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:04:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:05:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:05:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:05:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:05:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.10_summits.bed INFO @ Sun, 02 Jun 2019 22:05:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (342 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:05:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.20_summits.bed INFO @ Sun, 02 Jun 2019 22:05:31: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (123 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:05:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5073500/SRX5073500.05_summits.bed INFO @ Sun, 02 Jun 2019 22:05:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (773 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。