Job ID = 2590796 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,244,185 reads read : 68,488,370 reads written : 34,244,185 reads 0-length : 34,244,185 rm: cannot remove ‘[DSE]RR*’: 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: 00:14:07 34244185 reads; of these: 34244185 (100.00%) were unpaired; of these: 731212 (2.14%) aligned 0 times 23883506 (69.74%) aligned exactly 1 time 9629467 (28.12%) aligned >1 times 97.86% overall alignment rate Time searching: 00:14:07 Overall time: 00:14:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 15464985 / 33512973 = 0.4615 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 @ Mon, 12 Aug 2019 23:41:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 23:41:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:41:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:41:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 23:41:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:41:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:41:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 23:41:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:41:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:41:23: 1000000 INFO @ Mon, 12 Aug 2019 23:41:25: 1000000 INFO @ Mon, 12 Aug 2019 23:41:26: 1000000 INFO @ Mon, 12 Aug 2019 23:41:30: 2000000 INFO @ Mon, 12 Aug 2019 23:41:32: 2000000 INFO @ Mon, 12 Aug 2019 23:41:34: 2000000 INFO @ Mon, 12 Aug 2019 23:41:37: 3000000 INFO @ Mon, 12 Aug 2019 23:41:40: 3000000 INFO @ Mon, 12 Aug 2019 23:41:43: 3000000 INFO @ Mon, 12 Aug 2019 23:41:45: 4000000 INFO @ Mon, 12 Aug 2019 23:41:47: 4000000 INFO @ Mon, 12 Aug 2019 23:41:51: 4000000 INFO @ Mon, 12 Aug 2019 23:41:52: 5000000 INFO @ Mon, 12 Aug 2019 23:41:54: 5000000 INFO @ Mon, 12 Aug 2019 23:41:59: 6000000 INFO @ Mon, 12 Aug 2019 23:42:00: 5000000 INFO @ Mon, 12 Aug 2019 23:42:02: 6000000 INFO @ Mon, 12 Aug 2019 23:42:07: 7000000 INFO @ Mon, 12 Aug 2019 23:42:08: 6000000 INFO @ Mon, 12 Aug 2019 23:42:09: 7000000 INFO @ Mon, 12 Aug 2019 23:42:14: 8000000 INFO @ Mon, 12 Aug 2019 23:42:16: 8000000 INFO @ Mon, 12 Aug 2019 23:42:17: 7000000 INFO @ Mon, 12 Aug 2019 23:42:21: 9000000 INFO @ Mon, 12 Aug 2019 23:42:24: 9000000 INFO @ Mon, 12 Aug 2019 23:42:25: 8000000 INFO @ Mon, 12 Aug 2019 23:42:29: 10000000 INFO @ Mon, 12 Aug 2019 23:42:31: 10000000 INFO @ Mon, 12 Aug 2019 23:42:34: 9000000 INFO @ Mon, 12 Aug 2019 23:42:36: 11000000 INFO @ Mon, 12 Aug 2019 23:42:38: 11000000 INFO @ Mon, 12 Aug 2019 23:42:42: 10000000 INFO @ Mon, 12 Aug 2019 23:42:43: 12000000 INFO @ Mon, 12 Aug 2019 23:42:46: 12000000 INFO @ Mon, 12 Aug 2019 23:42:50: 11000000 INFO @ Mon, 12 Aug 2019 23:42:51: 13000000 INFO @ Mon, 12 Aug 2019 23:42:53: 13000000 INFO @ Mon, 12 Aug 2019 23:42:58: 12000000 INFO @ Mon, 12 Aug 2019 23:42:58: 14000000 INFO @ Mon, 12 Aug 2019 23:43:00: 14000000 INFO @ Mon, 12 Aug 2019 23:43:06: 15000000 INFO @ Mon, 12 Aug 2019 23:43:06: 13000000 INFO @ Mon, 12 Aug 2019 23:43:08: 15000000 INFO @ Mon, 12 Aug 2019 23:43:13: 16000000 INFO @ Mon, 12 Aug 2019 23:43:15: 16000000 INFO @ Mon, 12 Aug 2019 23:43:15: 14000000 INFO @ Mon, 12 Aug 2019 23:43:20: 17000000 INFO @ Mon, 12 Aug 2019 23:43:22: 17000000 INFO @ Mon, 12 Aug 2019 23:43:24: 15000000 INFO @ Mon, 12 Aug 2019 23:43:28: 18000000 INFO @ Mon, 12 Aug 2019 23:43:28: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:43:28: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:43:28: #1 total tags in treatment: 18047988 INFO @ Mon, 12 Aug 2019 23:43:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:43:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:43:28: #1 tags after filtering in treatment: 18047988 INFO @ Mon, 12 Aug 2019 23:43:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:43:28: #1 finished! INFO @ Mon, 12 Aug 2019 23:43:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:43:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:43:29: 18000000 INFO @ Mon, 12 Aug 2019 23:43:30: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:43:30: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:43:30: #1 total tags in treatment: 18047988 INFO @ Mon, 12 Aug 2019 23:43:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:43:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:43:30: #2 number of paired peaks: 605 WARNING @ Mon, 12 Aug 2019 23:43:30: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Mon, 12 Aug 2019 23:43:30: start model_add_line... INFO @ Mon, 12 Aug 2019 23:43:30: start X-correlation... INFO @ Mon, 12 Aug 2019 23:43:30: end of X-cor INFO @ Mon, 12 Aug 2019 23:43:30: #2 finished! INFO @ Mon, 12 Aug 2019 23:43:30: #2 predicted fragment length is 54 bps INFO @ Mon, 12 Aug 2019 23:43:30: #2 alternative fragment length(s) may be 3,54,595 bps INFO @ Mon, 12 Aug 2019 23:43:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.05_model.r WARNING @ Mon, 12 Aug 2019 23:43:30: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:43:30: #2 You may need to consider one of the other alternative d(s): 3,54,595 WARNING @ Mon, 12 Aug 2019 23:43:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:43:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:43:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:43:30: #1 tags after filtering in treatment: 18047988 INFO @ Mon, 12 Aug 2019 23:43:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:43:30: #1 finished! INFO @ Mon, 12 Aug 2019 23:43:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:43:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:43:32: 16000000 INFO @ Mon, 12 Aug 2019 23:43:32: #2 number of paired peaks: 605 WARNING @ Mon, 12 Aug 2019 23:43:32: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Mon, 12 Aug 2019 23:43:32: start model_add_line... INFO @ Mon, 12 Aug 2019 23:43:32: start X-correlation... INFO @ Mon, 12 Aug 2019 23:43:32: end of X-cor INFO @ Mon, 12 Aug 2019 23:43:32: #2 finished! INFO @ Mon, 12 Aug 2019 23:43:32: #2 predicted fragment length is 54 bps INFO @ Mon, 12 Aug 2019 23:43:32: #2 alternative fragment length(s) may be 3,54,595 bps INFO @ Mon, 12 Aug 2019 23:43:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.20_model.r WARNING @ Mon, 12 Aug 2019 23:43:32: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:43:32: #2 You may need to consider one of the other alternative d(s): 3,54,595 WARNING @ Mon, 12 Aug 2019 23:43:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:43:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:43:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:43:40: 17000000 INFO @ Mon, 12 Aug 2019 23:43:48: 18000000 INFO @ Mon, 12 Aug 2019 23:43:49: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:43:49: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:43:49: #1 total tags in treatment: 18047988 INFO @ Mon, 12 Aug 2019 23:43:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:43:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:43:49: #1 tags after filtering in treatment: 18047988 INFO @ Mon, 12 Aug 2019 23:43:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:43:49: #1 finished! INFO @ Mon, 12 Aug 2019 23:43:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:43:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:43:51: #2 number of paired peaks: 605 WARNING @ Mon, 12 Aug 2019 23:43:51: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Mon, 12 Aug 2019 23:43:51: start model_add_line... INFO @ Mon, 12 Aug 2019 23:43:51: start X-correlation... INFO @ Mon, 12 Aug 2019 23:43:51: end of X-cor INFO @ Mon, 12 Aug 2019 23:43:51: #2 finished! INFO @ Mon, 12 Aug 2019 23:43:51: #2 predicted fragment length is 54 bps INFO @ Mon, 12 Aug 2019 23:43:51: #2 alternative fragment length(s) may be 3,54,595 bps INFO @ Mon, 12 Aug 2019 23:43:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.10_model.r WARNING @ Mon, 12 Aug 2019 23:43:51: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:43:51: #2 You may need to consider one of the other alternative d(s): 3,54,595 WARNING @ Mon, 12 Aug 2019 23:43:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:43:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:43:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:44:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:44:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:44:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:44:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:44:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:44:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.05_summits.bed INFO @ Mon, 12 Aug 2019 23:44:40: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3839 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:44:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:44:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:44:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.20_summits.bed INFO @ Mon, 12 Aug 2019 23:44:41: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1041 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:45:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:45:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:45:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011038/SRX5011038.10_summits.bed INFO @ Mon, 12 Aug 2019 23:45:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2216 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。