Job ID = 1294128 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,046,993 reads read : 18,046,993 reads written : 18,046,993 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: 00:07:23 18046993 reads; of these: 18046993 (100.00%) were unpaired; of these: 701010 (3.88%) aligned 0 times 11573614 (64.13%) aligned exactly 1 time 5772369 (31.99%) aligned >1 times 96.12% overall alignment rate Time searching: 00:07:23 Overall time: 00:07:23 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 8 files... [bam_rmdupse_core] 2645290 / 17345983 = 0.1525 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, 03 Jun 2019 05:09:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.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, 03 Jun 2019 05:09:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:09:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:09:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.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, 03 Jun 2019 05:09:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:09:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:09:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.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, 03 Jun 2019 05:09:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:09:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:09:14: 1000000 INFO @ Mon, 03 Jun 2019 05:09:16: 1000000 INFO @ Mon, 03 Jun 2019 05:09:17: 1000000 INFO @ Mon, 03 Jun 2019 05:09:21: 2000000 INFO @ Mon, 03 Jun 2019 05:09:23: 2000000 INFO @ Mon, 03 Jun 2019 05:09:26: 2000000 INFO @ Mon, 03 Jun 2019 05:09:28: 3000000 INFO @ Mon, 03 Jun 2019 05:09:31: 3000000 INFO @ Mon, 03 Jun 2019 05:09:35: 4000000 INFO @ Mon, 03 Jun 2019 05:09:36: 3000000 INFO @ Mon, 03 Jun 2019 05:09:39: 4000000 INFO @ Mon, 03 Jun 2019 05:09:41: 5000000 INFO @ Mon, 03 Jun 2019 05:09:45: 4000000 INFO @ Mon, 03 Jun 2019 05:09:47: 5000000 INFO @ Mon, 03 Jun 2019 05:09:48: 6000000 INFO @ Mon, 03 Jun 2019 05:09:55: 6000000 INFO @ Mon, 03 Jun 2019 05:09:55: 5000000 INFO @ Mon, 03 Jun 2019 05:09:55: 7000000 INFO @ Mon, 03 Jun 2019 05:10:01: 8000000 INFO @ Mon, 03 Jun 2019 05:10:02: 7000000 INFO @ Mon, 03 Jun 2019 05:10:04: 6000000 INFO @ Mon, 03 Jun 2019 05:10:08: 9000000 INFO @ Mon, 03 Jun 2019 05:10:10: 8000000 INFO @ Mon, 03 Jun 2019 05:10:12: 7000000 INFO @ Mon, 03 Jun 2019 05:10:14: 10000000 INFO @ Mon, 03 Jun 2019 05:10:17: 9000000 INFO @ Mon, 03 Jun 2019 05:10:20: 8000000 INFO @ Mon, 03 Jun 2019 05:10:21: 11000000 INFO @ Mon, 03 Jun 2019 05:10:25: 10000000 INFO @ Mon, 03 Jun 2019 05:10:27: 12000000 INFO @ Mon, 03 Jun 2019 05:10:28: 9000000 INFO @ Mon, 03 Jun 2019 05:10:32: 11000000 INFO @ Mon, 03 Jun 2019 05:10:34: 13000000 INFO @ Mon, 03 Jun 2019 05:10:36: 10000000 INFO @ Mon, 03 Jun 2019 05:10:40: 12000000 INFO @ Mon, 03 Jun 2019 05:10:41: 14000000 INFO @ Mon, 03 Jun 2019 05:10:44: 11000000 INFO @ Mon, 03 Jun 2019 05:10:45: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:10:45: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:10:45: #1 total tags in treatment: 14700693 INFO @ Mon, 03 Jun 2019 05:10:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:10:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:10:46: #1 tags after filtering in treatment: 14700693 INFO @ Mon, 03 Jun 2019 05:10:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:10:46: #1 finished! INFO @ Mon, 03 Jun 2019 05:10:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:10:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:10:47: #2 number of paired peaks: 611 WARNING @ Mon, 03 Jun 2019 05:10:47: Fewer paired peaks (611) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 611 pairs to build model! INFO @ Mon, 03 Jun 2019 05:10:47: start model_add_line... INFO @ Mon, 03 Jun 2019 05:10:47: 13000000 INFO @ Mon, 03 Jun 2019 05:10:47: start X-correlation... INFO @ Mon, 03 Jun 2019 05:10:47: end of X-cor INFO @ Mon, 03 Jun 2019 05:10:47: #2 finished! INFO @ Mon, 03 Jun 2019 05:10:47: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 05:10:47: #2 alternative fragment length(s) may be 3,56 bps INFO @ Mon, 03 Jun 2019 05:10:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.20_model.r WARNING @ Mon, 03 Jun 2019 05:10:47: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:10:47: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Mon, 03 Jun 2019 05:10:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:10:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:10:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:10:52: 12000000 INFO @ Mon, 03 Jun 2019 05:10:55: 14000000 INFO @ Mon, 03 Jun 2019 05:11:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:11:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:11:00: #1 total tags in treatment: 14700693 INFO @ Mon, 03 Jun 2019 05:11:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:11:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:11:00: 13000000 INFO @ Mon, 03 Jun 2019 05:11:00: #1 tags after filtering in treatment: 14700693 INFO @ Mon, 03 Jun 2019 05:11:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:11:00: #1 finished! INFO @ Mon, 03 Jun 2019 05:11:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:11:02: #2 number of paired peaks: 611 WARNING @ Mon, 03 Jun 2019 05:11:02: Fewer paired peaks (611) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 611 pairs to build model! INFO @ Mon, 03 Jun 2019 05:11:02: start model_add_line... INFO @ Mon, 03 Jun 2019 05:11:02: start X-correlation... INFO @ Mon, 03 Jun 2019 05:11:02: end of X-cor INFO @ Mon, 03 Jun 2019 05:11:02: #2 finished! INFO @ Mon, 03 Jun 2019 05:11:02: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 05:11:02: #2 alternative fragment length(s) may be 3,56 bps INFO @ Mon, 03 Jun 2019 05:11:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.05_model.r WARNING @ Mon, 03 Jun 2019 05:11:02: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:11:02: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Mon, 03 Jun 2019 05:11:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:11:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:11:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:11:08: 14000000 INFO @ Mon, 03 Jun 2019 05:11:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:11:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:11:14: #1 total tags in treatment: 14700693 INFO @ Mon, 03 Jun 2019 05:11:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:11:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:11:14: #1 tags after filtering in treatment: 14700693 INFO @ Mon, 03 Jun 2019 05:11:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:11:14: #1 finished! INFO @ Mon, 03 Jun 2019 05:11:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:11:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:11:15: #2 number of paired peaks: 611 WARNING @ Mon, 03 Jun 2019 05:11:15: Fewer paired peaks (611) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 611 pairs to build model! INFO @ Mon, 03 Jun 2019 05:11:15: start model_add_line... INFO @ Mon, 03 Jun 2019 05:11:15: start X-correlation... INFO @ Mon, 03 Jun 2019 05:11:15: end of X-cor INFO @ Mon, 03 Jun 2019 05:11:15: #2 finished! INFO @ Mon, 03 Jun 2019 05:11:15: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 05:11:15: #2 alternative fragment length(s) may be 3,56 bps INFO @ Mon, 03 Jun 2019 05:11:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.10_model.r WARNING @ Mon, 03 Jun 2019 05:11:15: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:11:15: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Mon, 03 Jun 2019 05:11:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:11:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:11:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:11:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:11:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:11:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:11:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:11:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.20_summits.bed INFO @ Mon, 03 Jun 2019 05:11:45: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (976 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:11:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:12:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:12:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:12:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.05_summits.bed INFO @ Mon, 03 Jun 2019 05:12:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3365 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:12:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:12:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:12:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193308/SRX193308.10_summits.bed INFO @ Mon, 03 Jun 2019 05:12:14: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2246 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。