Job ID = 1294972 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,930,693 reads read : 19,930,693 reads written : 19,930,693 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: 00:08:53 19930693 reads; of these: 19930693 (100.00%) were unpaired; of these: 1257582 (6.31%) aligned 0 times 12953047 (64.99%) aligned exactly 1 time 5720064 (28.70%) aligned >1 times 93.69% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 2338738 / 18673111 = 0.1252 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 11:23:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.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 11:23:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:23:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:23:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.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 11:23:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:23:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:23:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.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 11:23:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:23:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:23:42: 1000000 INFO @ Mon, 03 Jun 2019 11:23:43: 1000000 INFO @ Mon, 03 Jun 2019 11:23:44: 1000000 INFO @ Mon, 03 Jun 2019 11:23:49: 2000000 INFO @ Mon, 03 Jun 2019 11:23:52: 2000000 INFO @ Mon, 03 Jun 2019 11:23:53: 2000000 INFO @ Mon, 03 Jun 2019 11:23:57: 3000000 INFO @ Mon, 03 Jun 2019 11:24:00: 3000000 INFO @ Mon, 03 Jun 2019 11:24:01: 3000000 INFO @ Mon, 03 Jun 2019 11:24:04: 4000000 INFO @ Mon, 03 Jun 2019 11:24:08: 4000000 INFO @ Mon, 03 Jun 2019 11:24:09: 4000000 INFO @ Mon, 03 Jun 2019 11:24:12: 5000000 INFO @ Mon, 03 Jun 2019 11:24:17: 5000000 INFO @ Mon, 03 Jun 2019 11:24:18: 5000000 INFO @ Mon, 03 Jun 2019 11:24:19: 6000000 INFO @ Mon, 03 Jun 2019 11:24:25: 6000000 INFO @ Mon, 03 Jun 2019 11:24:27: 7000000 INFO @ Mon, 03 Jun 2019 11:24:27: 6000000 INFO @ Mon, 03 Jun 2019 11:24:34: 8000000 INFO @ Mon, 03 Jun 2019 11:24:35: 7000000 INFO @ Mon, 03 Jun 2019 11:24:35: 7000000 INFO @ Mon, 03 Jun 2019 11:24:41: 9000000 INFO @ Mon, 03 Jun 2019 11:24:43: 8000000 INFO @ Mon, 03 Jun 2019 11:24:43: 8000000 INFO @ Mon, 03 Jun 2019 11:24:49: 10000000 INFO @ Mon, 03 Jun 2019 11:24:51: 9000000 INFO @ Mon, 03 Jun 2019 11:24:52: 9000000 INFO @ Mon, 03 Jun 2019 11:24:56: 11000000 INFO @ Mon, 03 Jun 2019 11:25:00: 10000000 INFO @ Mon, 03 Jun 2019 11:25:01: 10000000 INFO @ Mon, 03 Jun 2019 11:25:03: 12000000 INFO @ Mon, 03 Jun 2019 11:25:08: 11000000 INFO @ Mon, 03 Jun 2019 11:25:09: 11000000 INFO @ Mon, 03 Jun 2019 11:25:10: 13000000 INFO @ Mon, 03 Jun 2019 11:25:16: 12000000 INFO @ Mon, 03 Jun 2019 11:25:17: 12000000 INFO @ Mon, 03 Jun 2019 11:25:18: 14000000 INFO @ Mon, 03 Jun 2019 11:25:24: 13000000 INFO @ Mon, 03 Jun 2019 11:25:25: 15000000 INFO @ Mon, 03 Jun 2019 11:25:26: 13000000 INFO @ Mon, 03 Jun 2019 11:25:32: 16000000 INFO @ Mon, 03 Jun 2019 11:25:33: 14000000 INFO @ Mon, 03 Jun 2019 11:25:34: 14000000 INFO @ Mon, 03 Jun 2019 11:25:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:25:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:25:35: #1 total tags in treatment: 16334373 INFO @ Mon, 03 Jun 2019 11:25:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:25:35: #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 11:25:35: #1 tags after filtering in treatment: 16334373 INFO @ Mon, 03 Jun 2019 11:25:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:25:35: #1 finished! INFO @ Mon, 03 Jun 2019 11:25:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:25:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:25:37: #2 number of paired peaks: 203 WARNING @ Mon, 03 Jun 2019 11:25:37: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Mon, 03 Jun 2019 11:25:37: start model_add_line... INFO @ Mon, 03 Jun 2019 11:25:37: start X-correlation... INFO @ Mon, 03 Jun 2019 11:25:37: end of X-cor INFO @ Mon, 03 Jun 2019 11:25:37: #2 finished! INFO @ Mon, 03 Jun 2019 11:25:37: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 11:25:37: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 11:25:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.20_model.r WARNING @ Mon, 03 Jun 2019 11:25:37: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:25:37: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 11:25:37: #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 11:25:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:25:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:25:41: 15000000 INFO @ Mon, 03 Jun 2019 11:25:41: 15000000 INFO @ Mon, 03 Jun 2019 11:25:49: 16000000 INFO @ Mon, 03 Jun 2019 11:25:50: 16000000 INFO @ Mon, 03 Jun 2019 11:25:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:25:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:25:52: #1 total tags in treatment: 16334373 INFO @ Mon, 03 Jun 2019 11:25:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:25:52: #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 11:25:53: #1 tags after filtering in treatment: 16334373 INFO @ Mon, 03 Jun 2019 11:25:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:25:53: #1 finished! INFO @ Mon, 03 Jun 2019 11:25:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:25:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:25:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:25:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:25:53: #1 total tags in treatment: 16334373 INFO @ Mon, 03 Jun 2019 11:25:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:25:53: #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 11:25:53: #1 tags after filtering in treatment: 16334373 INFO @ Mon, 03 Jun 2019 11:25:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:25:53: #1 finished! INFO @ Mon, 03 Jun 2019 11:25:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:25:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:25:54: #2 number of paired peaks: 203 WARNING @ Mon, 03 Jun 2019 11:25:54: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Mon, 03 Jun 2019 11:25:54: start model_add_line... INFO @ Mon, 03 Jun 2019 11:25:54: start X-correlation... INFO @ Mon, 03 Jun 2019 11:25:54: end of X-cor INFO @ Mon, 03 Jun 2019 11:25:54: #2 finished! INFO @ Mon, 03 Jun 2019 11:25:54: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 11:25:54: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 11:25:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.10_model.r WARNING @ Mon, 03 Jun 2019 11:25:54: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:25:54: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 11:25:54: #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 11:25:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:25:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:25:54: #2 number of paired peaks: 203 WARNING @ Mon, 03 Jun 2019 11:25:54: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Mon, 03 Jun 2019 11:25:54: start model_add_line... INFO @ Mon, 03 Jun 2019 11:25:55: start X-correlation... INFO @ Mon, 03 Jun 2019 11:25:55: end of X-cor INFO @ Mon, 03 Jun 2019 11:25:55: #2 finished! INFO @ Mon, 03 Jun 2019 11:25:55: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 11:25:55: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 11:25:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.05_model.r WARNING @ Mon, 03 Jun 2019 11:25:55: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:25:55: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 11:25:55: #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 11:25:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:25:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:26:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:26:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:26:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:26:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:26:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:26:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.20_summits.bed INFO @ Mon, 03 Jun 2019 11:26:41: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1363 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:26:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:26:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:26:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.10_summits.bed INFO @ Mon, 03 Jun 2019 11:26:58: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1858 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:26:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:26:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:26:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288031/SRX288031.05_summits.bed INFO @ Mon, 03 Jun 2019 11:26:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2093 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。