Job ID = 1295129 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,580,056 reads read : 12,580,056 reads written : 12,580,056 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: 00:05:12 12580056 reads; of these: 12580056 (100.00%) were unpaired; of these: 271331 (2.16%) aligned 0 times 8598143 (68.35%) aligned exactly 1 time 3710582 (29.50%) aligned >1 times 97.84% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 819445 / 12308725 = 0.0666 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 12:20:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.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 12:20:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:20:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:20:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.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 12:20:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:20:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:20:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.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 12:20:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:20:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:20:29: 1000000 INFO @ Mon, 03 Jun 2019 12:20:30: 1000000 INFO @ Mon, 03 Jun 2019 12:20:31: 1000000 INFO @ Mon, 03 Jun 2019 12:20:36: 2000000 INFO @ Mon, 03 Jun 2019 12:20:38: 2000000 INFO @ Mon, 03 Jun 2019 12:20:39: 2000000 INFO @ Mon, 03 Jun 2019 12:20:43: 3000000 INFO @ Mon, 03 Jun 2019 12:20:46: 3000000 INFO @ Mon, 03 Jun 2019 12:20:47: 3000000 INFO @ Mon, 03 Jun 2019 12:20:50: 4000000 INFO @ Mon, 03 Jun 2019 12:20:55: 4000000 INFO @ Mon, 03 Jun 2019 12:20:55: 4000000 INFO @ Mon, 03 Jun 2019 12:20:57: 5000000 INFO @ Mon, 03 Jun 2019 12:21:03: 5000000 INFO @ Mon, 03 Jun 2019 12:21:03: 5000000 INFO @ Mon, 03 Jun 2019 12:21:04: 6000000 INFO @ Mon, 03 Jun 2019 12:21:11: 6000000 INFO @ Mon, 03 Jun 2019 12:21:11: 6000000 INFO @ Mon, 03 Jun 2019 12:21:11: 7000000 INFO @ Mon, 03 Jun 2019 12:21:18: 8000000 INFO @ Mon, 03 Jun 2019 12:21:19: 7000000 INFO @ Mon, 03 Jun 2019 12:21:20: 7000000 INFO @ Mon, 03 Jun 2019 12:21:25: 9000000 INFO @ Mon, 03 Jun 2019 12:21:26: 8000000 INFO @ Mon, 03 Jun 2019 12:21:28: 8000000 INFO @ Mon, 03 Jun 2019 12:21:32: 10000000 INFO @ Mon, 03 Jun 2019 12:21:34: 9000000 INFO @ Mon, 03 Jun 2019 12:21:37: 9000000 INFO @ Mon, 03 Jun 2019 12:21:39: 11000000 INFO @ Mon, 03 Jun 2019 12:21:41: 10000000 INFO @ Mon, 03 Jun 2019 12:21:43: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 12:21:43: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 12:21:43: #1 total tags in treatment: 11489280 INFO @ Mon, 03 Jun 2019 12:21:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:21:43: #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 12:21:43: #1 tags after filtering in treatment: 11489280 INFO @ Mon, 03 Jun 2019 12:21:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:21:43: #1 finished! INFO @ Mon, 03 Jun 2019 12:21:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:21:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:21:44: #2 number of paired peaks: 738 WARNING @ Mon, 03 Jun 2019 12:21:44: Fewer paired peaks (738) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 738 pairs to build model! INFO @ Mon, 03 Jun 2019 12:21:44: start model_add_line... INFO @ Mon, 03 Jun 2019 12:21:44: start X-correlation... INFO @ Mon, 03 Jun 2019 12:21:44: end of X-cor INFO @ Mon, 03 Jun 2019 12:21:44: #2 finished! INFO @ Mon, 03 Jun 2019 12:21:44: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 12:21:44: #2 alternative fragment length(s) may be 4,46 bps INFO @ Mon, 03 Jun 2019 12:21:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.05_model.r WARNING @ Mon, 03 Jun 2019 12:21:44: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:21:44: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Mon, 03 Jun 2019 12:21:44: #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 12:21:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:21:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:21:45: 10000000 INFO @ Mon, 03 Jun 2019 12:21:49: 11000000 INFO @ Mon, 03 Jun 2019 12:21:53: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 12:21:53: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 12:21:53: #1 total tags in treatment: 11489280 INFO @ Mon, 03 Jun 2019 12:21:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:21:53: #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 12:21:53: #1 tags after filtering in treatment: 11489280 INFO @ Mon, 03 Jun 2019 12:21:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:21:53: #1 finished! INFO @ Mon, 03 Jun 2019 12:21:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:21:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:21:54: 11000000 INFO @ Mon, 03 Jun 2019 12:21:54: #2 number of paired peaks: 738 WARNING @ Mon, 03 Jun 2019 12:21:54: Fewer paired peaks (738) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 738 pairs to build model! INFO @ Mon, 03 Jun 2019 12:21:54: start model_add_line... INFO @ Mon, 03 Jun 2019 12:21:54: start X-correlation... INFO @ Mon, 03 Jun 2019 12:21:54: end of X-cor INFO @ Mon, 03 Jun 2019 12:21:54: #2 finished! INFO @ Mon, 03 Jun 2019 12:21:54: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 12:21:54: #2 alternative fragment length(s) may be 4,46 bps INFO @ Mon, 03 Jun 2019 12:21:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.20_model.r WARNING @ Mon, 03 Jun 2019 12:21:54: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:21:54: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Mon, 03 Jun 2019 12:21:54: #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 12:21:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:21:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:21:58: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 12:21:58: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 12:21:58: #1 total tags in treatment: 11489280 INFO @ Mon, 03 Jun 2019 12:21:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:21:58: #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 12:21:58: #1 tags after filtering in treatment: 11489280 INFO @ Mon, 03 Jun 2019 12:21:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:21:58: #1 finished! INFO @ Mon, 03 Jun 2019 12:21:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:21:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:21:59: #2 number of paired peaks: 738 WARNING @ Mon, 03 Jun 2019 12:21:59: Fewer paired peaks (738) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 738 pairs to build model! INFO @ Mon, 03 Jun 2019 12:21:59: start model_add_line... INFO @ Mon, 03 Jun 2019 12:21:59: start X-correlation... INFO @ Mon, 03 Jun 2019 12:21:59: end of X-cor INFO @ Mon, 03 Jun 2019 12:21:59: #2 finished! INFO @ Mon, 03 Jun 2019 12:21:59: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 12:21:59: #2 alternative fragment length(s) may be 4,46 bps INFO @ Mon, 03 Jun 2019 12:21:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.10_model.r WARNING @ Mon, 03 Jun 2019 12:21:59: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:21:59: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Mon, 03 Jun 2019 12:21:59: #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 12:21:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:21:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:22:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:22:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:22:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:22:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:22:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:22:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.05_summits.bed INFO @ Mon, 03 Jun 2019 12:22:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3099 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:22:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:22:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.20_summits.bed INFO @ Mon, 03 Jun 2019 12:22:43: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (764 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:22:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:22:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:22:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX326969/SRX326969.10_summits.bed INFO @ Mon, 03 Jun 2019 12:22:48: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1868 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。