Job ID = 1294578 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,539,414 reads read : 16,539,414 reads written : 16,539,414 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: 00:08:13 16539414 reads; of these: 16539414 (100.00%) were unpaired; of these: 698542 (4.22%) aligned 0 times 10319644 (62.39%) aligned exactly 1 time 5521228 (33.38%) aligned >1 times 95.78% overall alignment rate Time searching: 00:08:13 Overall time: 00:08:13 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] 2191349 / 15840872 = 0.1383 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 09:21:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.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 09:21:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:21:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:21:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.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 09:21:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:21:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:21:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.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 09:21:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:21:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:21:10: 1000000 INFO @ Mon, 03 Jun 2019 09:21:13: 1000000 INFO @ Mon, 03 Jun 2019 09:21:13: 1000000 INFO @ Mon, 03 Jun 2019 09:21:18: 2000000 INFO @ Mon, 03 Jun 2019 09:21:23: 2000000 INFO @ Mon, 03 Jun 2019 09:21:23: 2000000 INFO @ Mon, 03 Jun 2019 09:21:26: 3000000 INFO @ Mon, 03 Jun 2019 09:21:33: 3000000 INFO @ Mon, 03 Jun 2019 09:21:33: 3000000 INFO @ Mon, 03 Jun 2019 09:21:34: 4000000 INFO @ Mon, 03 Jun 2019 09:21:42: 5000000 INFO @ Mon, 03 Jun 2019 09:21:43: 4000000 INFO @ Mon, 03 Jun 2019 09:21:43: 4000000 INFO @ Mon, 03 Jun 2019 09:21:50: 6000000 INFO @ Mon, 03 Jun 2019 09:21:53: 5000000 INFO @ Mon, 03 Jun 2019 09:21:53: 5000000 INFO @ Mon, 03 Jun 2019 09:21:58: 7000000 INFO @ Mon, 03 Jun 2019 09:22:03: 6000000 INFO @ Mon, 03 Jun 2019 09:22:03: 6000000 INFO @ Mon, 03 Jun 2019 09:22:06: 8000000 INFO @ Mon, 03 Jun 2019 09:22:13: 7000000 INFO @ Mon, 03 Jun 2019 09:22:13: 7000000 INFO @ Mon, 03 Jun 2019 09:22:14: 9000000 INFO @ Mon, 03 Jun 2019 09:22:22: 10000000 INFO @ Mon, 03 Jun 2019 09:22:23: 8000000 INFO @ Mon, 03 Jun 2019 09:22:23: 8000000 INFO @ Mon, 03 Jun 2019 09:22:30: 11000000 INFO @ Mon, 03 Jun 2019 09:22:33: 9000000 INFO @ Mon, 03 Jun 2019 09:22:33: 9000000 INFO @ Mon, 03 Jun 2019 09:22:38: 12000000 INFO @ Mon, 03 Jun 2019 09:22:43: 10000000 INFO @ Mon, 03 Jun 2019 09:22:43: 10000000 INFO @ Mon, 03 Jun 2019 09:22:46: 13000000 INFO @ Mon, 03 Jun 2019 09:22:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:22:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:22:51: #1 total tags in treatment: 13649523 INFO @ Mon, 03 Jun 2019 09:22:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:22:51: #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 09:22:51: #1 tags after filtering in treatment: 13649523 INFO @ Mon, 03 Jun 2019 09:22:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:22:51: #1 finished! INFO @ Mon, 03 Jun 2019 09:22:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:22:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:22:52: #2 number of paired peaks: 402 WARNING @ Mon, 03 Jun 2019 09:22:52: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Mon, 03 Jun 2019 09:22:52: start model_add_line... INFO @ Mon, 03 Jun 2019 09:22:52: 11000000 INFO @ Mon, 03 Jun 2019 09:22:52: start X-correlation... INFO @ Mon, 03 Jun 2019 09:22:52: end of X-cor INFO @ Mon, 03 Jun 2019 09:22:52: #2 finished! INFO @ Mon, 03 Jun 2019 09:22:52: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 09:22:52: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 09:22:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.10_model.r WARNING @ Mon, 03 Jun 2019 09:22:52: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:22:52: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 09:22:52: #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 09:22:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:22:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:22:52: 11000000 INFO @ Mon, 03 Jun 2019 09:23:02: 12000000 INFO @ Mon, 03 Jun 2019 09:23:02: 12000000 INFO @ Mon, 03 Jun 2019 09:23:12: 13000000 INFO @ Mon, 03 Jun 2019 09:23:12: 13000000 INFO @ Mon, 03 Jun 2019 09:23:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:23:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:23:18: #1 total tags in treatment: 13649523 INFO @ Mon, 03 Jun 2019 09:23:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:23:18: #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 09:23:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:23:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:23:18: #1 total tags in treatment: 13649523 INFO @ Mon, 03 Jun 2019 09:23:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:23:18: #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 09:23:18: #1 tags after filtering in treatment: 13649523 INFO @ Mon, 03 Jun 2019 09:23:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:23:18: #1 finished! INFO @ Mon, 03 Jun 2019 09:23:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:23:18: #1 tags after filtering in treatment: 13649523 INFO @ Mon, 03 Jun 2019 09:23:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:23:18: #1 finished! INFO @ Mon, 03 Jun 2019 09:23:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:23:20: #2 number of paired peaks: 402 WARNING @ Mon, 03 Jun 2019 09:23:20: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Mon, 03 Jun 2019 09:23:20: start model_add_line... INFO @ Mon, 03 Jun 2019 09:23:20: #2 number of paired peaks: 402 WARNING @ Mon, 03 Jun 2019 09:23:20: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Mon, 03 Jun 2019 09:23:20: start model_add_line... INFO @ Mon, 03 Jun 2019 09:23:20: start X-correlation... INFO @ Mon, 03 Jun 2019 09:23:20: end of X-cor INFO @ Mon, 03 Jun 2019 09:23:20: #2 finished! INFO @ Mon, 03 Jun 2019 09:23:20: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 09:23:20: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 09:23:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.05_model.r WARNING @ Mon, 03 Jun 2019 09:23:20: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:23:20: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 09:23:20: #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 09:23:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:23:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:23:20: start X-correlation... INFO @ Mon, 03 Jun 2019 09:23:20: end of X-cor INFO @ Mon, 03 Jun 2019 09:23:20: #2 finished! INFO @ Mon, 03 Jun 2019 09:23:20: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 09:23:20: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 09:23:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.20_model.r WARNING @ Mon, 03 Jun 2019 09:23:20: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:23:20: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 09:23:20: #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 09:23:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:23:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:23:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:23:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:23:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:23:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.10_summits.bed INFO @ Mon, 03 Jun 2019 09:23:47: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1933 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:23:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:23:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:24:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:24:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:24:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.20_summits.bed INFO @ Mon, 03 Jun 2019 09:24:14: Done! pass1 - making usageList (13 chroms): 0 millis INFO @ Mon, 03 Jun 2019 09:24:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.05_peaks.xls pass2 - checking and writing primary data (1526 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:24:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:24:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287753/SRX287753.05_summits.bed INFO @ Mon, 03 Jun 2019 09:24:14: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2227 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。