Job ID = 1294856 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,587,705 reads read : 16,587,705 reads written : 16,587,705 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: 00:07:24 16587705 reads; of these: 16587705 (100.00%) were unpaired; of these: 805563 (4.86%) aligned 0 times 9764966 (58.87%) aligned exactly 1 time 6017176 (36.27%) aligned >1 times 95.14% overall alignment rate Time searching: 00:07:24 Overall time: 00:07:24 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] 1636620 / 15782142 = 0.1037 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 10:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.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 10:45:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:45:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.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 10:45:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:45:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.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 10:45:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:45:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:45:07: 1000000 INFO @ Mon, 03 Jun 2019 10:45:08: 1000000 INFO @ Mon, 03 Jun 2019 10:45:08: 1000000 INFO @ Mon, 03 Jun 2019 10:45:14: 2000000 INFO @ Mon, 03 Jun 2019 10:45:16: 2000000 INFO @ Mon, 03 Jun 2019 10:45:16: 2000000 INFO @ Mon, 03 Jun 2019 10:45:21: 3000000 INFO @ Mon, 03 Jun 2019 10:45:23: 3000000 INFO @ Mon, 03 Jun 2019 10:45:23: 3000000 INFO @ Mon, 03 Jun 2019 10:45:27: 4000000 INFO @ Mon, 03 Jun 2019 10:45:31: 4000000 INFO @ Mon, 03 Jun 2019 10:45:31: 4000000 INFO @ Mon, 03 Jun 2019 10:45:34: 5000000 INFO @ Mon, 03 Jun 2019 10:45:38: 5000000 INFO @ Mon, 03 Jun 2019 10:45:38: 5000000 INFO @ Mon, 03 Jun 2019 10:45:41: 6000000 INFO @ Mon, 03 Jun 2019 10:45:46: 6000000 INFO @ Mon, 03 Jun 2019 10:45:46: 6000000 INFO @ Mon, 03 Jun 2019 10:45:47: 7000000 INFO @ Mon, 03 Jun 2019 10:45:53: 7000000 INFO @ Mon, 03 Jun 2019 10:45:53: 7000000 INFO @ Mon, 03 Jun 2019 10:45:54: 8000000 INFO @ Mon, 03 Jun 2019 10:46:01: 8000000 INFO @ Mon, 03 Jun 2019 10:46:01: 8000000 INFO @ Mon, 03 Jun 2019 10:46:01: 9000000 INFO @ Mon, 03 Jun 2019 10:46:08: 10000000 INFO @ Mon, 03 Jun 2019 10:46:08: 9000000 INFO @ Mon, 03 Jun 2019 10:46:08: 9000000 INFO @ Mon, 03 Jun 2019 10:46:14: 11000000 INFO @ Mon, 03 Jun 2019 10:46:16: 10000000 INFO @ Mon, 03 Jun 2019 10:46:16: 10000000 INFO @ Mon, 03 Jun 2019 10:46:21: 12000000 INFO @ Mon, 03 Jun 2019 10:46:23: 11000000 INFO @ Mon, 03 Jun 2019 10:46:23: 11000000 INFO @ Mon, 03 Jun 2019 10:46:28: 13000000 INFO @ Mon, 03 Jun 2019 10:46:30: 12000000 INFO @ Mon, 03 Jun 2019 10:46:31: 12000000 INFO @ Mon, 03 Jun 2019 10:46:34: 14000000 INFO @ Mon, 03 Jun 2019 10:46:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:46:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:46:35: #1 total tags in treatment: 14145522 INFO @ Mon, 03 Jun 2019 10:46:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:46:35: #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 10:46:36: #1 tags after filtering in treatment: 14145522 INFO @ Mon, 03 Jun 2019 10:46:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:46:36: #1 finished! INFO @ Mon, 03 Jun 2019 10:46:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:46:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:46:37: #2 number of paired peaks: 367 WARNING @ Mon, 03 Jun 2019 10:46:37: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Mon, 03 Jun 2019 10:46:37: start model_add_line... INFO @ Mon, 03 Jun 2019 10:46:37: start X-correlation... INFO @ Mon, 03 Jun 2019 10:46:37: end of X-cor INFO @ Mon, 03 Jun 2019 10:46:37: #2 finished! INFO @ Mon, 03 Jun 2019 10:46:37: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 10:46:37: #2 alternative fragment length(s) may be 86 bps INFO @ Mon, 03 Jun 2019 10:46:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.10_model.r WARNING @ Mon, 03 Jun 2019 10:46:37: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:46:37: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Mon, 03 Jun 2019 10:46:37: #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 10:46:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:46:38: 13000000 INFO @ Mon, 03 Jun 2019 10:46:38: 13000000 INFO @ Mon, 03 Jun 2019 10:46:45: 14000000 INFO @ Mon, 03 Jun 2019 10:46:45: 14000000 INFO @ Mon, 03 Jun 2019 10:46:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:46:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:46:46: #1 total tags in treatment: 14145522 INFO @ Mon, 03 Jun 2019 10:46:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:46:46: #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 10:46:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:46:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:46:47: #1 total tags in treatment: 14145522 INFO @ Mon, 03 Jun 2019 10:46:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:46:47: #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 10:46:47: #1 tags after filtering in treatment: 14145522 INFO @ Mon, 03 Jun 2019 10:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:46:47: #1 finished! INFO @ Mon, 03 Jun 2019 10:46:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:46:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:46:47: #1 tags after filtering in treatment: 14145522 INFO @ Mon, 03 Jun 2019 10:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:46:47: #1 finished! INFO @ Mon, 03 Jun 2019 10:46:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:46:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:46:48: #2 number of paired peaks: 367 WARNING @ Mon, 03 Jun 2019 10:46:48: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Mon, 03 Jun 2019 10:46:48: start model_add_line... INFO @ Mon, 03 Jun 2019 10:46:48: start X-correlation... INFO @ Mon, 03 Jun 2019 10:46:48: end of X-cor INFO @ Mon, 03 Jun 2019 10:46:48: #2 finished! INFO @ Mon, 03 Jun 2019 10:46:48: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 10:46:48: #2 alternative fragment length(s) may be 86 bps INFO @ Mon, 03 Jun 2019 10:46:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.20_model.r WARNING @ Mon, 03 Jun 2019 10:46:48: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:46:48: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Mon, 03 Jun 2019 10:46:48: #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 10:46:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:46:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:46:48: #2 number of paired peaks: 367 WARNING @ Mon, 03 Jun 2019 10:46:48: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Mon, 03 Jun 2019 10:46:48: start model_add_line... INFO @ Mon, 03 Jun 2019 10:46:48: start X-correlation... INFO @ Mon, 03 Jun 2019 10:46:48: end of X-cor INFO @ Mon, 03 Jun 2019 10:46:48: #2 finished! INFO @ Mon, 03 Jun 2019 10:46:48: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 10:46:48: #2 alternative fragment length(s) may be 86 bps INFO @ Mon, 03 Jun 2019 10:46:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.05_model.r WARNING @ Mon, 03 Jun 2019 10:46:48: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:46:48: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Mon, 03 Jun 2019 10:46:48: #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 10:46:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:46:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:47:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:47:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:47:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:47:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:47:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:47:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.10_summits.bed INFO @ Mon, 03 Jun 2019 10:47:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1697 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:47:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:47:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.20_summits.bed INFO @ Mon, 03 Jun 2019 10:47:46: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1035 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:47:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:47:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287949/SRX287949.05_summits.bed INFO @ Mon, 03 Jun 2019 10:47:46: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2761 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。