Job ID = 1295079 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,493,128 reads read : 18,493,128 reads written : 18,493,128 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: 00:07:34 18493128 reads; of these: 18493128 (100.00%) were unpaired; of these: 1124923 (6.08%) aligned 0 times 13121027 (70.95%) aligned exactly 1 time 4247178 (22.97%) aligned >1 times 93.92% overall alignment rate Time searching: 00:07:34 Overall time: 00:07:34 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] 1482310 / 17368205 = 0.0853 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 11:55:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.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 11:55:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:55:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:55:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.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 11:55:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:55:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:55:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.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 11:55:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:55:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:55:17: 1000000 INFO @ Mon, 03 Jun 2019 11:55:18: 1000000 INFO @ Mon, 03 Jun 2019 11:55:18: 1000000 INFO @ Mon, 03 Jun 2019 11:55:25: 2000000 INFO @ Mon, 03 Jun 2019 11:55:27: 2000000 INFO @ Mon, 03 Jun 2019 11:55:28: 2000000 INFO @ Mon, 03 Jun 2019 11:55:33: 3000000 INFO @ Mon, 03 Jun 2019 11:55:36: 3000000 INFO @ Mon, 03 Jun 2019 11:55:37: 3000000 INFO @ Mon, 03 Jun 2019 11:55:42: 4000000 INFO @ Mon, 03 Jun 2019 11:55:46: 4000000 INFO @ Mon, 03 Jun 2019 11:55:48: 4000000 INFO @ Mon, 03 Jun 2019 11:55:52: 5000000 INFO @ Mon, 03 Jun 2019 11:55:56: 5000000 INFO @ Mon, 03 Jun 2019 11:55:57: 5000000 INFO @ Mon, 03 Jun 2019 11:56:00: 6000000 INFO @ Mon, 03 Jun 2019 11:56:05: 6000000 INFO @ Mon, 03 Jun 2019 11:56:06: 6000000 INFO @ Mon, 03 Jun 2019 11:56:08: 7000000 INFO @ Mon, 03 Jun 2019 11:56:14: 7000000 INFO @ Mon, 03 Jun 2019 11:56:15: 7000000 INFO @ Mon, 03 Jun 2019 11:56:17: 8000000 INFO @ Mon, 03 Jun 2019 11:56:23: 8000000 INFO @ Mon, 03 Jun 2019 11:56:25: 8000000 INFO @ Mon, 03 Jun 2019 11:56:25: 9000000 INFO @ Mon, 03 Jun 2019 11:56:31: 9000000 INFO @ Mon, 03 Jun 2019 11:56:34: 10000000 INFO @ Mon, 03 Jun 2019 11:56:35: 9000000 INFO @ Mon, 03 Jun 2019 11:56:41: 10000000 INFO @ Mon, 03 Jun 2019 11:56:42: 11000000 INFO @ Mon, 03 Jun 2019 11:56:45: 10000000 INFO @ Mon, 03 Jun 2019 11:56:49: 11000000 INFO @ Mon, 03 Jun 2019 11:56:50: 12000000 INFO @ Mon, 03 Jun 2019 11:56:54: 11000000 INFO @ Mon, 03 Jun 2019 11:56:58: 12000000 INFO @ Mon, 03 Jun 2019 11:56:58: 13000000 INFO @ Mon, 03 Jun 2019 11:57:04: 12000000 INFO @ Mon, 03 Jun 2019 11:57:08: 13000000 INFO @ Mon, 03 Jun 2019 11:57:09: 14000000 INFO @ Mon, 03 Jun 2019 11:57:14: 13000000 INFO @ Mon, 03 Jun 2019 11:57:17: 14000000 INFO @ Mon, 03 Jun 2019 11:57:17: 15000000 INFO @ Mon, 03 Jun 2019 11:57:23: 14000000 INFO @ Mon, 03 Jun 2019 11:57:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:57:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:57:25: #1 total tags in treatment: 15885895 INFO @ Mon, 03 Jun 2019 11:57:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:57:25: #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 11:57:25: #1 tags after filtering in treatment: 15885895 INFO @ Mon, 03 Jun 2019 11:57:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:57:25: #1 finished! INFO @ Mon, 03 Jun 2019 11:57:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:57:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:57:26: 15000000 INFO @ Mon, 03 Jun 2019 11:57:27: #2 number of paired peaks: 164 WARNING @ Mon, 03 Jun 2019 11:57:27: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Mon, 03 Jun 2019 11:57:27: start model_add_line... INFO @ Mon, 03 Jun 2019 11:57:27: start X-correlation... INFO @ Mon, 03 Jun 2019 11:57:27: end of X-cor INFO @ Mon, 03 Jun 2019 11:57:27: #2 finished! INFO @ Mon, 03 Jun 2019 11:57:27: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 11:57:27: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 11:57:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.10_model.r WARNING @ Mon, 03 Jun 2019 11:57:27: #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 11:57:27: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 11:57:27: #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 11:57:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:57:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:57:32: 15000000 INFO @ Mon, 03 Jun 2019 11:57:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:57:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:57:34: #1 total tags in treatment: 15885895 INFO @ Mon, 03 Jun 2019 11:57:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:57:34: #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 11:57:35: #1 tags after filtering in treatment: 15885895 INFO @ Mon, 03 Jun 2019 11:57:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:57:35: #1 finished! INFO @ Mon, 03 Jun 2019 11:57:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:57:36: #2 number of paired peaks: 164 WARNING @ Mon, 03 Jun 2019 11:57:36: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Mon, 03 Jun 2019 11:57:36: start model_add_line... INFO @ Mon, 03 Jun 2019 11:57:36: start X-correlation... INFO @ Mon, 03 Jun 2019 11:57:36: end of X-cor INFO @ Mon, 03 Jun 2019 11:57:36: #2 finished! INFO @ Mon, 03 Jun 2019 11:57:36: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 11:57:36: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 11:57:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.05_model.r WARNING @ Mon, 03 Jun 2019 11:57:36: #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 11:57:36: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 11:57:36: #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 11:57:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:57:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:57:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:57:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:57:40: #1 total tags in treatment: 15885895 INFO @ Mon, 03 Jun 2019 11:57:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:57:40: #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 11:57:40: #1 tags after filtering in treatment: 15885895 INFO @ Mon, 03 Jun 2019 11:57:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:57:40: #1 finished! INFO @ Mon, 03 Jun 2019 11:57:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:57:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:57:42: #2 number of paired peaks: 164 WARNING @ Mon, 03 Jun 2019 11:57:42: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Mon, 03 Jun 2019 11:57:42: start model_add_line... INFO @ Mon, 03 Jun 2019 11:57:42: start X-correlation... INFO @ Mon, 03 Jun 2019 11:57:42: end of X-cor INFO @ Mon, 03 Jun 2019 11:57:42: #2 finished! INFO @ Mon, 03 Jun 2019 11:57:42: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 11:57:42: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 11:57:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.20_model.r WARNING @ Mon, 03 Jun 2019 11:57:42: #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 11:57:42: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 11:57:42: #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 11:57:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:57:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:58:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:58:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:58:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:58:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:58:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:58:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.10_summits.bed INFO @ Mon, 03 Jun 2019 11:58:28: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1607 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:58:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:58:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:58:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.05_summits.bed INFO @ Mon, 03 Jun 2019 11:58:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1994 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:58:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:58:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:58:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318778/SRX318778.20_summits.bed INFO @ Mon, 03 Jun 2019 11:58:44: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1055 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。