Job ID = 1294627 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,258,758 reads read : 11,258,758 reads written : 11,258,758 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: 00:05:18 11258758 reads; of these: 11258758 (100.00%) were unpaired; of these: 550926 (4.89%) aligned 0 times 7134557 (63.37%) aligned exactly 1 time 3573275 (31.74%) aligned >1 times 95.11% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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] 1087106 / 10707832 = 0.1015 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 09:32:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.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 09:32:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:32:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:32:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.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 09:32:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:32:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:32:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.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 09:32:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:32:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:32:48: 1000000 INFO @ Mon, 03 Jun 2019 09:32:51: 1000000 INFO @ Mon, 03 Jun 2019 09:32:52: 1000000 INFO @ Mon, 03 Jun 2019 09:32:57: 2000000 INFO @ Mon, 03 Jun 2019 09:33:02: 2000000 INFO @ Mon, 03 Jun 2019 09:33:04: 2000000 INFO @ Mon, 03 Jun 2019 09:33:05: 3000000 INFO @ Mon, 03 Jun 2019 09:33:13: 4000000 INFO @ Mon, 03 Jun 2019 09:33:15: 3000000 INFO @ Mon, 03 Jun 2019 09:33:17: 3000000 INFO @ Mon, 03 Jun 2019 09:33:22: 5000000 INFO @ Mon, 03 Jun 2019 09:33:26: 4000000 INFO @ Mon, 03 Jun 2019 09:33:29: 4000000 INFO @ Mon, 03 Jun 2019 09:33:30: 6000000 INFO @ Mon, 03 Jun 2019 09:33:38: 5000000 INFO @ Mon, 03 Jun 2019 09:33:38: 7000000 INFO @ Mon, 03 Jun 2019 09:33:41: 5000000 INFO @ Mon, 03 Jun 2019 09:33:47: 8000000 INFO @ Mon, 03 Jun 2019 09:33:50: 6000000 INFO @ Mon, 03 Jun 2019 09:33:53: 6000000 INFO @ Mon, 03 Jun 2019 09:33:55: 9000000 INFO @ Mon, 03 Jun 2019 09:34:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:34:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:34:00: #1 total tags in treatment: 9620726 INFO @ Mon, 03 Jun 2019 09:34:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:34:00: #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 09:34:00: #1 tags after filtering in treatment: 9620726 INFO @ Mon, 03 Jun 2019 09:34:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:34:00: #1 finished! INFO @ Mon, 03 Jun 2019 09:34:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:34:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:34:01: 7000000 INFO @ Mon, 03 Jun 2019 09:34:01: #2 number of paired peaks: 366 WARNING @ Mon, 03 Jun 2019 09:34:01: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Mon, 03 Jun 2019 09:34:01: start model_add_line... INFO @ Mon, 03 Jun 2019 09:34:01: start X-correlation... INFO @ Mon, 03 Jun 2019 09:34:01: end of X-cor INFO @ Mon, 03 Jun 2019 09:34:01: #2 finished! INFO @ Mon, 03 Jun 2019 09:34:01: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 09:34:01: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 09:34:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.20_model.r WARNING @ Mon, 03 Jun 2019 09:34:01: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:34:01: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 09:34:01: #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 09:34:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:34:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:34:06: 7000000 INFO @ Mon, 03 Jun 2019 09:34:12: 8000000 INFO @ Mon, 03 Jun 2019 09:34:16: 8000000 INFO @ Mon, 03 Jun 2019 09:34:24: 9000000 INFO @ Mon, 03 Jun 2019 09:34:27: 9000000 INFO @ Mon, 03 Jun 2019 09:34:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:34:32: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:34:32: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:34:32: #1 total tags in treatment: 9620726 INFO @ Mon, 03 Jun 2019 09:34:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:34:32: #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 09:34:32: #1 tags after filtering in treatment: 9620726 INFO @ Mon, 03 Jun 2019 09:34:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:34:32: #1 finished! INFO @ Mon, 03 Jun 2019 09:34:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:34:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:34:33: #2 number of paired peaks: 366 WARNING @ Mon, 03 Jun 2019 09:34:33: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Mon, 03 Jun 2019 09:34:33: start model_add_line... INFO @ Mon, 03 Jun 2019 09:34:33: start X-correlation... INFO @ Mon, 03 Jun 2019 09:34:33: end of X-cor INFO @ Mon, 03 Jun 2019 09:34:33: #2 finished! INFO @ Mon, 03 Jun 2019 09:34:33: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 09:34:33: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 09:34:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.10_model.r WARNING @ Mon, 03 Jun 2019 09:34:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:34:33: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 09:34:33: #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 09:34:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:34:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:34:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:34:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:34:34: #1 total tags in treatment: 9620726 INFO @ Mon, 03 Jun 2019 09:34:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:34:34: #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 09:34:34: #1 tags after filtering in treatment: 9620726 INFO @ Mon, 03 Jun 2019 09:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:34:34: #1 finished! INFO @ Mon, 03 Jun 2019 09:34:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:34:35: #2 number of paired peaks: 366 WARNING @ Mon, 03 Jun 2019 09:34:35: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Mon, 03 Jun 2019 09:34:35: start model_add_line... INFO @ Mon, 03 Jun 2019 09:34:35: start X-correlation... INFO @ Mon, 03 Jun 2019 09:34:35: end of X-cor INFO @ Mon, 03 Jun 2019 09:34:35: #2 finished! INFO @ Mon, 03 Jun 2019 09:34:35: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 09:34:35: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 09:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.05_model.r WARNING @ Mon, 03 Jun 2019 09:34:35: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:34:35: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 09:34:35: #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 09:34:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:34:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:34:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:34:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:34:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.20_summits.bed INFO @ Mon, 03 Jun 2019 09:34:42: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1185 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:35:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:35:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:35:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:35:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:35:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.10_summits.bed INFO @ Mon, 03 Jun 2019 09:35:13: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1645 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:35:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:35:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:35:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287790/SRX287790.05_summits.bed INFO @ Mon, 03 Jun 2019 09:35:15: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1956 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。