Job ID = 4178605 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,468,445 reads read : 36,468,445 reads written : 36,468,445 rm: cannot remove ‘[DSE]RR*’: 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: 00:07:48 36468445 reads; of these: 36468445 (100.00%) were unpaired; of these: 23234660 (63.71%) aligned 0 times 10849582 (29.75%) aligned exactly 1 time 2384203 (6.54%) aligned >1 times 36.29% overall alignment rate Time searching: 00:07:48 Overall time: 00:07:48 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] 9720772 / 13233785 = 0.7345 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:44:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.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 @ Thu, 05 Dec 2019 13:44:37: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:44:37: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:44:45: 1000000 INFO @ Thu, 05 Dec 2019 13:44:52: 2000000 INFO @ Thu, 05 Dec 2019 13:45:00: 3000000 INFO @ Thu, 05 Dec 2019 13:45:04: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:45:04: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:45:04: #1 total tags in treatment: 3513013 INFO @ Thu, 05 Dec 2019 13:45:04: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:45:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:45:04: #1 tags after filtering in treatment: 3513013 INFO @ Thu, 05 Dec 2019 13:45:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:45:04: #1 finished! INFO @ Thu, 05 Dec 2019 13:45:04: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:45:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:45:04: #2 number of paired peaks: 488 WARNING @ Thu, 05 Dec 2019 13:45:04: Fewer paired peaks (488) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 488 pairs to build model! INFO @ Thu, 05 Dec 2019 13:45:04: start model_add_line... INFO @ Thu, 05 Dec 2019 13:45:04: start X-correlation... INFO @ Thu, 05 Dec 2019 13:45:04: end of X-cor INFO @ Thu, 05 Dec 2019 13:45:04: #2 finished! INFO @ Thu, 05 Dec 2019 13:45:04: #2 predicted fragment length is 97 bps INFO @ Thu, 05 Dec 2019 13:45:04: #2 alternative fragment length(s) may be 97 bps INFO @ Thu, 05 Dec 2019 13:45:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.05_model.r WARNING @ Thu, 05 Dec 2019 13:45:05: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:45:05: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Thu, 05 Dec 2019 13:45:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:45:05: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:45:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:45:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.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 @ Thu, 05 Dec 2019 13:45:07: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:45:07: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:45:15: 1000000 INFO @ Thu, 05 Dec 2019 13:45:15: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:45:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:45:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:45:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.05_summits.bed INFO @ Thu, 05 Dec 2019 13:45:21: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2041 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:45:22: 2000000 INFO @ Thu, 05 Dec 2019 13:45:29: 3000000 INFO @ Thu, 05 Dec 2019 13:45:33: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:45:33: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:45:33: #1 total tags in treatment: 3513013 INFO @ Thu, 05 Dec 2019 13:45:33: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:45:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:45:33: #1 tags after filtering in treatment: 3513013 INFO @ Thu, 05 Dec 2019 13:45:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:45:33: #1 finished! INFO @ Thu, 05 Dec 2019 13:45:33: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:45:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:45:34: #2 number of paired peaks: 488 WARNING @ Thu, 05 Dec 2019 13:45:34: Fewer paired peaks (488) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 488 pairs to build model! INFO @ Thu, 05 Dec 2019 13:45:34: start model_add_line... INFO @ Thu, 05 Dec 2019 13:45:34: start X-correlation... INFO @ Thu, 05 Dec 2019 13:45:34: end of X-cor INFO @ Thu, 05 Dec 2019 13:45:34: #2 finished! INFO @ Thu, 05 Dec 2019 13:45:34: #2 predicted fragment length is 97 bps INFO @ Thu, 05 Dec 2019 13:45:34: #2 alternative fragment length(s) may be 97 bps INFO @ Thu, 05 Dec 2019 13:45:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.10_model.r WARNING @ Thu, 05 Dec 2019 13:45:34: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:45:34: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Thu, 05 Dec 2019 13:45:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:45:34: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:45:34: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:45:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.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 @ Thu, 05 Dec 2019 13:45:37: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:45:37: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:45:45: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:45:45: 1000000 INFO @ Thu, 05 Dec 2019 13:45:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:45:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:45:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.10_summits.bed INFO @ Thu, 05 Dec 2019 13:45:50: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (611 records, 4 fields): 58 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:45:52: 2000000 INFO @ Thu, 05 Dec 2019 13:46:00: 3000000 INFO @ Thu, 05 Dec 2019 13:46:04: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:46:04: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:46:04: #1 total tags in treatment: 3513013 INFO @ Thu, 05 Dec 2019 13:46:04: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:46:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:46:04: #1 tags after filtering in treatment: 3513013 INFO @ Thu, 05 Dec 2019 13:46:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:46:04: #1 finished! INFO @ Thu, 05 Dec 2019 13:46:04: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:46:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:46:04: #2 number of paired peaks: 488 WARNING @ Thu, 05 Dec 2019 13:46:04: Fewer paired peaks (488) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 488 pairs to build model! INFO @ Thu, 05 Dec 2019 13:46:04: start model_add_line... INFO @ Thu, 05 Dec 2019 13:46:04: start X-correlation... INFO @ Thu, 05 Dec 2019 13:46:04: end of X-cor INFO @ Thu, 05 Dec 2019 13:46:04: #2 finished! INFO @ Thu, 05 Dec 2019 13:46:04: #2 predicted fragment length is 97 bps INFO @ Thu, 05 Dec 2019 13:46:04: #2 alternative fragment length(s) may be 97 bps INFO @ Thu, 05 Dec 2019 13:46:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.20_model.r WARNING @ Thu, 05 Dec 2019 13:46:05: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:46:05: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Thu, 05 Dec 2019 13:46:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:46:05: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:46:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:46:16: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:46:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:46:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:46:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6468481/SRX6468481.20_summits.bed INFO @ Thu, 05 Dec 2019 13:46:22: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (200 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。