Job ID = 4178546 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,632,362 reads read : 19,264,724 reads written : 9,632,362 reads 0-length : 9,632,362 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:56 9632362 reads; of these: 9632362 (100.00%) were unpaired; of these: 2808997 (29.16%) aligned 0 times 5340613 (55.44%) aligned exactly 1 time 1482752 (15.39%) aligned >1 times 70.84% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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_rmdupse_core] 3865929 / 6823365 = 0.5666 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:59:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.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 12:59:47: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:59:47: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:59:55: 1000000 INFO @ Thu, 05 Dec 2019 13:00:02: 2000000 INFO @ Thu, 05 Dec 2019 13:00:09: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:00:09: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:00:09: #1 total tags in treatment: 2957436 INFO @ Thu, 05 Dec 2019 13:00:09: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:00:09: #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 13:00:09: #1 tags after filtering in treatment: 2957436 INFO @ Thu, 05 Dec 2019 13:00:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:00:09: #1 finished! INFO @ Thu, 05 Dec 2019 13:00:09: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:00:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:00:09: #2 number of paired peaks: 556 WARNING @ Thu, 05 Dec 2019 13:00:09: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Thu, 05 Dec 2019 13:00:09: start model_add_line... INFO @ Thu, 05 Dec 2019 13:00:09: start X-correlation... INFO @ Thu, 05 Dec 2019 13:00:09: end of X-cor INFO @ Thu, 05 Dec 2019 13:00:09: #2 finished! INFO @ Thu, 05 Dec 2019 13:00:09: #2 predicted fragment length is 96 bps INFO @ Thu, 05 Dec 2019 13:00:09: #2 alternative fragment length(s) may be 96 bps INFO @ Thu, 05 Dec 2019 13:00:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.05_model.r WARNING @ Thu, 05 Dec 2019 13:00:09: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:00:09: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Thu, 05 Dec 2019 13:00:09: #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 13:00:09: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:00:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:00:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.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 13:00:17: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:00:17: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:00:19: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:00:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:00:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:00:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.05_summits.bed INFO @ Thu, 05 Dec 2019 13:00:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1045 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:00:26: 1000000 INFO @ Thu, 05 Dec 2019 13:00:35: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:00:45: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:00:45: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:00:45: #1 total tags in treatment: 2957436 INFO @ Thu, 05 Dec 2019 13:00:45: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:00:45: #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 13:00:45: #1 tags after filtering in treatment: 2957436 INFO @ Thu, 05 Dec 2019 13:00:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:00:45: #1 finished! INFO @ Thu, 05 Dec 2019 13:00:45: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:00:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:00:46: #2 number of paired peaks: 556 WARNING @ Thu, 05 Dec 2019 13:00:46: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Thu, 05 Dec 2019 13:00:46: start model_add_line... INFO @ Thu, 05 Dec 2019 13:00:46: start X-correlation... INFO @ Thu, 05 Dec 2019 13:00:46: end of X-cor INFO @ Thu, 05 Dec 2019 13:00:46: #2 finished! INFO @ Thu, 05 Dec 2019 13:00:46: #2 predicted fragment length is 96 bps INFO @ Thu, 05 Dec 2019 13:00:46: #2 alternative fragment length(s) may be 96 bps INFO @ Thu, 05 Dec 2019 13:00:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.10_model.r WARNING @ Thu, 05 Dec 2019 13:00:46: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:00:46: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Thu, 05 Dec 2019 13:00:46: #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 13:00:46: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:00:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:00:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.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 13:00:47: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:00:47: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:00:56: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:00:57: 1000000 INFO @ Thu, 05 Dec 2019 13:01:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:01:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:01:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.10_summits.bed INFO @ Thu, 05 Dec 2019 13:01:00: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (714 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:01:06: 2000000 INFO @ Thu, 05 Dec 2019 13:01:15: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:01:15: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:01:15: #1 total tags in treatment: 2957436 INFO @ Thu, 05 Dec 2019 13:01:15: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:01:15: #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 13:01:15: #1 tags after filtering in treatment: 2957436 INFO @ Thu, 05 Dec 2019 13:01:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:01:15: #1 finished! INFO @ Thu, 05 Dec 2019 13:01:15: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:01:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:01:15: #2 number of paired peaks: 556 WARNING @ Thu, 05 Dec 2019 13:01:15: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Thu, 05 Dec 2019 13:01:15: start model_add_line... INFO @ Thu, 05 Dec 2019 13:01:16: start X-correlation... INFO @ Thu, 05 Dec 2019 13:01:16: end of X-cor INFO @ Thu, 05 Dec 2019 13:01:16: #2 finished! INFO @ Thu, 05 Dec 2019 13:01:16: #2 predicted fragment length is 96 bps INFO @ Thu, 05 Dec 2019 13:01:16: #2 alternative fragment length(s) may be 96 bps INFO @ Thu, 05 Dec 2019 13:01:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.20_model.r WARNING @ Thu, 05 Dec 2019 13:01:16: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:01:16: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Thu, 05 Dec 2019 13:01:16: #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 13:01:16: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:01:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:01:25: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:01:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:01:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:01:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827818/SRX5827818.20_summits.bed INFO @ Thu, 05 Dec 2019 13:01:30: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (343 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。