Job ID = 4178465 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,183,061 reads read : 4,366,122 reads written : 2,183,061 reads 0-length : 2,183,061 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: 00:00:01 Multiseed full-index search: 00:00:46 2183061 reads; of these: 2183061 (100.00%) were unpaired; of these: 863 (0.04%) aligned 0 times 1564258 (71.65%) aligned exactly 1 time 617940 (28.31%) aligned >1 times 99.96% overall alignment rate Time searching: 00:00:47 Overall time: 00:00:47 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] 147951 / 2182198 = 0.0678 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:24:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.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 12:24:20: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:24:20: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:24:25: 1000000 INFO @ Thu, 05 Dec 2019 12:24:30: 2000000 INFO @ Thu, 05 Dec 2019 12:24:30: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:24:30: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:24:30: #1 total tags in treatment: 2034247 INFO @ Thu, 05 Dec 2019 12:24:30: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:24:30: #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 12:24:30: #1 tags after filtering in treatment: 2034247 INFO @ Thu, 05 Dec 2019 12:24:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:24:30: #1 finished! INFO @ Thu, 05 Dec 2019 12:24:30: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:24:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:24:30: #2 number of paired peaks: 346 WARNING @ Thu, 05 Dec 2019 12:24:30: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Thu, 05 Dec 2019 12:24:30: start model_add_line... INFO @ Thu, 05 Dec 2019 12:24:30: start X-correlation... INFO @ Thu, 05 Dec 2019 12:24:30: end of X-cor INFO @ Thu, 05 Dec 2019 12:24:30: #2 finished! INFO @ Thu, 05 Dec 2019 12:24:30: #2 predicted fragment length is 48 bps INFO @ Thu, 05 Dec 2019 12:24:30: #2 alternative fragment length(s) may be 48 bps INFO @ Thu, 05 Dec 2019 12:24:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.05_model.r WARNING @ Thu, 05 Dec 2019 12:24:30: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:24:30: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Thu, 05 Dec 2019 12:24:30: #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 12:24:30: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:24:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:24:34: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:24:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:24:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:24:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.05_summits.bed INFO @ Thu, 05 Dec 2019 12:24:37: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (352 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:24:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.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 12:24:49: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:24:49: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:24:54: 1000000 INFO @ Thu, 05 Dec 2019 12:24:59: 2000000 INFO @ Thu, 05 Dec 2019 12:24:59: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:24:59: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:24:59: #1 total tags in treatment: 2034247 INFO @ Thu, 05 Dec 2019 12:24:59: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:24:59: #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 12:24:59: #1 tags after filtering in treatment: 2034247 INFO @ Thu, 05 Dec 2019 12:24:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:24:59: #1 finished! INFO @ Thu, 05 Dec 2019 12:24:59: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:24:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:24:59: #2 number of paired peaks: 346 WARNING @ Thu, 05 Dec 2019 12:24:59: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Thu, 05 Dec 2019 12:24:59: start model_add_line... INFO @ Thu, 05 Dec 2019 12:24:59: start X-correlation... INFO @ Thu, 05 Dec 2019 12:24:59: end of X-cor INFO @ Thu, 05 Dec 2019 12:24:59: #2 finished! INFO @ Thu, 05 Dec 2019 12:24:59: #2 predicted fragment length is 48 bps INFO @ Thu, 05 Dec 2019 12:24:59: #2 alternative fragment length(s) may be 48 bps INFO @ Thu, 05 Dec 2019 12:24:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.10_model.r WARNING @ Thu, 05 Dec 2019 12:24:59: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:24:59: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Thu, 05 Dec 2019 12:24:59: #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 12:24:59: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:24:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:25:03: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:25:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:25:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:25:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.10_summits.bed INFO @ Thu, 05 Dec 2019 12:25:08: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:25:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.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 12:25:23: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:25:23: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:25:28: 1000000 INFO @ Thu, 05 Dec 2019 12:25:33: 2000000 INFO @ Thu, 05 Dec 2019 12:25:33: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:25:33: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:25:33: #1 total tags in treatment: 2034247 INFO @ Thu, 05 Dec 2019 12:25:33: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:25:33: #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 12:25:33: #1 tags after filtering in treatment: 2034247 INFO @ Thu, 05 Dec 2019 12:25:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:25:33: #1 finished! INFO @ Thu, 05 Dec 2019 12:25:33: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:25:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:25:33: #2 number of paired peaks: 346 WARNING @ Thu, 05 Dec 2019 12:25:33: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Thu, 05 Dec 2019 12:25:33: start model_add_line... INFO @ Thu, 05 Dec 2019 12:25:33: start X-correlation... INFO @ Thu, 05 Dec 2019 12:25:33: end of X-cor INFO @ Thu, 05 Dec 2019 12:25:33: #2 finished! INFO @ Thu, 05 Dec 2019 12:25:33: #2 predicted fragment length is 48 bps INFO @ Thu, 05 Dec 2019 12:25:33: #2 alternative fragment length(s) may be 48 bps INFO @ Thu, 05 Dec 2019 12:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.20_model.r WARNING @ Thu, 05 Dec 2019 12:25:33: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:25:33: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Thu, 05 Dec 2019 12:25:33: #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 12:25:33: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:25:37: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:25:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:25:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:25:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5515080/SRX5515080.20_summits.bed INFO @ Thu, 05 Dec 2019 12:25:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (113 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。