Job ID = 2590869 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,938,319 reads read : 19,876,638 reads written : 9,938,319 reads 0-length : 9,938,319 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: 00:05:08 9938319 reads; of these: 9938319 (100.00%) were unpaired; of these: 1071057 (10.78%) aligned 0 times 6333748 (63.73%) aligned exactly 1 time 2533514 (25.49%) aligned >1 times 89.22% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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] 2418276 / 8867262 = 0.2727 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, 12 Aug 2019 23:55:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.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, 12 Aug 2019 23:55:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:55:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:55:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.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, 12 Aug 2019 23:55:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:55:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:55:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.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, 12 Aug 2019 23:55:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:55:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:55:13: 1000000 INFO @ Mon, 12 Aug 2019 23:55:15: 1000000 INFO @ Mon, 12 Aug 2019 23:55:18: 1000000 INFO @ Mon, 12 Aug 2019 23:55:22: 2000000 INFO @ Mon, 12 Aug 2019 23:55:23: 2000000 INFO @ Mon, 12 Aug 2019 23:55:30: 3000000 INFO @ Mon, 12 Aug 2019 23:55:31: 2000000 INFO @ Mon, 12 Aug 2019 23:55:31: 3000000 INFO @ Mon, 12 Aug 2019 23:55:38: 4000000 INFO @ Mon, 12 Aug 2019 23:55:40: 4000000 INFO @ Mon, 12 Aug 2019 23:55:44: 3000000 INFO @ Mon, 12 Aug 2019 23:55:47: 5000000 INFO @ Mon, 12 Aug 2019 23:55:49: 5000000 INFO @ Mon, 12 Aug 2019 23:55:55: 6000000 INFO @ Mon, 12 Aug 2019 23:55:57: 4000000 INFO @ Mon, 12 Aug 2019 23:55:57: 6000000 INFO @ Mon, 12 Aug 2019 23:55:59: #1 tag size is determined as 75 bps INFO @ Mon, 12 Aug 2019 23:55:59: #1 tag size = 75 INFO @ Mon, 12 Aug 2019 23:55:59: #1 total tags in treatment: 6448986 INFO @ Mon, 12 Aug 2019 23:55:59: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:55:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:55:59: #1 tags after filtering in treatment: 6448986 INFO @ Mon, 12 Aug 2019 23:55:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:55:59: #1 finished! INFO @ Mon, 12 Aug 2019 23:55:59: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:56:00: #2 number of paired peaks: 1288 INFO @ Mon, 12 Aug 2019 23:56:00: start model_add_line... INFO @ Mon, 12 Aug 2019 23:56:00: start X-correlation... INFO @ Mon, 12 Aug 2019 23:56:00: end of X-cor INFO @ Mon, 12 Aug 2019 23:56:00: #2 finished! INFO @ Mon, 12 Aug 2019 23:56:00: #2 predicted fragment length is 79 bps INFO @ Mon, 12 Aug 2019 23:56:00: #2 alternative fragment length(s) may be 79 bps INFO @ Mon, 12 Aug 2019 23:56:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.05_model.r WARNING @ Mon, 12 Aug 2019 23:56:00: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:56:00: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Mon, 12 Aug 2019 23:56:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:56:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:56:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:56:01: #1 tag size is determined as 75 bps INFO @ Mon, 12 Aug 2019 23:56:01: #1 tag size = 75 INFO @ Mon, 12 Aug 2019 23:56:01: #1 total tags in treatment: 6448986 INFO @ Mon, 12 Aug 2019 23:56:01: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:56:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:56:01: #1 tags after filtering in treatment: 6448986 INFO @ Mon, 12 Aug 2019 23:56:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:56:01: #1 finished! INFO @ Mon, 12 Aug 2019 23:56:01: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:56:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:56:02: #2 number of paired peaks: 1288 INFO @ Mon, 12 Aug 2019 23:56:02: start model_add_line... INFO @ Mon, 12 Aug 2019 23:56:02: start X-correlation... INFO @ Mon, 12 Aug 2019 23:56:02: end of X-cor INFO @ Mon, 12 Aug 2019 23:56:02: #2 finished! INFO @ Mon, 12 Aug 2019 23:56:02: #2 predicted fragment length is 79 bps INFO @ Mon, 12 Aug 2019 23:56:02: #2 alternative fragment length(s) may be 79 bps INFO @ Mon, 12 Aug 2019 23:56:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.20_model.r WARNING @ Mon, 12 Aug 2019 23:56:02: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:56:02: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Mon, 12 Aug 2019 23:56:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:56:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:56:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:56:09: 5000000 INFO @ Mon, 12 Aug 2019 23:56:20: 6000000 INFO @ Mon, 12 Aug 2019 23:56:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:56:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:56:25: #1 tag size is determined as 75 bps INFO @ Mon, 12 Aug 2019 23:56:25: #1 tag size = 75 INFO @ Mon, 12 Aug 2019 23:56:25: #1 total tags in treatment: 6448986 INFO @ Mon, 12 Aug 2019 23:56:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:56:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:56:25: #1 tags after filtering in treatment: 6448986 INFO @ Mon, 12 Aug 2019 23:56:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:56:25: #1 finished! INFO @ Mon, 12 Aug 2019 23:56:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:56:26: #2 number of paired peaks: 1288 INFO @ Mon, 12 Aug 2019 23:56:26: start model_add_line... INFO @ Mon, 12 Aug 2019 23:56:26: start X-correlation... INFO @ Mon, 12 Aug 2019 23:56:26: end of X-cor INFO @ Mon, 12 Aug 2019 23:56:26: #2 finished! INFO @ Mon, 12 Aug 2019 23:56:26: #2 predicted fragment length is 79 bps INFO @ Mon, 12 Aug 2019 23:56:26: #2 alternative fragment length(s) may be 79 bps INFO @ Mon, 12 Aug 2019 23:56:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.10_model.r WARNING @ Mon, 12 Aug 2019 23:56:26: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:56:26: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Mon, 12 Aug 2019 23:56:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:56:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:56:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:56:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:56:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:56:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.05_summits.bed INFO @ Mon, 12 Aug 2019 23:56:30: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (2455 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:56:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:56:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:56:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.20_summits.bed INFO @ Mon, 12 Aug 2019 23:56:32: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (755 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:56:46: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:56:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:56:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:56:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5053152/SRX5053152.10_summits.bed INFO @ Mon, 12 Aug 2019 23:56:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1501 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。