Job ID = 1309299 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,446,090 reads read : 12,892,180 reads written : 6,446,090 reads 0-length : 6,446,090 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: 00:05:05 6446090 reads; of these: 6446090 (100.00%) were unpaired; of these: 145902 (2.26%) aligned 0 times 5476211 (84.95%) aligned exactly 1 time 823977 (12.78%) aligned >1 times 97.74% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 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] 595816 / 6300188 = 0.0946 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 23:31:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.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 23:31:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:31:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:31:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.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 23:31:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:31:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:31:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.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 23:31:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:31:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:31:52: 1000000 INFO @ Mon, 03 Jun 2019 23:31:56: 1000000 INFO @ Mon, 03 Jun 2019 23:31:57: 1000000 INFO @ Mon, 03 Jun 2019 23:32:04: 2000000 INFO @ Mon, 03 Jun 2019 23:32:11: 2000000 INFO @ Mon, 03 Jun 2019 23:32:13: 2000000 INFO @ Mon, 03 Jun 2019 23:32:16: 3000000 INFO @ Mon, 03 Jun 2019 23:32:26: 3000000 INFO @ Mon, 03 Jun 2019 23:32:29: 4000000 INFO @ Mon, 03 Jun 2019 23:32:30: 3000000 INFO @ Mon, 03 Jun 2019 23:32:40: 4000000 INFO @ Mon, 03 Jun 2019 23:32:41: 5000000 INFO @ Mon, 03 Jun 2019 23:32:46: 4000000 INFO @ Mon, 03 Jun 2019 23:32:50: #1 tag size is determined as 148 bps INFO @ Mon, 03 Jun 2019 23:32:50: #1 tag size = 148 INFO @ Mon, 03 Jun 2019 23:32:50: #1 total tags in treatment: 5704372 INFO @ Mon, 03 Jun 2019 23:32:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:32:50: #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 23:32:50: #1 tags after filtering in treatment: 5704372 INFO @ Mon, 03 Jun 2019 23:32:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:32:50: #1 finished! INFO @ Mon, 03 Jun 2019 23:32:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:32:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:32:51: #2 number of paired peaks: 2235 INFO @ Mon, 03 Jun 2019 23:32:51: start model_add_line... INFO @ Mon, 03 Jun 2019 23:32:51: start X-correlation... INFO @ Mon, 03 Jun 2019 23:32:51: end of X-cor INFO @ Mon, 03 Jun 2019 23:32:51: #2 finished! INFO @ Mon, 03 Jun 2019 23:32:51: #2 predicted fragment length is 182 bps INFO @ Mon, 03 Jun 2019 23:32:51: #2 alternative fragment length(s) may be 182 bps INFO @ Mon, 03 Jun 2019 23:32:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.10_model.r WARNING @ Mon, 03 Jun 2019 23:32:51: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:32:51: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Mon, 03 Jun 2019 23:32:51: #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 23:32:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:32:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:32:53: 5000000 INFO @ Mon, 03 Jun 2019 23:33:02: #1 tag size is determined as 148 bps INFO @ Mon, 03 Jun 2019 23:33:02: #1 tag size = 148 INFO @ Mon, 03 Jun 2019 23:33:02: #1 total tags in treatment: 5704372 INFO @ Mon, 03 Jun 2019 23:33:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:33:02: #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 23:33:02: #1 tags after filtering in treatment: 5704372 INFO @ Mon, 03 Jun 2019 23:33:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:33:02: #1 finished! INFO @ Mon, 03 Jun 2019 23:33:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:33:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:33:02: 5000000 INFO @ Mon, 03 Jun 2019 23:33:03: #2 number of paired peaks: 2235 INFO @ Mon, 03 Jun 2019 23:33:03: start model_add_line... INFO @ Mon, 03 Jun 2019 23:33:03: start X-correlation... INFO @ Mon, 03 Jun 2019 23:33:03: end of X-cor INFO @ Mon, 03 Jun 2019 23:33:03: #2 finished! INFO @ Mon, 03 Jun 2019 23:33:03: #2 predicted fragment length is 182 bps INFO @ Mon, 03 Jun 2019 23:33:03: #2 alternative fragment length(s) may be 182 bps INFO @ Mon, 03 Jun 2019 23:33:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.20_model.r WARNING @ Mon, 03 Jun 2019 23:33:03: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:33:03: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Mon, 03 Jun 2019 23:33:03: #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 23:33:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:33:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:33:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:33:13: #1 tag size is determined as 148 bps INFO @ Mon, 03 Jun 2019 23:33:13: #1 tag size = 148 INFO @ Mon, 03 Jun 2019 23:33:13: #1 total tags in treatment: 5704372 INFO @ Mon, 03 Jun 2019 23:33:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:33:13: #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 23:33:13: #1 tags after filtering in treatment: 5704372 INFO @ Mon, 03 Jun 2019 23:33:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:33:13: #1 finished! INFO @ Mon, 03 Jun 2019 23:33:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:33:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:33:14: #2 number of paired peaks: 2235 INFO @ Mon, 03 Jun 2019 23:33:14: start model_add_line... INFO @ Mon, 03 Jun 2019 23:33:14: start X-correlation... INFO @ Mon, 03 Jun 2019 23:33:14: end of X-cor INFO @ Mon, 03 Jun 2019 23:33:14: #2 finished! INFO @ Mon, 03 Jun 2019 23:33:14: #2 predicted fragment length is 182 bps INFO @ Mon, 03 Jun 2019 23:33:14: #2 alternative fragment length(s) may be 182 bps INFO @ Mon, 03 Jun 2019 23:33:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.05_model.r WARNING @ Mon, 03 Jun 2019 23:33:14: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:33:14: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Mon, 03 Jun 2019 23:33:14: #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 23:33:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:33:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:33:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:33:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:33:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.10_summits.bed INFO @ Mon, 03 Jun 2019 23:33:20: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (4023 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:33:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:33:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:33:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:33:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.20_summits.bed INFO @ Mon, 03 Jun 2019 23:33:32: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1880 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:33:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:33:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:33:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:33:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864533/SRX864533.05_summits.bed INFO @ Mon, 03 Jun 2019 23:33:42: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (6938 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。