Job ID = 1294260 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,201,806 reads read : 6,403,612 reads written : 6,403,612 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: 00:23:42 3201806 reads; of these: 3201806 (100.00%) were paired; of these: 246720 (7.71%) aligned concordantly 0 times 694165 (21.68%) aligned concordantly exactly 1 time 2260921 (70.61%) aligned concordantly >1 times ---- 246720 pairs aligned concordantly 0 times; of these: 8058 (3.27%) aligned discordantly 1 time ---- 238662 pairs aligned 0 times concordantly or discordantly; of these: 477324 mates make up the pairs; of these: 349922 (73.31%) aligned 0 times 26131 (5.47%) aligned exactly 1 time 101271 (21.22%) aligned >1 times 94.54% overall alignment rate Time searching: 00:23:42 Overall time: 00:23:42 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 157263 / 2947248 = 0.0534 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 06:20:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.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 06:20:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:20:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:20:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.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 06:20:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:20:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:20:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.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 06:20:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:20:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:20:29: 1000000 INFO @ Mon, 03 Jun 2019 06:20:29: 1000000 INFO @ Mon, 03 Jun 2019 06:20:34: 1000000 INFO @ Mon, 03 Jun 2019 06:20:38: 2000000 INFO @ Mon, 03 Jun 2019 06:20:38: 2000000 INFO @ Mon, 03 Jun 2019 06:20:48: 3000000 INFO @ Mon, 03 Jun 2019 06:20:48: 3000000 INFO @ Mon, 03 Jun 2019 06:20:49: 2000000 INFO @ Mon, 03 Jun 2019 06:20:57: 4000000 INFO @ Mon, 03 Jun 2019 06:20:57: 4000000 INFO @ Mon, 03 Jun 2019 06:21:04: 3000000 INFO @ Mon, 03 Jun 2019 06:21:08: 5000000 INFO @ Mon, 03 Jun 2019 06:21:08: 5000000 INFO @ Mon, 03 Jun 2019 06:21:14: #1 tag size is determined as 70 bps INFO @ Mon, 03 Jun 2019 06:21:14: #1 tag size = 70 INFO @ Mon, 03 Jun 2019 06:21:14: #1 total tags in treatment: 2797919 INFO @ Mon, 03 Jun 2019 06:21:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:21:14: #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 06:21:14: #1 tags after filtering in treatment: 2226312 INFO @ Mon, 03 Jun 2019 06:21:14: #1 Redundant rate of treatment: 0.20 INFO @ Mon, 03 Jun 2019 06:21:14: #1 finished! INFO @ Mon, 03 Jun 2019 06:21:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:21:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:21:14: #1 tag size is determined as 70 bps INFO @ Mon, 03 Jun 2019 06:21:14: #1 tag size = 70 INFO @ Mon, 03 Jun 2019 06:21:14: #1 total tags in treatment: 2797919 INFO @ Mon, 03 Jun 2019 06:21:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:21:14: #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 06:21:14: #1 tags after filtering in treatment: 2226312 INFO @ Mon, 03 Jun 2019 06:21:14: #1 Redundant rate of treatment: 0.20 INFO @ Mon, 03 Jun 2019 06:21:14: #1 finished! INFO @ Mon, 03 Jun 2019 06:21:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:21:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:21:15: #2 number of paired peaks: 5524 INFO @ Mon, 03 Jun 2019 06:21:15: start model_add_line... INFO @ Mon, 03 Jun 2019 06:21:15: start X-correlation... INFO @ Mon, 03 Jun 2019 06:21:15: end of X-cor INFO @ Mon, 03 Jun 2019 06:21:15: #2 finished! INFO @ Mon, 03 Jun 2019 06:21:15: #2 predicted fragment length is 119 bps INFO @ Mon, 03 Jun 2019 06:21:15: #2 alternative fragment length(s) may be 119 bps INFO @ Mon, 03 Jun 2019 06:21:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.05_model.r WARNING @ Mon, 03 Jun 2019 06:21:15: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:21:15: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Mon, 03 Jun 2019 06:21:15: #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 06:21:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:21:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:21:15: #2 number of paired peaks: 5524 INFO @ Mon, 03 Jun 2019 06:21:15: start model_add_line... INFO @ Mon, 03 Jun 2019 06:21:15: start X-correlation... INFO @ Mon, 03 Jun 2019 06:21:15: end of X-cor INFO @ Mon, 03 Jun 2019 06:21:15: #2 finished! INFO @ Mon, 03 Jun 2019 06:21:15: #2 predicted fragment length is 119 bps INFO @ Mon, 03 Jun 2019 06:21:15: #2 alternative fragment length(s) may be 119 bps INFO @ Mon, 03 Jun 2019 06:21:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.20_model.r WARNING @ Mon, 03 Jun 2019 06:21:15: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:21:15: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Mon, 03 Jun 2019 06:21:15: #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 06:21:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:21:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:21:19: 4000000 INFO @ Mon, 03 Jun 2019 06:21:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:21:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:21:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:21:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:21:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.05_summits.bed INFO @ Mon, 03 Jun 2019 06:21:26: Done! INFO @ Mon, 03 Jun 2019 06:21:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.20_peaks.xls pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3572 records, 4 fields): 11 millis INFO @ Mon, 03 Jun 2019 06:21:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.20_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:21:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.20_summits.bed INFO @ Mon, 03 Jun 2019 06:21:27: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (812 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:21:34: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 06:21:45: #1 tag size is determined as 70 bps INFO @ Mon, 03 Jun 2019 06:21:45: #1 tag size = 70 INFO @ Mon, 03 Jun 2019 06:21:45: #1 total tags in treatment: 2797919 INFO @ Mon, 03 Jun 2019 06:21:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:21:45: #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 06:21:45: #1 tags after filtering in treatment: 2226312 INFO @ Mon, 03 Jun 2019 06:21:45: #1 Redundant rate of treatment: 0.20 INFO @ Mon, 03 Jun 2019 06:21:45: #1 finished! INFO @ Mon, 03 Jun 2019 06:21:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:21:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:21:45: #2 number of paired peaks: 5524 INFO @ Mon, 03 Jun 2019 06:21:45: start model_add_line... INFO @ Mon, 03 Jun 2019 06:21:45: start X-correlation... INFO @ Mon, 03 Jun 2019 06:21:45: end of X-cor INFO @ Mon, 03 Jun 2019 06:21:45: #2 finished! INFO @ Mon, 03 Jun 2019 06:21:45: #2 predicted fragment length is 119 bps INFO @ Mon, 03 Jun 2019 06:21:45: #2 alternative fragment length(s) may be 119 bps INFO @ Mon, 03 Jun 2019 06:21:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.10_model.r WARNING @ Mon, 03 Jun 2019 06:21:45: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:21:45: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Mon, 03 Jun 2019 06:21:45: #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 06:21:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:21:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:21:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:21:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:21:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:21:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215624/SRX215624.10_summits.bed INFO @ Mon, 03 Jun 2019 06:21:58: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1527 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。