Job ID = 1294263 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,373,796 reads read : 6,747,592 reads written : 6,747,592 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:24:04 3373796 reads; of these: 3373796 (100.00%) were paired; of these: 409701 (12.14%) aligned concordantly 0 times 679888 (20.15%) aligned concordantly exactly 1 time 2284207 (67.70%) aligned concordantly >1 times ---- 409701 pairs aligned concordantly 0 times; of these: 7550 (1.84%) aligned discordantly 1 time ---- 402151 pairs aligned 0 times concordantly or discordantly; of these: 804302 mates make up the pairs; of these: 671516 (83.49%) aligned 0 times 26742 (3.32%) aligned exactly 1 time 106044 (13.18%) aligned >1 times 90.05% overall alignment rate Time searching: 00:24:05 Overall time: 00:24:05 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_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] 172774 / 2955763 = 0.0585 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 06:21:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.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 06:21:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.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 06:21:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:21:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:21:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:21:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:21:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.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 06:21:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:21:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:21:40: 1000000 INFO @ Mon, 03 Jun 2019 06:21:41: 1000000 INFO @ Mon, 03 Jun 2019 06:21:41: 1000000 INFO @ Mon, 03 Jun 2019 06:21:50: 2000000 INFO @ Mon, 03 Jun 2019 06:21:50: 2000000 INFO @ Mon, 03 Jun 2019 06:21:50: 2000000 INFO @ Mon, 03 Jun 2019 06:22:00: 3000000 INFO @ Mon, 03 Jun 2019 06:22:00: 3000000 INFO @ Mon, 03 Jun 2019 06:22:00: 3000000 INFO @ Mon, 03 Jun 2019 06:22:09: 4000000 INFO @ Mon, 03 Jun 2019 06:22:09: 4000000 INFO @ Mon, 03 Jun 2019 06:22:09: 4000000 INFO @ Mon, 03 Jun 2019 06:22:18: 5000000 INFO @ Mon, 03 Jun 2019 06:22:19: 5000000 INFO @ Mon, 03 Jun 2019 06:22:19: 5000000 INFO @ Mon, 03 Jun 2019 06:22:24: #1 tag size is determined as 70 bps INFO @ Mon, 03 Jun 2019 06:22:24: #1 tag size = 70 INFO @ Mon, 03 Jun 2019 06:22:24: #1 total tags in treatment: 2791442 INFO @ Mon, 03 Jun 2019 06:22:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:22:24: #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 06:22:24: #1 tags after filtering in treatment: 2207147 INFO @ Mon, 03 Jun 2019 06:22:24: #1 Redundant rate of treatment: 0.21 INFO @ Mon, 03 Jun 2019 06:22:24: #1 finished! INFO @ Mon, 03 Jun 2019 06:22:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:22:25: #2 number of paired peaks: 5559 INFO @ Mon, 03 Jun 2019 06:22:25: start model_add_line... INFO @ Mon, 03 Jun 2019 06:22:25: start X-correlation... INFO @ Mon, 03 Jun 2019 06:22:25: end of X-cor INFO @ Mon, 03 Jun 2019 06:22:25: #2 finished! INFO @ Mon, 03 Jun 2019 06:22:25: #2 predicted fragment length is 122 bps INFO @ Mon, 03 Jun 2019 06:22:25: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 03 Jun 2019 06:22:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.05_model.r WARNING @ Mon, 03 Jun 2019 06:22:25: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:22:25: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Mon, 03 Jun 2019 06:22:25: #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 06:22:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:22:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:22:25: #1 tag size is determined as 70 bps INFO @ Mon, 03 Jun 2019 06:22:25: #1 tag size = 70 INFO @ Mon, 03 Jun 2019 06:22:25: #1 total tags in treatment: 2791442 INFO @ Mon, 03 Jun 2019 06:22:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:22:25: #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 06:22:25: #1 tag size is determined as 70 bps INFO @ Mon, 03 Jun 2019 06:22:25: #1 tag size = 70 INFO @ Mon, 03 Jun 2019 06:22:25: #1 total tags in treatment: 2791442 INFO @ Mon, 03 Jun 2019 06:22:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:22:25: #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 06:22:25: #1 tags after filtering in treatment: 2207147 INFO @ Mon, 03 Jun 2019 06:22:25: #1 Redundant rate of treatment: 0.21 INFO @ Mon, 03 Jun 2019 06:22:25: #1 finished! INFO @ Mon, 03 Jun 2019 06:22:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:22:25: #1 tags after filtering in treatment: 2207147 INFO @ Mon, 03 Jun 2019 06:22:25: #1 Redundant rate of treatment: 0.21 INFO @ Mon, 03 Jun 2019 06:22:25: #1 finished! INFO @ Mon, 03 Jun 2019 06:22:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:22:26: #2 number of paired peaks: 5559 INFO @ Mon, 03 Jun 2019 06:22:26: start model_add_line... INFO @ Mon, 03 Jun 2019 06:22:26: start X-correlation... INFO @ Mon, 03 Jun 2019 06:22:26: #2 number of paired peaks: 5559 INFO @ Mon, 03 Jun 2019 06:22:26: start model_add_line... INFO @ Mon, 03 Jun 2019 06:22:26: end of X-cor INFO @ Mon, 03 Jun 2019 06:22:26: #2 finished! INFO @ Mon, 03 Jun 2019 06:22:26: #2 predicted fragment length is 122 bps INFO @ Mon, 03 Jun 2019 06:22:26: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 03 Jun 2019 06:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.20_model.r WARNING @ Mon, 03 Jun 2019 06:22:26: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:22:26: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Mon, 03 Jun 2019 06:22:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 06:22:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:22:26: start X-correlation... INFO @ Mon, 03 Jun 2019 06:22:26: end of X-cor INFO @ Mon, 03 Jun 2019 06:22:26: #2 finished! INFO @ Mon, 03 Jun 2019 06:22:26: #2 predicted fragment length is 122 bps INFO @ Mon, 03 Jun 2019 06:22:26: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 03 Jun 2019 06:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.10_model.r WARNING @ Mon, 03 Jun 2019 06:22:26: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:22:26: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Mon, 03 Jun 2019 06:22:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 06:22:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:22:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:22:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:22:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:22:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:22:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:22:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.05_summits.bed INFO @ Mon, 03 Jun 2019 06:22:37: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (3859 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:22:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:22:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:22:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.10_summits.bed INFO @ Mon, 03 Jun 2019 06:22:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1844 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:22:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:22:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:22:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215626/SRX215626.20_summits.bed INFO @ Mon, 03 Jun 2019 06:22:40: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (936 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。