Job ID = 2590981 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 581,272 reads read : 1,162,544 reads written : 1,162,544 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: 00:00:00 Multiseed full-index search: 00:01:05 581272 reads; of these: 581272 (100.00%) were paired; of these: 112520 (19.36%) aligned concordantly 0 times 384013 (66.06%) aligned concordantly exactly 1 time 84739 (14.58%) aligned concordantly >1 times ---- 112520 pairs aligned concordantly 0 times; of these: 18732 (16.65%) aligned discordantly 1 time ---- 93788 pairs aligned 0 times concordantly or discordantly; of these: 187576 mates make up the pairs; of these: 127847 (68.16%) aligned 0 times 40769 (21.73%) aligned exactly 1 time 18960 (10.11%) aligned >1 times 89.00% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 354394 / 486794 = 0.7280 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 @ Tue, 13 Aug 2019 00:13:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.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 @ Tue, 13 Aug 2019 00:13:09: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:13:09: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:13:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.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 @ Tue, 13 Aug 2019 00:13:10: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:13:10: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:13:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.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 @ Tue, 13 Aug 2019 00:13:11: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:13:11: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:13:12: #1 tag size is determined as 75 bps INFO @ Tue, 13 Aug 2019 00:13:12: #1 tag size = 75 INFO @ Tue, 13 Aug 2019 00:13:12: #1 total tags in treatment: 123810 INFO @ Tue, 13 Aug 2019 00:13:12: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:13:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:13:12: #1 tags after filtering in treatment: 115942 INFO @ Tue, 13 Aug 2019 00:13:12: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 13 Aug 2019 00:13:12: #1 finished! INFO @ Tue, 13 Aug 2019 00:13:12: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:13:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:13:12: #2 number of paired peaks: 7964 INFO @ Tue, 13 Aug 2019 00:13:12: start model_add_line... INFO @ Tue, 13 Aug 2019 00:13:12: start X-correlation... INFO @ Tue, 13 Aug 2019 00:13:12: end of X-cor INFO @ Tue, 13 Aug 2019 00:13:12: #2 finished! INFO @ Tue, 13 Aug 2019 00:13:12: #2 predicted fragment length is 3 bps INFO @ Tue, 13 Aug 2019 00:13:12: #2 alternative fragment length(s) may be 3,84,160,187,225,242,286,322,348,361 bps INFO @ Tue, 13 Aug 2019 00:13:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.05_model.r WARNING @ Tue, 13 Aug 2019 00:13:12: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:13:12: #2 You may need to consider one of the other alternative d(s): 3,84,160,187,225,242,286,322,348,361 WARNING @ Tue, 13 Aug 2019 00:13:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:13:12: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:13:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:13:13: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:13:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:13:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:13:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.05_summits.bed INFO @ Tue, 13 Aug 2019 00:13:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 INFO @ Tue, 13 Aug 2019 00:13:14: #1 tag size is determined as 75 bps INFO @ Tue, 13 Aug 2019 00:13:14: #1 tag size = 75 INFO @ Tue, 13 Aug 2019 00:13:14: #1 total tags in treatment: 123810 INFO @ Tue, 13 Aug 2019 00:13:14: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:13:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換中... INFO @ Tue, 13 Aug 2019 00:13:14: #1 tags after filtering in treatment: 115942 INFO @ Tue, 13 Aug 2019 00:13:14: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 13 Aug 2019 00:13:14: #1 finished! INFO @ Tue, 13 Aug 2019 00:13:14: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:13:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:13:15: #2 number of paired peaks: 7964 INFO @ Tue, 13 Aug 2019 00:13:15: start model_add_line... INFO @ Tue, 13 Aug 2019 00:13:15: start X-correlation... INFO @ Tue, 13 Aug 2019 00:13:15: end of X-cor INFO @ Tue, 13 Aug 2019 00:13:15: #2 finished! INFO @ Tue, 13 Aug 2019 00:13:15: #2 predicted fragment length is 3 bps INFO @ Tue, 13 Aug 2019 00:13:15: #2 alternative fragment length(s) may be 3,84,160,187,225,242,286,322,348,361 bps INFO @ Tue, 13 Aug 2019 00:13:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.10_model.r WARNING @ Tue, 13 Aug 2019 00:13:15: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:13:15: #2 You may need to consider one of the other alternative d(s): 3,84,160,187,225,242,286,322,348,361 WARNING @ Tue, 13 Aug 2019 00:13:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:13:15: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:13:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 13 Aug 2019 00:13:15: #1 tag size is determined as 75 bps INFO @ Tue, 13 Aug 2019 00:13:15: #1 tag size = 75 INFO @ Tue, 13 Aug 2019 00:13:15: #1 total tags in treatment: 123810 INFO @ Tue, 13 Aug 2019 00:13:15: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:13:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:13:15: #1 tags after filtering in treatment: 115942 INFO @ Tue, 13 Aug 2019 00:13:15: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 13 Aug 2019 00:13:15: #1 finished! INFO @ Tue, 13 Aug 2019 00:13:15: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:13:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:13:15: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:13:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:13:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:13:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.10_summits.bed INFO @ Tue, 13 Aug 2019 00:13:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:13:15: #2 number of paired peaks: 7964 INFO @ Tue, 13 Aug 2019 00:13:15: start model_add_line... INFO @ Tue, 13 Aug 2019 00:13:15: start X-correlation... INFO @ Tue, 13 Aug 2019 00:13:15: end of X-cor INFO @ Tue, 13 Aug 2019 00:13:15: #2 finished! INFO @ Tue, 13 Aug 2019 00:13:15: #2 predicted fragment length is 3 bps INFO @ Tue, 13 Aug 2019 00:13:15: #2 alternative fragment length(s) may be 3,84,160,187,225,242,286,322,348,361 bps INFO @ Tue, 13 Aug 2019 00:13:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.20_model.r WARNING @ Tue, 13 Aug 2019 00:13:16: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:13:16: #2 You may need to consider one of the other alternative d(s): 3,84,160,187,225,242,286,322,348,361 WARNING @ Tue, 13 Aug 2019 00:13:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:13:16: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:13:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:13:16: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:13:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:13:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:13:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441111/SRX6441111.20_summits.bed INFO @ Tue, 13 Aug 2019 00:13:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling