Job ID = 4303089 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,253,356 reads read : 14,506,712 reads written : 14,506,712 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1151101.sra.cache’: 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: 00:06:25 7253356 reads; of these: 7253356 (100.00%) were paired; of these: 4404415 (60.72%) aligned concordantly 0 times 2160367 (29.78%) aligned concordantly exactly 1 time 688574 (9.49%) aligned concordantly >1 times ---- 4404415 pairs aligned concordantly 0 times; of these: 2070 (0.05%) aligned discordantly 1 time ---- 4402345 pairs aligned 0 times concordantly or discordantly; of these: 8804690 mates make up the pairs; of these: 8744345 (99.31%) aligned 0 times 46611 (0.53%) aligned exactly 1 time 13734 (0.16%) aligned >1 times 39.72% overall alignment rate Time searching: 00:06:26 Overall time: 00:06:26 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] 2350630 / 2847686 = 0.8255 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:48:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.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 @ Thu, 12 Dec 2019 00:48:09: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:48:09: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:48:16: 1000000 INFO @ Thu, 12 Dec 2019 00:48:16: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:48:16: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:48:16: #1 total tags in treatment: 498979 INFO @ Thu, 12 Dec 2019 00:48:16: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:48:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:48:16: #1 tags after filtering in treatment: 399918 INFO @ Thu, 12 Dec 2019 00:48:16: #1 Redundant rate of treatment: 0.20 INFO @ Thu, 12 Dec 2019 00:48:16: #1 finished! INFO @ Thu, 12 Dec 2019 00:48:16: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:48:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:48:16: #2 number of paired peaks: 4225 INFO @ Thu, 12 Dec 2019 00:48:16: start model_add_line... INFO @ Thu, 12 Dec 2019 00:48:16: start X-correlation... INFO @ Thu, 12 Dec 2019 00:48:16: end of X-cor INFO @ Thu, 12 Dec 2019 00:48:16: #2 finished! INFO @ Thu, 12 Dec 2019 00:48:16: #2 predicted fragment length is 85 bps INFO @ Thu, 12 Dec 2019 00:48:16: #2 alternative fragment length(s) may be 85 bps INFO @ Thu, 12 Dec 2019 00:48:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.05_model.r WARNING @ Thu, 12 Dec 2019 00:48:16: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:48:16: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Thu, 12 Dec 2019 00:48:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:48:16: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:48:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:48:17: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:48:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:48:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:48:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.05_summits.bed INFO @ Thu, 12 Dec 2019 00:48:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1123 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:48:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.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 @ Thu, 12 Dec 2019 00:48:39: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:48:39: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:48:46: 1000000 INFO @ Thu, 12 Dec 2019 00:48:46: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:48:46: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:48:46: #1 total tags in treatment: 498979 INFO @ Thu, 12 Dec 2019 00:48:46: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:48:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:48:46: #1 tags after filtering in treatment: 399918 INFO @ Thu, 12 Dec 2019 00:48:46: #1 Redundant rate of treatment: 0.20 INFO @ Thu, 12 Dec 2019 00:48:46: #1 finished! INFO @ Thu, 12 Dec 2019 00:48:46: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:48:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:48:46: #2 number of paired peaks: 4225 INFO @ Thu, 12 Dec 2019 00:48:46: start model_add_line... INFO @ Thu, 12 Dec 2019 00:48:46: start X-correlation... INFO @ Thu, 12 Dec 2019 00:48:46: end of X-cor INFO @ Thu, 12 Dec 2019 00:48:46: #2 finished! INFO @ Thu, 12 Dec 2019 00:48:46: #2 predicted fragment length is 85 bps INFO @ Thu, 12 Dec 2019 00:48:46: #2 alternative fragment length(s) may be 85 bps INFO @ Thu, 12 Dec 2019 00:48:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.10_model.r WARNING @ Thu, 12 Dec 2019 00:48:46: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:48:46: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Thu, 12 Dec 2019 00:48:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:48:46: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:48:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:48:47: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:48:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:48:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:48:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.10_summits.bed INFO @ Thu, 12 Dec 2019 00:48:47: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (525 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:49:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.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 @ Thu, 12 Dec 2019 00:49:09: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:49:09: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:49:16: 1000000 INFO @ Thu, 12 Dec 2019 00:49:16: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:49:16: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:49:16: #1 total tags in treatment: 498979 INFO @ Thu, 12 Dec 2019 00:49:16: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:49:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:49:16: #1 tags after filtering in treatment: 399918 INFO @ Thu, 12 Dec 2019 00:49:16: #1 Redundant rate of treatment: 0.20 INFO @ Thu, 12 Dec 2019 00:49:16: #1 finished! INFO @ Thu, 12 Dec 2019 00:49:16: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:49:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:49:16: #2 number of paired peaks: 4225 INFO @ Thu, 12 Dec 2019 00:49:16: start model_add_line... INFO @ Thu, 12 Dec 2019 00:49:16: start X-correlation... INFO @ Thu, 12 Dec 2019 00:49:16: end of X-cor INFO @ Thu, 12 Dec 2019 00:49:16: #2 finished! INFO @ Thu, 12 Dec 2019 00:49:16: #2 predicted fragment length is 85 bps INFO @ Thu, 12 Dec 2019 00:49:16: #2 alternative fragment length(s) may be 85 bps INFO @ Thu, 12 Dec 2019 00:49:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.20_model.r WARNING @ Thu, 12 Dec 2019 00:49:16: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:49:16: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Thu, 12 Dec 2019 00:49:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:49:16: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:49:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:49:17: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:49:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:49:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:49:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456153/SRX456153.20_summits.bed INFO @ Thu, 12 Dec 2019 00:49:17: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (266 records, 4 fields): 32 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。