Job ID = 2590980 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,990,439 reads read : 3,980,878 reads written : 3,980,878 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: 00:09:37 1990439 reads; of these: 1990439 (100.00%) were paired; of these: 345908 (17.38%) aligned concordantly 0 times 480481 (24.14%) aligned concordantly exactly 1 time 1164050 (58.48%) aligned concordantly >1 times ---- 345908 pairs aligned concordantly 0 times; of these: 22405 (6.48%) aligned discordantly 1 time ---- 323503 pairs aligned 0 times concordantly or discordantly; of these: 647006 mates make up the pairs; of these: 324684 (50.18%) aligned 0 times 44703 (6.91%) aligned exactly 1 time 277619 (42.91%) aligned >1 times 91.84% overall alignment rate Time searching: 00:09:37 Overall time: 00:09:37 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] 1466130 / 1664866 = 0.8806 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 00:21:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.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 00:21:47: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:21:47: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:21:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.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 00:21:48: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:21:48: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:21:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.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 00:21:49: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:21:49: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:21:53: #1 tag size is determined as 81 bps INFO @ Tue, 13 Aug 2019 00:21:53: #1 tag size = 81 INFO @ Tue, 13 Aug 2019 00:21:53: #1 total tags in treatment: 194851 INFO @ Tue, 13 Aug 2019 00:21:53: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:21:53: #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 00:21:53: #1 tags after filtering in treatment: 151980 INFO @ Tue, 13 Aug 2019 00:21:53: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 13 Aug 2019 00:21:53: #1 finished! INFO @ Tue, 13 Aug 2019 00:21:53: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:21:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:21:53: #2 number of paired peaks: 7046 INFO @ Tue, 13 Aug 2019 00:21:53: start model_add_line... INFO @ Tue, 13 Aug 2019 00:21:53: start X-correlation... INFO @ Tue, 13 Aug 2019 00:21:53: end of X-cor INFO @ Tue, 13 Aug 2019 00:21:53: #2 finished! INFO @ Tue, 13 Aug 2019 00:21:53: #2 predicted fragment length is 314 bps INFO @ Tue, 13 Aug 2019 00:21:53: #2 alternative fragment length(s) may be 3,115,314 bps INFO @ Tue, 13 Aug 2019 00:21:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.05_model.r INFO @ Tue, 13 Aug 2019 00:21:53: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:21:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:21:54: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:21:54: #1 tag size is determined as 81 bps INFO @ Tue, 13 Aug 2019 00:21:54: #1 tag size = 81 INFO @ Tue, 13 Aug 2019 00:21:54: #1 total tags in treatment: 194851 INFO @ Tue, 13 Aug 2019 00:21:54: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:21:54: #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 00:21:54: #1 tags after filtering in treatment: 151980 INFO @ Tue, 13 Aug 2019 00:21:54: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 13 Aug 2019 00:21:54: #1 finished! INFO @ Tue, 13 Aug 2019 00:21:54: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:21:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:21:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:21:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:21:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.05_summits.bed INFO @ Tue, 13 Aug 2019 00:21:54: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (47 records, 4 fields): 2 millis INFO @ Tue, 13 Aug 2019 00:21:54: #2 number of paired peaks: 7046 INFO @ Tue, 13 Aug 2019 00:21:54: start model_add_line... INFO @ Tue, 13 Aug 2019 00:21:54: start X-correlation... CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:21:54: end of X-cor INFO @ Tue, 13 Aug 2019 00:21:54: #2 finished! INFO @ Tue, 13 Aug 2019 00:21:54: #2 predicted fragment length is 314 bps INFO @ Tue, 13 Aug 2019 00:21:54: #2 alternative fragment length(s) may be 3,115,314 bps INFO @ Tue, 13 Aug 2019 00:21:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.10_model.r INFO @ Tue, 13 Aug 2019 00:21:54: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:21:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:21:54: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:21:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:21:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:21:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.10_summits.bed INFO @ Tue, 13 Aug 2019 00:21:55: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:21:55: #1 tag size is determined as 81 bps INFO @ Tue, 13 Aug 2019 00:21:55: #1 tag size = 81 INFO @ Tue, 13 Aug 2019 00:21:55: #1 total tags in treatment: 194851 INFO @ Tue, 13 Aug 2019 00:21:55: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:21:55: #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 00:21:55: #1 tags after filtering in treatment: 151980 INFO @ Tue, 13 Aug 2019 00:21:55: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 13 Aug 2019 00:21:55: #1 finished! INFO @ Tue, 13 Aug 2019 00:21:55: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:21:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:21:55: #2 number of paired peaks: 7046 INFO @ Tue, 13 Aug 2019 00:21:55: start model_add_line... INFO @ Tue, 13 Aug 2019 00:21:55: start X-correlation... INFO @ Tue, 13 Aug 2019 00:21:55: end of X-cor INFO @ Tue, 13 Aug 2019 00:21:55: #2 finished! INFO @ Tue, 13 Aug 2019 00:21:55: #2 predicted fragment length is 314 bps INFO @ Tue, 13 Aug 2019 00:21:55: #2 alternative fragment length(s) may be 3,115,314 bps INFO @ Tue, 13 Aug 2019 00:21:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.20_model.r INFO @ Tue, 13 Aug 2019 00:21:55: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:21:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:21:56: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 13 Aug 2019 00:21:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:21:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:21:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441110/SRX6441110.20_summits.bed INFO @ Tue, 13 Aug 2019 00:21:56: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。