Job ID = 4178423 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,310,163 reads read : 2,620,326 reads written : 2,620,326 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 1310163 reads; of these: 1310163 (100.00%) were paired; of these: 740780 (56.54%) aligned concordantly 0 times 493351 (37.66%) aligned concordantly exactly 1 time 76032 (5.80%) aligned concordantly >1 times ---- 740780 pairs aligned concordantly 0 times; of these: 60033 (8.10%) aligned discordantly 1 time ---- 680747 pairs aligned 0 times concordantly or discordantly; of these: 1361494 mates make up the pairs; of these: 1299414 (95.44%) aligned 0 times 40036 (2.94%) aligned exactly 1 time 22044 (1.62%) aligned >1 times 50.41% 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] 4463 / 377878 = 0.0118 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:22:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.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, 05 Dec 2019 12:22:39: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:22:39: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:22:45: 1000000 INFO @ Thu, 05 Dec 2019 12:22:47: #1 tag size is determined as 71 bps INFO @ Thu, 05 Dec 2019 12:22:47: #1 tag size = 71 INFO @ Thu, 05 Dec 2019 12:22:47: #1 total tags in treatment: 564959 INFO @ Thu, 05 Dec 2019 12:22:47: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:22:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:22:47: #1 tags after filtering in treatment: 559453 INFO @ Thu, 05 Dec 2019 12:22:47: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 05 Dec 2019 12:22:47: #1 finished! INFO @ Thu, 05 Dec 2019 12:22:47: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:22:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:22:47: #2 number of paired peaks: 386 WARNING @ Thu, 05 Dec 2019 12:22:47: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Thu, 05 Dec 2019 12:22:47: start model_add_line... INFO @ Thu, 05 Dec 2019 12:22:47: start X-correlation... INFO @ Thu, 05 Dec 2019 12:22:47: end of X-cor INFO @ Thu, 05 Dec 2019 12:22:47: #2 finished! INFO @ Thu, 05 Dec 2019 12:22:47: #2 predicted fragment length is 207 bps INFO @ Thu, 05 Dec 2019 12:22:47: #2 alternative fragment length(s) may be 207 bps INFO @ Thu, 05 Dec 2019 12:22:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.05_model.r INFO @ Thu, 05 Dec 2019 12:22:47: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:22:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:22:48: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:22:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:22:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:22:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.05_summits.bed INFO @ Thu, 05 Dec 2019 12:22:49: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (17 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:23:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.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, 05 Dec 2019 12:23:07: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:23:07: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:23:13: 1000000 INFO @ Thu, 05 Dec 2019 12:23:15: #1 tag size is determined as 71 bps INFO @ Thu, 05 Dec 2019 12:23:15: #1 tag size = 71 INFO @ Thu, 05 Dec 2019 12:23:15: #1 total tags in treatment: 564959 INFO @ Thu, 05 Dec 2019 12:23:15: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:23:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:23:15: #1 tags after filtering in treatment: 559453 INFO @ Thu, 05 Dec 2019 12:23:15: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 05 Dec 2019 12:23:15: #1 finished! INFO @ Thu, 05 Dec 2019 12:23:15: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:23:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:23:15: #2 number of paired peaks: 386 WARNING @ Thu, 05 Dec 2019 12:23:15: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Thu, 05 Dec 2019 12:23:15: start model_add_line... INFO @ Thu, 05 Dec 2019 12:23:15: start X-correlation... INFO @ Thu, 05 Dec 2019 12:23:15: end of X-cor INFO @ Thu, 05 Dec 2019 12:23:15: #2 finished! INFO @ Thu, 05 Dec 2019 12:23:15: #2 predicted fragment length is 207 bps INFO @ Thu, 05 Dec 2019 12:23:15: #2 alternative fragment length(s) may be 207 bps INFO @ Thu, 05 Dec 2019 12:23:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.10_model.r INFO @ Thu, 05 Dec 2019 12:23:15: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:23:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:23:16: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:23:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:23:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:23:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.10_summits.bed INFO @ Thu, 05 Dec 2019 12:23:17: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:23:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.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, 05 Dec 2019 12:23:38: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:23:38: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:23:43: 1000000 INFO @ Thu, 05 Dec 2019 12:23:45: #1 tag size is determined as 71 bps INFO @ Thu, 05 Dec 2019 12:23:45: #1 tag size = 71 INFO @ Thu, 05 Dec 2019 12:23:45: #1 total tags in treatment: 564959 INFO @ Thu, 05 Dec 2019 12:23:45: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:23:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:23:45: #1 tags after filtering in treatment: 559453 INFO @ Thu, 05 Dec 2019 12:23:45: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 05 Dec 2019 12:23:45: #1 finished! INFO @ Thu, 05 Dec 2019 12:23:45: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:23:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:23:45: #2 number of paired peaks: 386 WARNING @ Thu, 05 Dec 2019 12:23:45: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Thu, 05 Dec 2019 12:23:45: start model_add_line... INFO @ Thu, 05 Dec 2019 12:23:45: start X-correlation... INFO @ Thu, 05 Dec 2019 12:23:45: end of X-cor INFO @ Thu, 05 Dec 2019 12:23:45: #2 finished! INFO @ Thu, 05 Dec 2019 12:23:45: #2 predicted fragment length is 207 bps INFO @ Thu, 05 Dec 2019 12:23:45: #2 alternative fragment length(s) may be 207 bps INFO @ Thu, 05 Dec 2019 12:23:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.20_model.r INFO @ Thu, 05 Dec 2019 12:23:45: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:23:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:23:46: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:23:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:23:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:23:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3434305/SRX3434305.20_summits.bed INFO @ Thu, 05 Dec 2019 12:23:47: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。