Job ID = 4178421 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,299,789 reads read : 4,599,578 reads written : 4,599,578 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: 00:06:24 2299789 reads; of these: 2299789 (100.00%) were paired; of these: 264006 (11.48%) aligned concordantly 0 times 1510104 (65.66%) aligned concordantly exactly 1 time 525679 (22.86%) aligned concordantly >1 times ---- 264006 pairs aligned concordantly 0 times; of these: 78712 (29.81%) aligned discordantly 1 time ---- 185294 pairs aligned 0 times concordantly or discordantly; of these: 370588 mates make up the pairs; of these: 251184 (67.78%) aligned 0 times 63648 (17.17%) aligned exactly 1 time 55756 (15.05%) aligned >1 times 94.54% overall alignment rate Time searching: 00:06:24 Overall time: 00:06:24 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] 577682 / 2111410 = 0.2736 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:28:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.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 12:28:07: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:28:07: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:28:13: 1000000 INFO @ Thu, 05 Dec 2019 12:28:18: 2000000 INFO @ Thu, 05 Dec 2019 12:28:24: 3000000 INFO @ Thu, 05 Dec 2019 12:28:25: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:28:25: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:28:25: #1 total tags in treatment: 1477829 INFO @ Thu, 05 Dec 2019 12:28:25: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:28:25: #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 12:28:25: #1 tags after filtering in treatment: 1443569 INFO @ Thu, 05 Dec 2019 12:28:25: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 05 Dec 2019 12:28:25: #1 finished! INFO @ Thu, 05 Dec 2019 12:28:25: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:28:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:28:25: #2 number of paired peaks: 374 WARNING @ Thu, 05 Dec 2019 12:28:25: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Thu, 05 Dec 2019 12:28:25: start model_add_line... INFO @ Thu, 05 Dec 2019 12:28:25: start X-correlation... INFO @ Thu, 05 Dec 2019 12:28:25: end of X-cor INFO @ Thu, 05 Dec 2019 12:28:25: #2 finished! INFO @ Thu, 05 Dec 2019 12:28:25: #2 predicted fragment length is 161 bps INFO @ Thu, 05 Dec 2019 12:28:25: #2 alternative fragment length(s) may be 161 bps INFO @ Thu, 05 Dec 2019 12:28:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.05_model.r INFO @ Thu, 05 Dec 2019 12:28:28: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:28:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:28:31: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:28:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:28:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:28:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.05_summits.bed INFO @ Thu, 05 Dec 2019 12:28:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (570 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:28:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.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 12:28:37: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:28:37: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:28:42: 1000000 INFO @ Thu, 05 Dec 2019 12:28:48: 2000000 INFO @ Thu, 05 Dec 2019 12:28:53: 3000000 INFO @ Thu, 05 Dec 2019 12:28:54: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:28:54: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:28:54: #1 total tags in treatment: 1477829 INFO @ Thu, 05 Dec 2019 12:28:54: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:28:54: #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 12:28:54: #1 tags after filtering in treatment: 1443569 INFO @ Thu, 05 Dec 2019 12:28:54: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 05 Dec 2019 12:28:54: #1 finished! INFO @ Thu, 05 Dec 2019 12:28:54: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:28:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:28:55: #2 number of paired peaks: 374 WARNING @ Thu, 05 Dec 2019 12:28:55: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Thu, 05 Dec 2019 12:28:55: start model_add_line... INFO @ Thu, 05 Dec 2019 12:28:55: start X-correlation... INFO @ Thu, 05 Dec 2019 12:28:55: end of X-cor INFO @ Thu, 05 Dec 2019 12:28:55: #2 finished! INFO @ Thu, 05 Dec 2019 12:28:55: #2 predicted fragment length is 161 bps INFO @ Thu, 05 Dec 2019 12:28:55: #2 alternative fragment length(s) may be 161 bps INFO @ Thu, 05 Dec 2019 12:28:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.10_model.r INFO @ Thu, 05 Dec 2019 12:28:55: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:28:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:28:58: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:28:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:28:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:28:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.10_summits.bed INFO @ Thu, 05 Dec 2019 12:28:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (420 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:29:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.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 12:29:07: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:07: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:12: 1000000 INFO @ Thu, 05 Dec 2019 12:29:19: 2000000 INFO @ Thu, 05 Dec 2019 12:29:24: 3000000 INFO @ Thu, 05 Dec 2019 12:29:25: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:29:25: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:29:25: #1 total tags in treatment: 1477829 INFO @ Thu, 05 Dec 2019 12:29:25: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:29:25: #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 12:29:26: #1 tags after filtering in treatment: 1443569 INFO @ Thu, 05 Dec 2019 12:29:26: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 05 Dec 2019 12:29:26: #1 finished! INFO @ Thu, 05 Dec 2019 12:29:26: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:29:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:29:26: #2 number of paired peaks: 374 WARNING @ Thu, 05 Dec 2019 12:29:26: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Thu, 05 Dec 2019 12:29:26: start model_add_line... INFO @ Thu, 05 Dec 2019 12:29:26: start X-correlation... INFO @ Thu, 05 Dec 2019 12:29:26: end of X-cor INFO @ Thu, 05 Dec 2019 12:29:26: #2 finished! INFO @ Thu, 05 Dec 2019 12:29:26: #2 predicted fragment length is 161 bps INFO @ Thu, 05 Dec 2019 12:29:26: #2 alternative fragment length(s) may be 161 bps INFO @ Thu, 05 Dec 2019 12:29:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.20_model.r INFO @ Thu, 05 Dec 2019 12:29:26: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:29:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:29:29: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:29:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:29:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:29:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095159/SRX2095159.20_summits.bed INFO @ Thu, 05 Dec 2019 12:29:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (269 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。