Job ID = 2011919 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,250,445 reads read : 6,500,890 reads written : 6,500,890 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: 00:02:22 3250445 reads; of these: 3250445 (100.00%) were paired; of these: 453877 (13.96%) aligned concordantly 0 times 2439391 (75.05%) aligned concordantly exactly 1 time 357177 (10.99%) aligned concordantly >1 times ---- 453877 pairs aligned concordantly 0 times; of these: 281508 (62.02%) aligned discordantly 1 time ---- 172369 pairs aligned 0 times concordantly or discordantly; of these: 344738 mates make up the pairs; of these: 180534 (52.37%) aligned 0 times 70519 (20.46%) aligned exactly 1 time 93685 (27.18%) aligned >1 times 97.22% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 87398 / 3076871 = 0.0284 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 @ Sat, 06 Jul 2019 03:23:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 06 Jul 2019 03:23:03: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:23:03: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:23:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 06 Jul 2019 03:23:04: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:23:04: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:23:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 06 Jul 2019 03:23:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:23:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:23:10: 1000000 INFO @ Sat, 06 Jul 2019 03:23:12: 1000000 INFO @ Sat, 06 Jul 2019 03:23:12: 1000000 INFO @ Sat, 06 Jul 2019 03:23:16: 2000000 INFO @ Sat, 06 Jul 2019 03:23:19: 2000000 INFO @ Sat, 06 Jul 2019 03:23:19: 2000000 INFO @ Sat, 06 Jul 2019 03:23:23: 3000000 INFO @ Sat, 06 Jul 2019 03:23:25: 3000000 INFO @ Sat, 06 Jul 2019 03:23:26: 3000000 INFO @ Sat, 06 Jul 2019 03:23:29: 4000000 INFO @ Sat, 06 Jul 2019 03:23:32: 4000000 INFO @ Sat, 06 Jul 2019 03:23:34: 4000000 INFO @ Sat, 06 Jul 2019 03:23:35: 5000000 INFO @ Sat, 06 Jul 2019 03:23:38: 5000000 INFO @ Sat, 06 Jul 2019 03:23:41: 5000000 INFO @ Sat, 06 Jul 2019 03:23:42: 6000000 INFO @ Sat, 06 Jul 2019 03:23:43: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:23:43: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:23:43: #1 total tags in treatment: 2714640 INFO @ Sat, 06 Jul 2019 03:23:43: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:23:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:23:43: #1 tags after filtering in treatment: 2325111 INFO @ Sat, 06 Jul 2019 03:23:43: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 06 Jul 2019 03:23:43: #1 finished! INFO @ Sat, 06 Jul 2019 03:23:43: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:23:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:23:43: #2 number of paired peaks: 170 WARNING @ Sat, 06 Jul 2019 03:23:43: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 06 Jul 2019 03:23:43: start model_add_line... INFO @ Sat, 06 Jul 2019 03:23:43: start X-correlation... INFO @ Sat, 06 Jul 2019 03:23:43: end of X-cor INFO @ Sat, 06 Jul 2019 03:23:43: #2 finished! INFO @ Sat, 06 Jul 2019 03:23:43: #2 predicted fragment length is 246 bps INFO @ Sat, 06 Jul 2019 03:23:43: #2 alternative fragment length(s) may be 0,16,73,93,121,144,152,173,208,225,246,278,294,314,332,353,402,430,479,492,527,556,598 bps INFO @ Sat, 06 Jul 2019 03:23:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.05_model.r INFO @ Sat, 06 Jul 2019 03:23:43: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:23:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:23:44: 6000000 INFO @ Sat, 06 Jul 2019 03:23:45: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:23:45: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:23:45: #1 total tags in treatment: 2714640 INFO @ Sat, 06 Jul 2019 03:23:45: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:23:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:23:45: #1 tags after filtering in treatment: 2325111 INFO @ Sat, 06 Jul 2019 03:23:45: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 06 Jul 2019 03:23:45: #1 finished! INFO @ Sat, 06 Jul 2019 03:23:45: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:23:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:23:45: #2 number of paired peaks: 170 WARNING @ Sat, 06 Jul 2019 03:23:45: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 06 Jul 2019 03:23:45: start model_add_line... INFO @ Sat, 06 Jul 2019 03:23:45: start X-correlation... INFO @ Sat, 06 Jul 2019 03:23:45: end of X-cor INFO @ Sat, 06 Jul 2019 03:23:45: #2 finished! INFO @ Sat, 06 Jul 2019 03:23:45: #2 predicted fragment length is 246 bps INFO @ Sat, 06 Jul 2019 03:23:45: #2 alternative fragment length(s) may be 0,16,73,93,121,144,152,173,208,225,246,278,294,314,332,353,402,430,479,492,527,556,598 bps INFO @ Sat, 06 Jul 2019 03:23:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.20_model.r INFO @ Sat, 06 Jul 2019 03:23:45: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:23:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:23:48: 6000000 INFO @ Sat, 06 Jul 2019 03:23:49: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:23:49: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:23:49: #1 total tags in treatment: 2714640 INFO @ Sat, 06 Jul 2019 03:23:49: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:23:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:23:49: #1 tags after filtering in treatment: 2325111 INFO @ Sat, 06 Jul 2019 03:23:49: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 06 Jul 2019 03:23:49: #1 finished! INFO @ Sat, 06 Jul 2019 03:23:49: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:23:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:23:49: #2 number of paired peaks: 170 WARNING @ Sat, 06 Jul 2019 03:23:49: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 06 Jul 2019 03:23:49: start model_add_line... INFO @ Sat, 06 Jul 2019 03:23:49: start X-correlation... INFO @ Sat, 06 Jul 2019 03:23:49: end of X-cor INFO @ Sat, 06 Jul 2019 03:23:49: #2 finished! INFO @ Sat, 06 Jul 2019 03:23:49: #2 predicted fragment length is 246 bps INFO @ Sat, 06 Jul 2019 03:23:49: #2 alternative fragment length(s) may be 0,16,73,93,121,144,152,173,208,225,246,278,294,314,332,353,402,430,479,492,527,556,598 bps INFO @ Sat, 06 Jul 2019 03:23:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.10_model.r INFO @ Sat, 06 Jul 2019 03:23:49: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:23:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:23:50: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:23:52: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:23:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:23:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:23:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.05_summits.bed INFO @ Sat, 06 Jul 2019 03:23:53: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (36 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:23:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:23:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:23:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.20_summits.bed INFO @ Sat, 06 Jul 2019 03:23:55: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:23:56: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:23:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:23:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:23:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383692/SRX5383692.10_summits.bed INFO @ Sat, 06 Jul 2019 03:23:59: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。