Job ID = 2010917 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 31,108,626 reads read : 62,217,252 reads written : 62,217,252 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: 00:36:25 31108626 reads; of these: 31108626 (100.00%) were paired; of these: 7234156 (23.25%) aligned concordantly 0 times 9060280 (29.12%) aligned concordantly exactly 1 time 14814190 (47.62%) aligned concordantly >1 times ---- 7234156 pairs aligned concordantly 0 times; of these: 32034 (0.44%) aligned discordantly 1 time ---- 7202122 pairs aligned 0 times concordantly or discordantly; of these: 14404244 mates make up the pairs; of these: 12154887 (84.38%) aligned 0 times 1032759 (7.17%) aligned exactly 1 time 1216598 (8.45%) aligned >1 times 80.46% overall alignment rate Time searching: 00:36:25 Overall time: 00:36:25 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_sort_core] merging from 16 files... [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] 16684917 / 23844373 = 0.6997 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 02:21:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.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 02:21:17: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:21:17: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:21:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.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 02:21:18: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:21:18: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:21:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.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 02:21:19: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:21:19: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:21:23: 1000000 INFO @ Sat, 06 Jul 2019 02:21:26: 1000000 INFO @ Sat, 06 Jul 2019 02:21:28: 1000000 INFO @ Sat, 06 Jul 2019 02:21:29: 2000000 INFO @ Sat, 06 Jul 2019 02:21:32: 2000000 INFO @ Sat, 06 Jul 2019 02:21:36: 3000000 INFO @ Sat, 06 Jul 2019 02:21:37: 2000000 INFO @ Sat, 06 Jul 2019 02:21:38: 3000000 INFO @ Sat, 06 Jul 2019 02:21:42: 4000000 INFO @ Sat, 06 Jul 2019 02:21:44: 4000000 INFO @ Sat, 06 Jul 2019 02:21:45: 3000000 INFO @ Sat, 06 Jul 2019 02:21:48: 5000000 INFO @ Sat, 06 Jul 2019 02:21:50: 5000000 INFO @ Sat, 06 Jul 2019 02:21:53: 4000000 INFO @ Sat, 06 Jul 2019 02:21:54: 6000000 INFO @ Sat, 06 Jul 2019 02:21:56: 6000000 INFO @ Sat, 06 Jul 2019 02:22:00: 7000000 INFO @ Sat, 06 Jul 2019 02:22:01: 5000000 INFO @ Sat, 06 Jul 2019 02:22:02: 7000000 INFO @ Sat, 06 Jul 2019 02:22:06: 8000000 INFO @ Sat, 06 Jul 2019 02:22:08: 8000000 INFO @ Sat, 06 Jul 2019 02:22:10: 6000000 INFO @ Sat, 06 Jul 2019 02:22:12: 9000000 INFO @ Sat, 06 Jul 2019 02:22:14: 9000000 INFO @ Sat, 06 Jul 2019 02:22:18: 7000000 INFO @ Sat, 06 Jul 2019 02:22:18: 10000000 INFO @ Sat, 06 Jul 2019 02:22:20: 10000000 INFO @ Sat, 06 Jul 2019 02:22:24: 11000000 INFO @ Sat, 06 Jul 2019 02:22:26: 8000000 INFO @ Sat, 06 Jul 2019 02:22:26: 11000000 INFO @ Sat, 06 Jul 2019 02:22:30: 12000000 INFO @ Sat, 06 Jul 2019 02:22:32: 12000000 INFO @ Sat, 06 Jul 2019 02:22:34: 9000000 INFO @ Sat, 06 Jul 2019 02:22:36: 13000000 INFO @ Sat, 06 Jul 2019 02:22:38: 13000000 INFO @ Sat, 06 Jul 2019 02:22:42: 14000000 INFO @ Sat, 06 Jul 2019 02:22:42: 10000000 INFO @ Sat, 06 Jul 2019 02:22:44: 14000000 INFO @ Sat, 06 Jul 2019 02:22:48: 15000000 INFO @ Sat, 06 Jul 2019 02:22:50: 11000000 INFO @ Sat, 06 Jul 2019 02:22:50: 15000000 INFO @ Sat, 06 Jul 2019 02:22:54: 16000000 INFO @ Sat, 06 Jul 2019 02:22:56: 16000000 INFO @ Sat, 06 Jul 2019 02:22:58: #1 tag size is determined as 40 bps INFO @ Sat, 06 Jul 2019 02:22:58: #1 tag size = 40 INFO @ Sat, 06 Jul 2019 02:22:58: #1 total tags in treatment: 7196724 INFO @ Sat, 06 Jul 2019 02:22:58: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:22:58: #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 02:22:58: 12000000 INFO @ Sat, 06 Jul 2019 02:22:59: #1 tags after filtering in treatment: 3302681 INFO @ Sat, 06 Jul 2019 02:22:59: #1 Redundant rate of treatment: 0.54 INFO @ Sat, 06 Jul 2019 02:22:59: #1 finished! INFO @ Sat, 06 Jul 2019 02:22:59: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:22:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:22:59: #2 number of paired peaks: 277 WARNING @ Sat, 06 Jul 2019 02:22:59: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 06 Jul 2019 02:22:59: start model_add_line... INFO @ Sat, 06 Jul 2019 02:22:59: start X-correlation... INFO @ Sat, 06 Jul 2019 02:22:59: end of X-cor INFO @ Sat, 06 Jul 2019 02:22:59: #2 finished! INFO @ Sat, 06 Jul 2019 02:22:59: #2 predicted fragment length is 140 bps INFO @ Sat, 06 Jul 2019 02:22:59: #2 alternative fragment length(s) may be 1,89,123,140,160 bps INFO @ Sat, 06 Jul 2019 02:22:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.05_model.r INFO @ Sat, 06 Jul 2019 02:22:59: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:22:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:23:01: #1 tag size is determined as 40 bps INFO @ Sat, 06 Jul 2019 02:23:01: #1 tag size = 40 INFO @ Sat, 06 Jul 2019 02:23:01: #1 total tags in treatment: 7196724 INFO @ Sat, 06 Jul 2019 02:23:01: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:23:01: #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 02:23:01: #1 tags after filtering in treatment: 3302681 INFO @ Sat, 06 Jul 2019 02:23:01: #1 Redundant rate of treatment: 0.54 INFO @ Sat, 06 Jul 2019 02:23:01: #1 finished! INFO @ Sat, 06 Jul 2019 02:23:01: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:23:01: #2 number of paired peaks: 277 WARNING @ Sat, 06 Jul 2019 02:23:01: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 06 Jul 2019 02:23:01: start model_add_line... INFO @ Sat, 06 Jul 2019 02:23:01: start X-correlation... INFO @ Sat, 06 Jul 2019 02:23:01: end of X-cor INFO @ Sat, 06 Jul 2019 02:23:01: #2 finished! INFO @ Sat, 06 Jul 2019 02:23:01: #2 predicted fragment length is 140 bps INFO @ Sat, 06 Jul 2019 02:23:01: #2 alternative fragment length(s) may be 1,89,123,140,160 bps INFO @ Sat, 06 Jul 2019 02:23:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.20_model.r INFO @ Sat, 06 Jul 2019 02:23:01: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:23:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:23:07: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:23:10: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:23:12: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:23:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.05_peaks.xls INFO @ Sat, 06 Jul 2019 02:23:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:23:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.05_summits.bed INFO @ Sat, 06 Jul 2019 02:23:13: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (1200 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:23:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.20_peaks.xls INFO @ Sat, 06 Jul 2019 02:23:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:23:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.20_summits.bed INFO @ Sat, 06 Jul 2019 02:23:15: Done! INFO @ Sat, 06 Jul 2019 02:23:15: 14000000 pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:23:23: 15000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 02:23:31: 16000000 INFO @ Sat, 06 Jul 2019 02:23:36: #1 tag size is determined as 40 bps INFO @ Sat, 06 Jul 2019 02:23:36: #1 tag size = 40 INFO @ Sat, 06 Jul 2019 02:23:36: #1 total tags in treatment: 7196724 INFO @ Sat, 06 Jul 2019 02:23:36: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:23:36: #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 02:23:37: #1 tags after filtering in treatment: 3302681 INFO @ Sat, 06 Jul 2019 02:23:37: #1 Redundant rate of treatment: 0.54 INFO @ Sat, 06 Jul 2019 02:23:37: #1 finished! INFO @ Sat, 06 Jul 2019 02:23:37: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:23:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:23:37: #2 number of paired peaks: 277 WARNING @ Sat, 06 Jul 2019 02:23:37: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 06 Jul 2019 02:23:37: start model_add_line... INFO @ Sat, 06 Jul 2019 02:23:37: start X-correlation... INFO @ Sat, 06 Jul 2019 02:23:37: end of X-cor INFO @ Sat, 06 Jul 2019 02:23:37: #2 finished! INFO @ Sat, 06 Jul 2019 02:23:37: #2 predicted fragment length is 140 bps INFO @ Sat, 06 Jul 2019 02:23:37: #2 alternative fragment length(s) may be 1,89,123,140,160 bps INFO @ Sat, 06 Jul 2019 02:23:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.10_model.r INFO @ Sat, 06 Jul 2019 02:23:37: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:23:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:23:48: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:23:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.10_peaks.xls INFO @ Sat, 06 Jul 2019 02:24:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:24:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX423270/SRX423270.10_summits.bed INFO @ Sat, 06 Jul 2019 02:24:11: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (606 records, 4 fields): 4 millis CompletedMACS2peakCalling