Job ID = 2641206 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,977,459 reads read : 23,954,918 reads written : 23,954,918 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: 00:09:48 11977459 reads; of these: 11977459 (100.00%) were paired; of these: 8527060 (71.19%) aligned concordantly 0 times 3036042 (25.35%) aligned concordantly exactly 1 time 414357 (3.46%) aligned concordantly >1 times ---- 8527060 pairs aligned concordantly 0 times; of these: 3167521 (37.15%) aligned discordantly 1 time ---- 5359539 pairs aligned 0 times concordantly or discordantly; of these: 10719078 mates make up the pairs; of these: 5634693 (52.57%) aligned 0 times 3886918 (36.26%) aligned exactly 1 time 1197467 (11.17%) aligned >1 times 76.48% overall alignment rate Time searching: 00:09:48 Overall time: 00:09:48 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 8 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] 225331 / 3711327 = 0.0607 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:04:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.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, 24 Aug 2019 22:04:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:04:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:04:51: 1000000 INFO @ Sat, 24 Aug 2019 22:04:58: 2000000 INFO @ Sat, 24 Aug 2019 22:05:05: 3000000 INFO @ Sat, 24 Aug 2019 22:05:11: 4000000 INFO @ Sat, 24 Aug 2019 22:05:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.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, 24 Aug 2019 22:05:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:05:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:05:18: 5000000 INFO @ Sat, 24 Aug 2019 22:05:22: 1000000 INFO @ Sat, 24 Aug 2019 22:05:24: 6000000 INFO @ Sat, 24 Aug 2019 22:05:28: 2000000 INFO @ Sat, 24 Aug 2019 22:05:31: 7000000 INFO @ Sat, 24 Aug 2019 22:05:35: 3000000 INFO @ Sat, 24 Aug 2019 22:05:38: 8000000 INFO @ Sat, 24 Aug 2019 22:05:42: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:05:44: 9000000 INFO @ Sat, 24 Aug 2019 22:05:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.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, 24 Aug 2019 22:05:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:05:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:05:48: 5000000 INFO @ Sat, 24 Aug 2019 22:05:51: 10000000 INFO @ Sat, 24 Aug 2019 22:05:52: 1000000 INFO @ Sat, 24 Aug 2019 22:05:55: 6000000 INFO @ Sat, 24 Aug 2019 22:05:58: 11000000 INFO @ Sat, 24 Aug 2019 22:05:59: 2000000 INFO @ Sat, 24 Aug 2019 22:06:02: 7000000 INFO @ Sat, 24 Aug 2019 22:06:05: 3000000 INFO @ Sat, 24 Aug 2019 22:06:07: 12000000 INFO @ Sat, 24 Aug 2019 22:06:08: 8000000 INFO @ Sat, 24 Aug 2019 22:06:12: 4000000 INFO @ Sat, 24 Aug 2019 22:06:14: 13000000 INFO @ Sat, 24 Aug 2019 22:06:15: 9000000 INFO @ Sat, 24 Aug 2019 22:06:19: 5000000 INFO @ Sat, 24 Aug 2019 22:06:20: 14000000 INFO @ Sat, 24 Aug 2019 22:06:22: 10000000 INFO @ Sat, 24 Aug 2019 22:06:25: 6000000 INFO @ Sat, 24 Aug 2019 22:06:27: 15000000 INFO @ Sat, 24 Aug 2019 22:06:28: 11000000 INFO @ Sat, 24 Aug 2019 22:06:32: 7000000 INFO @ Sat, 24 Aug 2019 22:06:34: 16000000 INFO @ Sat, 24 Aug 2019 22:06:35: 12000000 INFO @ Sat, 24 Aug 2019 22:06:39: 8000000 INFO @ Sat, 24 Aug 2019 22:06:41: 17000000 INFO @ Sat, 24 Aug 2019 22:06:42: 13000000 INFO @ Sat, 24 Aug 2019 22:06:47: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:06:47: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:06:47: #1 total tags in treatment: 3225564 INFO @ Sat, 24 Aug 2019 22:06:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:06:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:06:47: #1 tags after filtering in treatment: 2313947 INFO @ Sat, 24 Aug 2019 22:06:47: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 24 Aug 2019 22:06:47: #1 finished! INFO @ Sat, 24 Aug 2019 22:06:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:06:47: #2 number of paired peaks: 30 WARNING @ Sat, 24 Aug 2019 22:06:47: Too few paired peaks (30) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 22:06:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:06:49: 14000000 INFO @ Sat, 24 Aug 2019 22:06:49: 9000000 INFO @ Sat, 24 Aug 2019 22:06:55: 15000000 INFO @ Sat, 24 Aug 2019 22:06:55: 10000000 INFO @ Sat, 24 Aug 2019 22:07:02: 16000000 INFO @ Sat, 24 Aug 2019 22:07:03: 11000000 INFO @ Sat, 24 Aug 2019 22:07:09: 17000000 INFO @ Sat, 24 Aug 2019 22:07:10: 12000000 INFO @ Sat, 24 Aug 2019 22:07:15: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:07:15: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:07:15: #1 total tags in treatment: 3225564 INFO @ Sat, 24 Aug 2019 22:07:15: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:07:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:07:15: #1 tags after filtering in treatment: 2313947 INFO @ Sat, 24 Aug 2019 22:07:15: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 24 Aug 2019 22:07:15: #1 finished! INFO @ Sat, 24 Aug 2019 22:07:15: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:07:15: #2 number of paired peaks: 30 WARNING @ Sat, 24 Aug 2019 22:07:15: Too few paired peaks (30) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 22:07:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:07:17: 13000000 INFO @ Sat, 24 Aug 2019 22:07:24: 14000000 INFO @ Sat, 24 Aug 2019 22:07:30: 15000000 INFO @ Sat, 24 Aug 2019 22:07:37: 16000000 INFO @ Sat, 24 Aug 2019 22:07:44: 17000000 INFO @ Sat, 24 Aug 2019 22:07:49: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:07:49: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:07:49: #1 total tags in treatment: 3225564 INFO @ Sat, 24 Aug 2019 22:07:49: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:07:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:07:49: #1 tags after filtering in treatment: 2313947 INFO @ Sat, 24 Aug 2019 22:07:49: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 24 Aug 2019 22:07:49: #1 finished! INFO @ Sat, 24 Aug 2019 22:07:49: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:07:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:07:50: #2 number of paired peaks: 30 WARNING @ Sat, 24 Aug 2019 22:07:50: Too few paired peaks (30) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 22:07:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811107/SRX5811107.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。