Job ID = 2641143 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 27,848,013 reads read : 55,696,026 reads written : 55,696,026 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: 00:22:22 27848013 reads; of these: 27848013 (100.00%) were paired; of these: 6812627 (24.46%) aligned concordantly 0 times 18365675 (65.95%) aligned concordantly exactly 1 time 2669711 (9.59%) aligned concordantly >1 times ---- 6812627 pairs aligned concordantly 0 times; of these: 2952819 (43.34%) aligned discordantly 1 time ---- 3859808 pairs aligned 0 times concordantly or discordantly; of these: 7719616 mates make up the pairs; of these: 4869935 (63.09%) aligned 0 times 1647988 (21.35%) aligned exactly 1 time 1201693 (15.57%) aligned >1 times 91.26% overall alignment rate Time searching: 00:22:22 Overall time: 00:22:22 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_sort_core] merging from 24 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] 4706605 / 21481766 = 0.2191 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:24:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.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 22:24:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:24:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:24:41: 1000000 INFO @ Sat, 24 Aug 2019 22:24:48: 2000000 INFO @ Sat, 24 Aug 2019 22:24:56: 3000000 INFO @ Sat, 24 Aug 2019 22:25:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.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 22:25:02: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:25:02: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:25:03: 4000000 INFO @ Sat, 24 Aug 2019 22:25:09: 1000000 INFO @ Sat, 24 Aug 2019 22:25:11: 5000000 INFO @ Sat, 24 Aug 2019 22:25:15: 2000000 INFO @ Sat, 24 Aug 2019 22:25:18: 6000000 INFO @ Sat, 24 Aug 2019 22:25:22: 3000000 INFO @ Sat, 24 Aug 2019 22:25:26: 7000000 INFO @ Sat, 24 Aug 2019 22:25:28: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:25:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.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 22:25:32: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:25:32: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:25:34: 8000000 INFO @ Sat, 24 Aug 2019 22:25:35: 5000000 INFO @ Sat, 24 Aug 2019 22:25:40: 1000000 INFO @ Sat, 24 Aug 2019 22:25:41: 6000000 INFO @ Sat, 24 Aug 2019 22:25:41: 9000000 INFO @ Sat, 24 Aug 2019 22:25:47: 2000000 INFO @ Sat, 24 Aug 2019 22:25:47: 7000000 INFO @ Sat, 24 Aug 2019 22:25:49: 10000000 INFO @ Sat, 24 Aug 2019 22:25:54: 8000000 INFO @ Sat, 24 Aug 2019 22:25:55: 3000000 INFO @ Sat, 24 Aug 2019 22:25:56: 11000000 INFO @ Sat, 24 Aug 2019 22:26:01: 9000000 INFO @ Sat, 24 Aug 2019 22:26:03: 4000000 INFO @ Sat, 24 Aug 2019 22:26:04: 12000000 INFO @ Sat, 24 Aug 2019 22:26:07: 10000000 INFO @ Sat, 24 Aug 2019 22:26:11: 5000000 INFO @ Sat, 24 Aug 2019 22:26:12: 13000000 INFO @ Sat, 24 Aug 2019 22:26:14: 11000000 INFO @ Sat, 24 Aug 2019 22:26:19: 6000000 INFO @ Sat, 24 Aug 2019 22:26:20: 14000000 INFO @ Sat, 24 Aug 2019 22:26:20: 12000000 INFO @ Sat, 24 Aug 2019 22:26:27: 7000000 INFO @ Sat, 24 Aug 2019 22:26:27: 13000000 INFO @ Sat, 24 Aug 2019 22:26:28: 15000000 INFO @ Sat, 24 Aug 2019 22:26:33: 14000000 INFO @ Sat, 24 Aug 2019 22:26:35: 8000000 INFO @ Sat, 24 Aug 2019 22:26:36: 16000000 INFO @ Sat, 24 Aug 2019 22:26:40: 15000000 INFO @ Sat, 24 Aug 2019 22:26:42: 9000000 INFO @ Sat, 24 Aug 2019 22:26:43: 17000000 INFO @ Sat, 24 Aug 2019 22:26:46: 16000000 INFO @ Sat, 24 Aug 2019 22:26:50: 10000000 INFO @ Sat, 24 Aug 2019 22:26:51: 18000000 INFO @ Sat, 24 Aug 2019 22:26:53: 17000000 INFO @ Sat, 24 Aug 2019 22:26:58: 11000000 INFO @ Sat, 24 Aug 2019 22:26:58: 19000000 INFO @ Sat, 24 Aug 2019 22:26:59: 18000000 INFO @ Sat, 24 Aug 2019 22:27:06: 19000000 INFO @ Sat, 24 Aug 2019 22:27:06: 12000000 INFO @ Sat, 24 Aug 2019 22:27:06: 20000000 INFO @ Sat, 24 Aug 2019 22:27:12: 20000000 INFO @ Sat, 24 Aug 2019 22:27:13: 21000000 INFO @ Sat, 24 Aug 2019 22:27:14: 13000000 INFO @ Sat, 24 Aug 2019 22:27:19: 21000000 INFO @ Sat, 24 Aug 2019 22:27:21: 22000000 INFO @ Sat, 24 Aug 2019 22:27:22: 14000000 INFO @ Sat, 24 Aug 2019 22:27:25: 22000000 INFO @ Sat, 24 Aug 2019 22:27:29: 23000000 INFO @ Sat, 24 Aug 2019 22:27:29: 15000000 INFO @ Sat, 24 Aug 2019 22:27:31: 23000000 INFO @ Sat, 24 Aug 2019 22:27:37: 24000000 INFO @ Sat, 24 Aug 2019 22:27:37: 16000000 INFO @ Sat, 24 Aug 2019 22:27:37: 24000000 INFO @ Sat, 24 Aug 2019 22:27:44: 25000000 INFO @ Sat, 24 Aug 2019 22:27:44: 25000000 INFO @ Sat, 24 Aug 2019 22:27:45: 17000000 INFO @ Sat, 24 Aug 2019 22:27:50: 26000000 INFO @ Sat, 24 Aug 2019 22:27:52: 26000000 INFO @ Sat, 24 Aug 2019 22:27:53: 18000000 INFO @ Sat, 24 Aug 2019 22:27:56: 27000000 INFO @ Sat, 24 Aug 2019 22:27:59: 27000000 INFO @ Sat, 24 Aug 2019 22:28:01: 19000000 INFO @ Sat, 24 Aug 2019 22:28:03: 28000000 INFO @ Sat, 24 Aug 2019 22:28:07: 28000000 INFO @ Sat, 24 Aug 2019 22:28:08: 20000000 INFO @ Sat, 24 Aug 2019 22:28:09: 29000000 INFO @ Sat, 24 Aug 2019 22:28:15: 29000000 INFO @ Sat, 24 Aug 2019 22:28:15: 30000000 INFO @ Sat, 24 Aug 2019 22:28:16: 21000000 INFO @ Sat, 24 Aug 2019 22:28:21: 31000000 INFO @ Sat, 24 Aug 2019 22:28:22: 30000000 INFO @ Sat, 24 Aug 2019 22:28:22: 22000000 INFO @ Sat, 24 Aug 2019 22:28:27: 32000000 INFO @ Sat, 24 Aug 2019 22:28:30: 31000000 INFO @ Sat, 24 Aug 2019 22:28:30: 23000000 INFO @ Sat, 24 Aug 2019 22:28:34: 33000000 INFO @ Sat, 24 Aug 2019 22:28:38: 32000000 INFO @ Sat, 24 Aug 2019 22:28:38: 24000000 INFO @ Sat, 24 Aug 2019 22:28:40: 34000000 INFO @ Sat, 24 Aug 2019 22:28:45: 33000000 INFO @ Sat, 24 Aug 2019 22:28:45: 25000000 INFO @ Sat, 24 Aug 2019 22:28:46: 35000000 INFO @ Sat, 24 Aug 2019 22:28:53: 36000000 INFO @ Sat, 24 Aug 2019 22:28:53: 26000000 INFO @ Sat, 24 Aug 2019 22:28:53: 34000000 INFO @ Sat, 24 Aug 2019 22:28:59: 37000000 INFO @ Sat, 24 Aug 2019 22:29:00: 27000000 INFO @ Sat, 24 Aug 2019 22:29:01: 35000000 INFO @ Sat, 24 Aug 2019 22:29:05: 38000000 INFO @ Sat, 24 Aug 2019 22:29:08: 28000000 INFO @ Sat, 24 Aug 2019 22:29:08: 36000000 INFO @ Sat, 24 Aug 2019 22:29:11: 39000000 INFO @ Sat, 24 Aug 2019 22:29:15: 37000000 INFO @ Sat, 24 Aug 2019 22:29:15: 29000000 INFO @ Sat, 24 Aug 2019 22:29:17: 40000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:29:22: 38000000 INFO @ Sat, 24 Aug 2019 22:29:23: 41000000 INFO @ Sat, 24 Aug 2019 22:29:23: 30000000 INFO @ Sat, 24 Aug 2019 22:29:26: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:29:26: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:29:26: #1 total tags in treatment: 16357916 INFO @ Sat, 24 Aug 2019 22:29:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:29:26: #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 22:29:26: #1 tags after filtering in treatment: 6738074 INFO @ Sat, 24 Aug 2019 22:29:26: #1 Redundant rate of treatment: 0.59 INFO @ Sat, 24 Aug 2019 22:29:26: #1 finished! INFO @ Sat, 24 Aug 2019 22:29:26: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:29:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:29:27: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:29:27: Too few paired peaks (0) 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 22:29:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.10_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/SRX5811099/SRX5811099.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:29:30: 39000000 INFO @ Sat, 24 Aug 2019 22:29:31: 31000000 INFO @ Sat, 24 Aug 2019 22:29:37: 40000000 INFO @ Sat, 24 Aug 2019 22:29:38: 32000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:29:44: 41000000 INFO @ Sat, 24 Aug 2019 22:29:46: 33000000 INFO @ Sat, 24 Aug 2019 22:29:47: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:29:47: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:29:47: #1 total tags in treatment: 16357916 INFO @ Sat, 24 Aug 2019 22:29:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:29:47: #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 22:29:48: #1 tags after filtering in treatment: 6738074 INFO @ Sat, 24 Aug 2019 22:29:48: #1 Redundant rate of treatment: 0.59 INFO @ Sat, 24 Aug 2019 22:29:48: #1 finished! INFO @ Sat, 24 Aug 2019 22:29:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:29:48: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:29:48: Too few paired peaks (0) 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 22:29:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.05_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/SRX5811099/SRX5811099.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:29:53: 34000000 INFO @ Sat, 24 Aug 2019 22:30:01: 35000000 INFO @ Sat, 24 Aug 2019 22:30:08: 36000000 INFO @ Sat, 24 Aug 2019 22:30:16: 37000000 INFO @ Sat, 24 Aug 2019 22:30:23: 38000000 INFO @ Sat, 24 Aug 2019 22:30:30: 39000000 INFO @ Sat, 24 Aug 2019 22:30:39: 40000000 INFO @ Sat, 24 Aug 2019 22:30:46: 41000000 INFO @ Sat, 24 Aug 2019 22:30:49: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:30:49: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:30:49: #1 total tags in treatment: 16357916 INFO @ Sat, 24 Aug 2019 22:30:49: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:30:49: #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 22:30:50: #1 tags after filtering in treatment: 6738074 INFO @ Sat, 24 Aug 2019 22:30:50: #1 Redundant rate of treatment: 0.59 INFO @ Sat, 24 Aug 2019 22:30:50: #1 finished! INFO @ Sat, 24 Aug 2019 22:30:50: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:30:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:30:50: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:30:50: Too few paired peaks (0) 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 22:30:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.20_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/SRX5811099/SRX5811099.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811099/SRX5811099.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling