Job ID = 2641145 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 26,354,996 reads read : 52,709,992 reads written : 52,709,992 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: 00:19:06 26354996 reads; of these: 26354996 (100.00%) were paired; of these: 4308853 (16.35%) aligned concordantly 0 times 17644527 (66.95%) aligned concordantly exactly 1 time 4401616 (16.70%) aligned concordantly >1 times ---- 4308853 pairs aligned concordantly 0 times; of these: 662337 (15.37%) aligned discordantly 1 time ---- 3646516 pairs aligned 0 times concordantly or discordantly; of these: 7293032 mates make up the pairs; of these: 5611309 (76.94%) aligned 0 times 799818 (10.97%) aligned exactly 1 time 881905 (12.09%) aligned >1 times 89.35% overall alignment rate Time searching: 00:19:06 Overall time: 00:19:06 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 20 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] 7437502 / 22129347 = 0.3361 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:19:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.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 22:19:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:19:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:20:02: 1000000 INFO @ Sat, 24 Aug 2019 22:20:09: 2000000 INFO @ Sat, 24 Aug 2019 22:20:15: 3000000 INFO @ Sat, 24 Aug 2019 22:20:21: 4000000 INFO @ Sat, 24 Aug 2019 22:20:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.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 22:20:25: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:20:25: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:20:28: 5000000 INFO @ Sat, 24 Aug 2019 22:20:34: 6000000 INFO @ Sat, 24 Aug 2019 22:20:35: 1000000 INFO @ Sat, 24 Aug 2019 22:20:41: 7000000 INFO @ Sat, 24 Aug 2019 22:20:44: 2000000 INFO @ Sat, 24 Aug 2019 22:20:47: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:20:54: 3000000 INFO @ Sat, 24 Aug 2019 22:20:54: 9000000 INFO @ Sat, 24 Aug 2019 22:20:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.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 22:20:55: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:20:55: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:21:00: 10000000 INFO @ Sat, 24 Aug 2019 22:21:03: 1000000 INFO @ Sat, 24 Aug 2019 22:21:03: 4000000 INFO @ Sat, 24 Aug 2019 22:21:07: 11000000 INFO @ Sat, 24 Aug 2019 22:21:10: 2000000 INFO @ Sat, 24 Aug 2019 22:21:13: 5000000 INFO @ Sat, 24 Aug 2019 22:21:14: 12000000 INFO @ Sat, 24 Aug 2019 22:21:18: 3000000 INFO @ Sat, 24 Aug 2019 22:21:20: 13000000 INFO @ Sat, 24 Aug 2019 22:21:22: 6000000 INFO @ Sat, 24 Aug 2019 22:21:25: 4000000 INFO @ Sat, 24 Aug 2019 22:21:27: 14000000 INFO @ Sat, 24 Aug 2019 22:21:32: 7000000 INFO @ Sat, 24 Aug 2019 22:21:33: 5000000 INFO @ Sat, 24 Aug 2019 22:21:33: 15000000 INFO @ Sat, 24 Aug 2019 22:21:40: 16000000 INFO @ Sat, 24 Aug 2019 22:21:40: 6000000 INFO @ Sat, 24 Aug 2019 22:21:41: 8000000 INFO @ Sat, 24 Aug 2019 22:21:47: 17000000 INFO @ Sat, 24 Aug 2019 22:21:48: 7000000 INFO @ Sat, 24 Aug 2019 22:21:51: 9000000 INFO @ Sat, 24 Aug 2019 22:21:53: 18000000 INFO @ Sat, 24 Aug 2019 22:21:55: 8000000 INFO @ Sat, 24 Aug 2019 22:22:00: 19000000 INFO @ Sat, 24 Aug 2019 22:22:00: 10000000 INFO @ Sat, 24 Aug 2019 22:22:02: 9000000 INFO @ Sat, 24 Aug 2019 22:22:06: 20000000 INFO @ Sat, 24 Aug 2019 22:22:10: 11000000 INFO @ Sat, 24 Aug 2019 22:22:10: 10000000 INFO @ Sat, 24 Aug 2019 22:22:13: 21000000 INFO @ Sat, 24 Aug 2019 22:22:17: 11000000 INFO @ Sat, 24 Aug 2019 22:22:19: 22000000 INFO @ Sat, 24 Aug 2019 22:22:19: 12000000 INFO @ Sat, 24 Aug 2019 22:22:25: 12000000 INFO @ Sat, 24 Aug 2019 22:22:26: 23000000 INFO @ Sat, 24 Aug 2019 22:22:29: 13000000 INFO @ Sat, 24 Aug 2019 22:22:32: 24000000 INFO @ Sat, 24 Aug 2019 22:22:32: 13000000 INFO @ Sat, 24 Aug 2019 22:22:38: 14000000 INFO @ Sat, 24 Aug 2019 22:22:39: 25000000 INFO @ Sat, 24 Aug 2019 22:22:40: 14000000 INFO @ Sat, 24 Aug 2019 22:22:45: 26000000 INFO @ Sat, 24 Aug 2019 22:22:47: 15000000 INFO @ Sat, 24 Aug 2019 22:22:47: 15000000 INFO @ Sat, 24 Aug 2019 22:22:52: 27000000 INFO @ Sat, 24 Aug 2019 22:22:55: 16000000 INFO @ Sat, 24 Aug 2019 22:22:57: 16000000 INFO @ Sat, 24 Aug 2019 22:22:59: 28000000 INFO @ Sat, 24 Aug 2019 22:23:02: 17000000 INFO @ Sat, 24 Aug 2019 22:23:05: 29000000 INFO @ Sat, 24 Aug 2019 22:23:06: 17000000 INFO @ Sat, 24 Aug 2019 22:23:10: 18000000 INFO @ Sat, 24 Aug 2019 22:23:12: 30000000 INFO @ Sat, 24 Aug 2019 22:23:16: 18000000 INFO @ Sat, 24 Aug 2019 22:23:17: 19000000 INFO @ Sat, 24 Aug 2019 22:23:18: 31000000 INFO @ Sat, 24 Aug 2019 22:23:25: 20000000 INFO @ Sat, 24 Aug 2019 22:23:25: 32000000 INFO @ Sat, 24 Aug 2019 22:23:25: 19000000 INFO @ Sat, 24 Aug 2019 22:23:26: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:23:26: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:23:26: #1 total tags in treatment: 14620273 INFO @ Sat, 24 Aug 2019 22:23:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:23:26: #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 22:23:27: #1 tags after filtering in treatment: 6101366 INFO @ Sat, 24 Aug 2019 22:23:27: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 24 Aug 2019 22:23:27: #1 finished! INFO @ Sat, 24 Aug 2019 22:23:27: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:23:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:23:27: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:23:27: 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 22:23:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.05_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/SRX5811100/SRX5811100.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:23:32: 21000000 INFO @ Sat, 24 Aug 2019 22:23:34: 20000000 INFO @ Sat, 24 Aug 2019 22:23:39: 22000000 INFO @ Sat, 24 Aug 2019 22:23:43: 21000000 INFO @ Sat, 24 Aug 2019 22:23:46: 23000000 INFO @ Sat, 24 Aug 2019 22:23:52: 22000000 INFO @ Sat, 24 Aug 2019 22:23:54: 24000000 INFO @ Sat, 24 Aug 2019 22:24:01: 25000000 INFO @ Sat, 24 Aug 2019 22:24:02: 23000000 INFO @ Sat, 24 Aug 2019 22:24:09: 26000000 INFO @ Sat, 24 Aug 2019 22:24:11: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:24:16: 27000000 INFO @ Sat, 24 Aug 2019 22:24:21: 25000000 INFO @ Sat, 24 Aug 2019 22:24:23: 28000000 INFO @ Sat, 24 Aug 2019 22:24:30: 26000000 INFO @ Sat, 24 Aug 2019 22:24:31: 29000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:24:38: 30000000 INFO @ Sat, 24 Aug 2019 22:24:39: 27000000 INFO @ Sat, 24 Aug 2019 22:24:45: 31000000 INFO @ Sat, 24 Aug 2019 22:24:49: 28000000 INFO @ Sat, 24 Aug 2019 22:24:53: 32000000 INFO @ Sat, 24 Aug 2019 22:24:54: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:24:54: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:24:54: #1 total tags in treatment: 14620273 INFO @ Sat, 24 Aug 2019 22:24:54: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:24:54: #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 22:24:55: #1 tags after filtering in treatment: 6101366 INFO @ Sat, 24 Aug 2019 22:24:55: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 24 Aug 2019 22:24:55: #1 finished! INFO @ Sat, 24 Aug 2019 22:24:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:24:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:24:55: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:24:55: 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 22:24:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.20_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/SRX5811100/SRX5811100.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:24:58: 29000000 INFO @ Sat, 24 Aug 2019 22:25:07: 30000000 INFO @ Sat, 24 Aug 2019 22:25:15: 31000000 INFO @ Sat, 24 Aug 2019 22:25:24: 32000000 INFO @ Sat, 24 Aug 2019 22:25:26: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:25:26: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:25:26: #1 total tags in treatment: 14620273 INFO @ Sat, 24 Aug 2019 22:25:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:25:26: #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 22:25:27: #1 tags after filtering in treatment: 6101366 INFO @ Sat, 24 Aug 2019 22:25:27: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 24 Aug 2019 22:25:27: #1 finished! INFO @ Sat, 24 Aug 2019 22:25:27: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:25:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:25:27: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:25:27: 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 22:25:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.10_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/SRX5811100/SRX5811100.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811100/SRX5811100.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling