Job ID = 2641151 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 32,821,294 reads read : 65,642,588 reads written : 65,642,588 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: 00:16:05 32821294 reads; of these: 32821294 (100.00%) were paired; of these: 14605773 (44.50%) aligned concordantly 0 times 16192964 (49.34%) aligned concordantly exactly 1 time 2022557 (6.16%) aligned concordantly >1 times ---- 14605773 pairs aligned concordantly 0 times; of these: 270219 (1.85%) aligned discordantly 1 time ---- 14335554 pairs aligned 0 times concordantly or discordantly; of these: 28671108 mates make up the pairs; of these: 27948567 (97.48%) aligned 0 times 451570 (1.58%) aligned exactly 1 time 270971 (0.95%) aligned >1 times 57.42% overall alignment rate Time searching: 00:16:05 Overall time: 00:16:05 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] 2749617 / 18327994 = 0.1500 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:19:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.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 22:19:42: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:19:42: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:19:48: 1000000 INFO @ Sat, 24 Aug 2019 22:19:54: 2000000 INFO @ Sat, 24 Aug 2019 22:20:00: 3000000 INFO @ Sat, 24 Aug 2019 22:20:06: 4000000 INFO @ Sat, 24 Aug 2019 22:20:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.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 22:20:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:20:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:20:12: 5000000 INFO @ Sat, 24 Aug 2019 22:20:18: 6000000 INFO @ Sat, 24 Aug 2019 22:20:20: 1000000 INFO @ Sat, 24 Aug 2019 22:20:24: 7000000 INFO @ Sat, 24 Aug 2019 22:20:29: 2000000 INFO @ Sat, 24 Aug 2019 22:20:30: 8000000 INFO @ Sat, 24 Aug 2019 22:20:36: 9000000 INFO @ Sat, 24 Aug 2019 22:20:37: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:20:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.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 22:20:42: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:20:42: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:20:42: 10000000 INFO @ Sat, 24 Aug 2019 22:20:45: 4000000 INFO @ Sat, 24 Aug 2019 22:20:49: 11000000 INFO @ Sat, 24 Aug 2019 22:20:49: 1000000 INFO @ Sat, 24 Aug 2019 22:20:54: 5000000 INFO @ Sat, 24 Aug 2019 22:20:55: 12000000 INFO @ Sat, 24 Aug 2019 22:20:56: 2000000 INFO @ Sat, 24 Aug 2019 22:21:01: 13000000 INFO @ Sat, 24 Aug 2019 22:21:02: 6000000 INFO @ Sat, 24 Aug 2019 22:21:03: 3000000 INFO @ Sat, 24 Aug 2019 22:21:07: 14000000 INFO @ Sat, 24 Aug 2019 22:21:10: 4000000 INFO @ Sat, 24 Aug 2019 22:21:10: 7000000 INFO @ Sat, 24 Aug 2019 22:21:13: 15000000 INFO @ Sat, 24 Aug 2019 22:21:17: 5000000 INFO @ Sat, 24 Aug 2019 22:21:19: 8000000 INFO @ Sat, 24 Aug 2019 22:21:19: 16000000 INFO @ Sat, 24 Aug 2019 22:21:24: 6000000 INFO @ Sat, 24 Aug 2019 22:21:25: 17000000 INFO @ Sat, 24 Aug 2019 22:21:27: 9000000 INFO @ Sat, 24 Aug 2019 22:21:30: 7000000 INFO @ Sat, 24 Aug 2019 22:21:32: 18000000 INFO @ Sat, 24 Aug 2019 22:21:35: 10000000 INFO @ Sat, 24 Aug 2019 22:21:37: 8000000 INFO @ Sat, 24 Aug 2019 22:21:38: 19000000 INFO @ Sat, 24 Aug 2019 22:21:43: 11000000 INFO @ Sat, 24 Aug 2019 22:21:44: 20000000 INFO @ Sat, 24 Aug 2019 22:21:44: 9000000 INFO @ Sat, 24 Aug 2019 22:21:50: 21000000 INFO @ Sat, 24 Aug 2019 22:21:51: 10000000 INFO @ Sat, 24 Aug 2019 22:21:52: 12000000 INFO @ Sat, 24 Aug 2019 22:21:56: 22000000 INFO @ Sat, 24 Aug 2019 22:21:58: 11000000 INFO @ Sat, 24 Aug 2019 22:22:00: 13000000 INFO @ Sat, 24 Aug 2019 22:22:02: 23000000 INFO @ Sat, 24 Aug 2019 22:22:05: 12000000 INFO @ Sat, 24 Aug 2019 22:22:08: 14000000 INFO @ Sat, 24 Aug 2019 22:22:08: 24000000 INFO @ Sat, 24 Aug 2019 22:22:12: 13000000 INFO @ Sat, 24 Aug 2019 22:22:14: 25000000 INFO @ Sat, 24 Aug 2019 22:22:16: 15000000 INFO @ Sat, 24 Aug 2019 22:22:18: 14000000 INFO @ Sat, 24 Aug 2019 22:22:20: 26000000 INFO @ Sat, 24 Aug 2019 22:22:24: 16000000 INFO @ Sat, 24 Aug 2019 22:22:25: 15000000 INFO @ Sat, 24 Aug 2019 22:22:26: 27000000 INFO @ Sat, 24 Aug 2019 22:22:32: 16000000 INFO @ Sat, 24 Aug 2019 22:22:32: 28000000 INFO @ Sat, 24 Aug 2019 22:22:33: 17000000 INFO @ Sat, 24 Aug 2019 22:22:39: 29000000 INFO @ Sat, 24 Aug 2019 22:22:39: 17000000 INFO @ Sat, 24 Aug 2019 22:22:41: 18000000 INFO @ Sat, 24 Aug 2019 22:22:45: 30000000 INFO @ Sat, 24 Aug 2019 22:22:46: 18000000 INFO @ Sat, 24 Aug 2019 22:22:49: 19000000 INFO @ Sat, 24 Aug 2019 22:22:51: 31000000 INFO @ Sat, 24 Aug 2019 22:22:53: 19000000 INFO @ Sat, 24 Aug 2019 22:22:57: 32000000 INFO @ Sat, 24 Aug 2019 22:22:57: 20000000 INFO @ Sat, 24 Aug 2019 22:22:58: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:22:58: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:22:58: #1 total tags in treatment: 15473095 INFO @ Sat, 24 Aug 2019 22:22:58: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:22:58: #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 22:22:58: #1 tags after filtering in treatment: 7183869 INFO @ Sat, 24 Aug 2019 22:22:58: #1 Redundant rate of treatment: 0.54 INFO @ Sat, 24 Aug 2019 22:22:58: #1 finished! INFO @ Sat, 24 Aug 2019 22:22:58: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:22:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:22:59: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:22:59: 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 22:22:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.05_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/SRX5811104/SRX5811104.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:23:00: 20000000 INFO @ Sat, 24 Aug 2019 22:23:06: 21000000 INFO @ Sat, 24 Aug 2019 22:23:07: 21000000 INFO @ Sat, 24 Aug 2019 22:23:14: 22000000 INFO @ Sat, 24 Aug 2019 22:23:14: 22000000 INFO @ Sat, 24 Aug 2019 22:23:21: 23000000 INFO @ Sat, 24 Aug 2019 22:23:23: 23000000 INFO @ Sat, 24 Aug 2019 22:23:28: 24000000 INFO @ Sat, 24 Aug 2019 22:23:31: 24000000 INFO @ Sat, 24 Aug 2019 22:23:34: 25000000 INFO @ Sat, 24 Aug 2019 22:23:39: 25000000 INFO @ Sat, 24 Aug 2019 22:23:41: 26000000 INFO @ Sat, 24 Aug 2019 22:23:47: 26000000 INFO @ Sat, 24 Aug 2019 22:23:48: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:23:55: 28000000 INFO @ Sat, 24 Aug 2019 22:23:55: 27000000 INFO @ Sat, 24 Aug 2019 22:24:01: 29000000 INFO @ Sat, 24 Aug 2019 22:24:03: 28000000 INFO @ Sat, 24 Aug 2019 22:24:08: 30000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:24:11: 29000000 INFO @ Sat, 24 Aug 2019 22:24:15: 31000000 INFO @ Sat, 24 Aug 2019 22:24:19: 30000000 INFO @ Sat, 24 Aug 2019 22:24:22: 32000000 INFO @ Sat, 24 Aug 2019 22:24:23: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:24:23: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:24:23: #1 total tags in treatment: 15473095 INFO @ Sat, 24 Aug 2019 22:24:23: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:24:23: #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 22:24:23: #1 tags after filtering in treatment: 7183869 INFO @ Sat, 24 Aug 2019 22:24:23: #1 Redundant rate of treatment: 0.54 INFO @ Sat, 24 Aug 2019 22:24:23: #1 finished! INFO @ Sat, 24 Aug 2019 22:24:23: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:24:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:24:24: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:24:24: 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 22:24:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.20_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/SRX5811104/SRX5811104.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:24:27: 31000000 INFO @ Sat, 24 Aug 2019 22:24:35: 32000000 INFO @ Sat, 24 Aug 2019 22:24:36: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:24:36: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:24:36: #1 total tags in treatment: 15473095 INFO @ Sat, 24 Aug 2019 22:24:36: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:24:36: #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 22:24:37: #1 tags after filtering in treatment: 7183869 INFO @ Sat, 24 Aug 2019 22:24:37: #1 Redundant rate of treatment: 0.54 INFO @ Sat, 24 Aug 2019 22:24:37: #1 finished! INFO @ Sat, 24 Aug 2019 22:24:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:24:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:24:37: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:24:37: 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 22:24:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.10_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/SRX5811104/SRX5811104.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811104/SRX5811104.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling