Job ID = 2641155 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 36,466,487 reads read : 72,932,974 reads written : 72,932,974 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: 00:18:13 36466487 reads; of these: 36466487 (100.00%) were paired; of these: 15048775 (41.27%) aligned concordantly 0 times 18382210 (50.41%) aligned concordantly exactly 1 time 3035502 (8.32%) aligned concordantly >1 times ---- 15048775 pairs aligned concordantly 0 times; of these: 189383 (1.26%) aligned discordantly 1 time ---- 14859392 pairs aligned 0 times concordantly or discordantly; of these: 29718784 mates make up the pairs; of these: 28886753 (97.20%) aligned 0 times 476712 (1.60%) aligned exactly 1 time 355319 (1.20%) aligned >1 times 60.39% overall alignment rate Time searching: 00:18:13 Overall time: 00:18:13 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] 3934453 / 21512763 = 0.1829 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:26:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.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 22:26:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:26:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:26:45: 1000000 INFO @ Sat, 24 Aug 2019 22:26:52: 2000000 INFO @ Sat, 24 Aug 2019 22:26:57: 3000000 INFO @ Sat, 24 Aug 2019 22:27:03: 4000000 INFO @ Sat, 24 Aug 2019 22:27:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.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 22:27:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:27:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:27:08: 5000000 INFO @ Sat, 24 Aug 2019 22:27:13: 1000000 INFO @ Sat, 24 Aug 2019 22:27:14: 6000000 INFO @ Sat, 24 Aug 2019 22:27:19: 7000000 INFO @ Sat, 24 Aug 2019 22:27:20: 2000000 INFO @ Sat, 24 Aug 2019 22:27:25: 8000000 INFO @ Sat, 24 Aug 2019 22:27:26: 3000000 INFO @ Sat, 24 Aug 2019 22:27:30: 9000000 INFO @ Sat, 24 Aug 2019 22:27:33: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:27:36: 10000000 INFO @ Sat, 24 Aug 2019 22:27:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.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 22:27:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:27:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:27:40: 5000000 INFO @ Sat, 24 Aug 2019 22:27:41: 11000000 INFO @ Sat, 24 Aug 2019 22:27:44: 1000000 INFO @ Sat, 24 Aug 2019 22:27:47: 6000000 INFO @ Sat, 24 Aug 2019 22:27:47: 12000000 INFO @ Sat, 24 Aug 2019 22:27:50: 2000000 INFO @ Sat, 24 Aug 2019 22:27:53: 7000000 INFO @ Sat, 24 Aug 2019 22:27:54: 13000000 INFO @ Sat, 24 Aug 2019 22:27:57: 3000000 INFO @ Sat, 24 Aug 2019 22:28:00: 8000000 INFO @ Sat, 24 Aug 2019 22:28:01: 14000000 INFO @ Sat, 24 Aug 2019 22:28:04: 4000000 INFO @ Sat, 24 Aug 2019 22:28:06: 9000000 INFO @ Sat, 24 Aug 2019 22:28:08: 15000000 INFO @ Sat, 24 Aug 2019 22:28:10: 5000000 INFO @ Sat, 24 Aug 2019 22:28:13: 10000000 INFO @ Sat, 24 Aug 2019 22:28:15: 16000000 INFO @ Sat, 24 Aug 2019 22:28:17: 6000000 INFO @ Sat, 24 Aug 2019 22:28:19: 11000000 INFO @ Sat, 24 Aug 2019 22:28:22: 17000000 INFO @ Sat, 24 Aug 2019 22:28:24: 7000000 INFO @ Sat, 24 Aug 2019 22:28:26: 12000000 INFO @ Sat, 24 Aug 2019 22:28:29: 18000000 INFO @ Sat, 24 Aug 2019 22:28:30: 8000000 INFO @ Sat, 24 Aug 2019 22:28:32: 13000000 INFO @ Sat, 24 Aug 2019 22:28:35: 19000000 INFO @ Sat, 24 Aug 2019 22:28:37: 9000000 INFO @ Sat, 24 Aug 2019 22:28:38: 14000000 INFO @ Sat, 24 Aug 2019 22:28:42: 20000000 INFO @ Sat, 24 Aug 2019 22:28:43: 10000000 INFO @ Sat, 24 Aug 2019 22:28:44: 15000000 INFO @ Sat, 24 Aug 2019 22:28:49: 21000000 INFO @ Sat, 24 Aug 2019 22:28:50: 11000000 INFO @ Sat, 24 Aug 2019 22:28:50: 16000000 INFO @ Sat, 24 Aug 2019 22:28:56: 12000000 INFO @ Sat, 24 Aug 2019 22:28:56: 22000000 INFO @ Sat, 24 Aug 2019 22:28:56: 17000000 INFO @ Sat, 24 Aug 2019 22:29:02: 13000000 INFO @ Sat, 24 Aug 2019 22:29:03: 18000000 INFO @ Sat, 24 Aug 2019 22:29:03: 23000000 INFO @ Sat, 24 Aug 2019 22:29:08: 14000000 INFO @ Sat, 24 Aug 2019 22:29:09: 19000000 INFO @ Sat, 24 Aug 2019 22:29:10: 24000000 INFO @ Sat, 24 Aug 2019 22:29:14: 15000000 INFO @ Sat, 24 Aug 2019 22:29:15: 20000000 INFO @ Sat, 24 Aug 2019 22:29:17: 25000000 INFO @ Sat, 24 Aug 2019 22:29:20: 16000000 INFO @ Sat, 24 Aug 2019 22:29:21: 21000000 INFO @ Sat, 24 Aug 2019 22:29:25: 26000000 INFO @ Sat, 24 Aug 2019 22:29:27: 17000000 INFO @ Sat, 24 Aug 2019 22:29:28: 22000000 INFO @ Sat, 24 Aug 2019 22:29:32: 27000000 INFO @ Sat, 24 Aug 2019 22:29:33: 18000000 INFO @ Sat, 24 Aug 2019 22:29:34: 23000000 INFO @ Sat, 24 Aug 2019 22:29:39: 19000000 INFO @ Sat, 24 Aug 2019 22:29:39: 28000000 INFO @ Sat, 24 Aug 2019 22:29:40: 24000000 INFO @ Sat, 24 Aug 2019 22:29:45: 20000000 INFO @ Sat, 24 Aug 2019 22:29:46: 29000000 INFO @ Sat, 24 Aug 2019 22:29:46: 25000000 INFO @ Sat, 24 Aug 2019 22:29:51: 21000000 INFO @ Sat, 24 Aug 2019 22:29:53: 26000000 INFO @ Sat, 24 Aug 2019 22:29:53: 30000000 INFO @ Sat, 24 Aug 2019 22:29:57: 22000000 INFO @ Sat, 24 Aug 2019 22:29:59: 27000000 INFO @ Sat, 24 Aug 2019 22:30:00: 31000000 INFO @ Sat, 24 Aug 2019 22:30:03: 23000000 INFO @ Sat, 24 Aug 2019 22:30:05: 28000000 INFO @ Sat, 24 Aug 2019 22:30:07: 32000000 INFO @ Sat, 24 Aug 2019 22:30:10: 24000000 INFO @ Sat, 24 Aug 2019 22:30:12: 29000000 INFO @ Sat, 24 Aug 2019 22:30:14: 33000000 INFO @ Sat, 24 Aug 2019 22:30:17: 25000000 INFO @ Sat, 24 Aug 2019 22:30:18: 30000000 INFO @ Sat, 24 Aug 2019 22:30:21: 34000000 INFO @ Sat, 24 Aug 2019 22:30:23: 26000000 INFO @ Sat, 24 Aug 2019 22:30:25: 31000000 INFO @ Sat, 24 Aug 2019 22:30:28: 35000000 INFO @ Sat, 24 Aug 2019 22:30:30: 27000000 INFO @ Sat, 24 Aug 2019 22:30:31: 32000000 INFO @ Sat, 24 Aug 2019 22:30:36: 36000000 INFO @ Sat, 24 Aug 2019 22:30:36: 28000000 INFO @ Sat, 24 Aug 2019 22:30:37: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:30:37: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:30:37: #1 total tags in treatment: 17490301 INFO @ Sat, 24 Aug 2019 22:30:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:30:37: #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 22:30:38: 33000000 INFO @ Sat, 24 Aug 2019 22:30:38: #1 tags after filtering in treatment: 7602914 INFO @ Sat, 24 Aug 2019 22:30:38: #1 Redundant rate of treatment: 0.57 INFO @ Sat, 24 Aug 2019 22:30:38: #1 finished! INFO @ Sat, 24 Aug 2019 22:30:38: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:30:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:30:38: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:30:38: 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 22:30:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.05_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/SRX5811106/SRX5811106.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:30:43: 29000000 INFO @ Sat, 24 Aug 2019 22:30:44: 34000000 INFO @ Sat, 24 Aug 2019 22:30:49: 30000000 INFO @ Sat, 24 Aug 2019 22:30:50: 35000000 INFO @ Sat, 24 Aug 2019 22:30:56: 31000000 INFO @ Sat, 24 Aug 2019 22:30:57: 36000000 INFO @ Sat, 24 Aug 2019 22:30:58: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:30:58: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:30:58: #1 total tags in treatment: 17490301 INFO @ Sat, 24 Aug 2019 22:30:58: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:30:58: #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 22:30:58: #1 tags after filtering in treatment: 7602914 INFO @ Sat, 24 Aug 2019 22:30:58: #1 Redundant rate of treatment: 0.57 INFO @ Sat, 24 Aug 2019 22:30:58: #1 finished! INFO @ Sat, 24 Aug 2019 22:30:58: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:30:59: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:30:59: 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 22:30:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.10_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/SRX5811106/SRX5811106.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:31:02: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:31:07: 33000000 INFO @ Sat, 24 Aug 2019 22:31:13: 34000000 INFO @ Sat, 24 Aug 2019 22:31:20: 35000000 INFO @ Sat, 24 Aug 2019 22:31:25: 36000000 INFO @ Sat, 24 Aug 2019 22:31:27: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:31:27: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:31:27: #1 total tags in treatment: 17490301 INFO @ Sat, 24 Aug 2019 22:31:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:31:27: #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 22:31:27: #1 tags after filtering in treatment: 7602914 INFO @ Sat, 24 Aug 2019 22:31:27: #1 Redundant rate of treatment: 0.57 INFO @ Sat, 24 Aug 2019 22:31:27: #1 finished! INFO @ Sat, 24 Aug 2019 22:31:27: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:31:27: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:31:28: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:31:28: 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 22:31:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811106/SRX5811106.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling