Job ID = 2641140 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 25,712,174 reads read : 51,424,348 reads written : 51,424,348 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: 00:31:11 25712174 reads; of these: 25712174 (100.00%) were paired; of these: 9372299 (36.45%) aligned concordantly 0 times 13672380 (53.17%) aligned concordantly exactly 1 time 2667495 (10.37%) aligned concordantly >1 times ---- 9372299 pairs aligned concordantly 0 times; of these: 3843641 (41.01%) aligned discordantly 1 time ---- 5528658 pairs aligned 0 times concordantly or discordantly; of these: 11057316 mates make up the pairs; of these: 9100215 (82.30%) aligned 0 times 451695 (4.09%) aligned exactly 1 time 1505406 (13.61%) aligned >1 times 82.30% overall alignment rate Time searching: 00:31:11 Overall time: 00:31:11 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] 3889924 / 19931139 = 0.1952 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:40:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.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 22:40:24: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:40:24: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:40:36: 1000000 INFO @ Sat, 24 Aug 2019 22:40:47: 2000000 INFO @ Sat, 24 Aug 2019 22:40:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.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 22:40:54: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:40:54: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:40:58: 3000000 INFO @ Sat, 24 Aug 2019 22:41:06: 1000000 INFO @ Sat, 24 Aug 2019 22:41:10: 4000000 INFO @ Sat, 24 Aug 2019 22:41:17: 2000000 INFO @ Sat, 24 Aug 2019 22:41:22: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:41:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.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 22:41:24: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:41:24: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:41:29: 3000000 INFO @ Sat, 24 Aug 2019 22:41:33: 6000000 INFO @ Sat, 24 Aug 2019 22:41:36: 1000000 INFO @ Sat, 24 Aug 2019 22:41:41: 4000000 INFO @ Sat, 24 Aug 2019 22:41:45: 7000000 INFO @ Sat, 24 Aug 2019 22:41:47: 2000000 INFO @ Sat, 24 Aug 2019 22:41:53: 5000000 INFO @ Sat, 24 Aug 2019 22:41:57: 8000000 INFO @ Sat, 24 Aug 2019 22:41:58: 3000000 INFO @ Sat, 24 Aug 2019 22:42:05: 6000000 INFO @ Sat, 24 Aug 2019 22:42:08: 9000000 INFO @ Sat, 24 Aug 2019 22:42:09: 4000000 INFO @ Sat, 24 Aug 2019 22:42:17: 7000000 INFO @ Sat, 24 Aug 2019 22:42:20: 10000000 INFO @ Sat, 24 Aug 2019 22:42:20: 5000000 INFO @ Sat, 24 Aug 2019 22:42:28: 8000000 INFO @ Sat, 24 Aug 2019 22:42:31: 11000000 INFO @ Sat, 24 Aug 2019 22:42:31: 6000000 INFO @ Sat, 24 Aug 2019 22:42:40: 9000000 INFO @ Sat, 24 Aug 2019 22:42:42: 12000000 INFO @ Sat, 24 Aug 2019 22:42:43: 7000000 INFO @ Sat, 24 Aug 2019 22:42:51: 10000000 INFO @ Sat, 24 Aug 2019 22:42:54: 8000000 INFO @ Sat, 24 Aug 2019 22:42:54: 13000000 INFO @ Sat, 24 Aug 2019 22:43:03: 11000000 INFO @ Sat, 24 Aug 2019 22:43:05: 9000000 INFO @ Sat, 24 Aug 2019 22:43:05: 14000000 INFO @ Sat, 24 Aug 2019 22:43:14: 12000000 INFO @ Sat, 24 Aug 2019 22:43:15: 10000000 INFO @ Sat, 24 Aug 2019 22:43:17: 15000000 INFO @ Sat, 24 Aug 2019 22:43:26: 13000000 INFO @ Sat, 24 Aug 2019 22:43:26: 11000000 INFO @ Sat, 24 Aug 2019 22:43:28: 16000000 INFO @ Sat, 24 Aug 2019 22:43:37: 14000000 INFO @ Sat, 24 Aug 2019 22:43:37: 12000000 INFO @ Sat, 24 Aug 2019 22:43:39: 17000000 INFO @ Sat, 24 Aug 2019 22:43:48: 13000000 INFO @ Sat, 24 Aug 2019 22:43:48: 15000000 INFO @ Sat, 24 Aug 2019 22:43:51: 18000000 INFO @ Sat, 24 Aug 2019 22:43:59: 14000000 INFO @ Sat, 24 Aug 2019 22:44:00: 16000000 INFO @ Sat, 24 Aug 2019 22:44:02: 19000000 INFO @ Sat, 24 Aug 2019 22:44:10: 15000000 INFO @ Sat, 24 Aug 2019 22:44:11: 17000000 INFO @ Sat, 24 Aug 2019 22:44:13: 20000000 INFO @ Sat, 24 Aug 2019 22:44:20: 16000000 INFO @ Sat, 24 Aug 2019 22:44:23: 18000000 INFO @ Sat, 24 Aug 2019 22:44:25: 21000000 INFO @ Sat, 24 Aug 2019 22:44:31: 17000000 INFO @ Sat, 24 Aug 2019 22:44:34: 19000000 INFO @ Sat, 24 Aug 2019 22:44:35: 22000000 INFO @ Sat, 24 Aug 2019 22:44:42: 18000000 INFO @ Sat, 24 Aug 2019 22:44:45: 20000000 INFO @ Sat, 24 Aug 2019 22:44:46: 23000000 INFO @ Sat, 24 Aug 2019 22:44:53: 19000000 INFO @ Sat, 24 Aug 2019 22:44:57: 21000000 INFO @ Sat, 24 Aug 2019 22:44:57: 24000000 INFO @ Sat, 24 Aug 2019 22:45:03: 20000000 INFO @ Sat, 24 Aug 2019 22:45:08: 22000000 INFO @ Sat, 24 Aug 2019 22:45:08: 25000000 INFO @ Sat, 24 Aug 2019 22:45:14: 21000000 INFO @ Sat, 24 Aug 2019 22:45:18: 23000000 INFO @ Sat, 24 Aug 2019 22:45:19: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:45:25: 22000000 INFO @ Sat, 24 Aug 2019 22:45:29: 24000000 INFO @ Sat, 24 Aug 2019 22:45:30: 27000000 INFO @ Sat, 24 Aug 2019 22:45:35: 23000000 INFO @ Sat, 24 Aug 2019 22:45:40: 25000000 INFO @ Sat, 24 Aug 2019 22:45:41: 28000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:45:45: 24000000 INFO @ Sat, 24 Aug 2019 22:45:51: 26000000 INFO @ Sat, 24 Aug 2019 22:45:52: 29000000 INFO @ Sat, 24 Aug 2019 22:45:56: 25000000 INFO @ Sat, 24 Aug 2019 22:46:02: 27000000 INFO @ Sat, 24 Aug 2019 22:46:03: 30000000 INFO @ Sat, 24 Aug 2019 22:46:06: 26000000 INFO @ Sat, 24 Aug 2019 22:46:13: 28000000 INFO @ Sat, 24 Aug 2019 22:46:13: 31000000 INFO @ Sat, 24 Aug 2019 22:46:17: 27000000 INFO @ Sat, 24 Aug 2019 22:46:24: 29000000 INFO @ Sat, 24 Aug 2019 22:46:24: 32000000 INFO @ Sat, 24 Aug 2019 22:46:27: 28000000 INFO @ Sat, 24 Aug 2019 22:46:35: 33000000 INFO @ Sat, 24 Aug 2019 22:46:35: 30000000 INFO @ Sat, 24 Aug 2019 22:46:38: 29000000 INFO @ Sat, 24 Aug 2019 22:46:46: 34000000 INFO @ Sat, 24 Aug 2019 22:46:46: 31000000 INFO @ Sat, 24 Aug 2019 22:46:48: 30000000 INFO @ Sat, 24 Aug 2019 22:46:52: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:46:52: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:46:52: #1 total tags in treatment: 13124701 INFO @ Sat, 24 Aug 2019 22:46:52: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:46:52: #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 22:46:52: #1 tags after filtering in treatment: 9159980 INFO @ Sat, 24 Aug 2019 22:46:52: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 24 Aug 2019 22:46:52: #1 finished! INFO @ Sat, 24 Aug 2019 22:46:52: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:46:53: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:46:53: 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 22:46:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.05_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/SRX5781918/SRX5781918.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:46:57: 32000000 INFO @ Sat, 24 Aug 2019 22:46:58: 31000000 INFO @ Sat, 24 Aug 2019 22:47:08: 33000000 INFO @ Sat, 24 Aug 2019 22:47:09: 32000000 INFO @ Sat, 24 Aug 2019 22:47:19: 34000000 INFO @ Sat, 24 Aug 2019 22:47:19: 33000000 INFO @ Sat, 24 Aug 2019 22:47:25: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:47:25: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:47:25: #1 total tags in treatment: 13124701 INFO @ Sat, 24 Aug 2019 22:47:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:47:25: #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 22:47:25: #1 tags after filtering in treatment: 9159980 INFO @ Sat, 24 Aug 2019 22:47:25: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 24 Aug 2019 22:47:25: #1 finished! INFO @ Sat, 24 Aug 2019 22:47:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:47:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:47:26: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:47:26: 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 22:47:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.10_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/SRX5781918/SRX5781918.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:47:29: 34000000 INFO @ Sat, 24 Aug 2019 22:47:35: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:47:35: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:47:35: #1 total tags in treatment: 13124701 INFO @ Sat, 24 Aug 2019 22:47:35: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:47:35: #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 22:47:35: #1 tags after filtering in treatment: 9159980 INFO @ Sat, 24 Aug 2019 22:47:35: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 24 Aug 2019 22:47:35: #1 finished! INFO @ Sat, 24 Aug 2019 22:47:35: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:47:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:47:36: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:47:36: 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 22:47:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.20_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/SRX5781918/SRX5781918.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5781918/SRX5781918.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling