Job ID = 2641111 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,035,139 reads read : 24,070,278 reads written : 24,070,278 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: 00:18:33 12035139 reads; of these: 12035139 (100.00%) were paired; of these: 9221346 (76.62%) aligned concordantly 0 times 2503341 (20.80%) aligned concordantly exactly 1 time 310452 (2.58%) aligned concordantly >1 times ---- 9221346 pairs aligned concordantly 0 times; of these: 6903994 (74.87%) aligned discordantly 1 time ---- 2317352 pairs aligned 0 times concordantly or discordantly; of these: 4634704 mates make up the pairs; of these: 2642451 (57.01%) aligned 0 times 281283 (6.07%) aligned exactly 1 time 1710970 (36.92%) aligned >1 times 89.02% overall alignment rate Time searching: 00:18:33 Overall time: 00:18:33 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 12 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] 313958 / 9714714 = 0.0323 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:14:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.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 22:14:49: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:14:49: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:15:00: 1000000 INFO @ Sat, 24 Aug 2019 22:15:11: 2000000 INFO @ Sat, 24 Aug 2019 22:15:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.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 22:15:19: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:15:19: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:15:22: 3000000 INFO @ Sat, 24 Aug 2019 22:15:28: 1000000 INFO @ Sat, 24 Aug 2019 22:15:33: 4000000 INFO @ Sat, 24 Aug 2019 22:15:36: 2000000 INFO @ Sat, 24 Aug 2019 22:15:44: 5000000 INFO @ Sat, 24 Aug 2019 22:15:44: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:15:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.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 22:15:49: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:15:49: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:15:52: 4000000 INFO @ Sat, 24 Aug 2019 22:15:55: 6000000 INFO @ Sat, 24 Aug 2019 22:15:58: 1000000 INFO @ Sat, 24 Aug 2019 22:16:00: 5000000 INFO @ Sat, 24 Aug 2019 22:16:06: 2000000 INFO @ Sat, 24 Aug 2019 22:16:06: 7000000 INFO @ Sat, 24 Aug 2019 22:16:08: 6000000 INFO @ Sat, 24 Aug 2019 22:16:15: 3000000 INFO @ Sat, 24 Aug 2019 22:16:16: 7000000 INFO @ Sat, 24 Aug 2019 22:16:17: 8000000 INFO @ Sat, 24 Aug 2019 22:16:23: 4000000 INFO @ Sat, 24 Aug 2019 22:16:24: 8000000 INFO @ Sat, 24 Aug 2019 22:16:28: 9000000 INFO @ Sat, 24 Aug 2019 22:16:31: 5000000 INFO @ Sat, 24 Aug 2019 22:16:33: 9000000 INFO @ Sat, 24 Aug 2019 22:16:40: 10000000 INFO @ Sat, 24 Aug 2019 22:16:40: 6000000 INFO @ Sat, 24 Aug 2019 22:16:41: 10000000 INFO @ Sat, 24 Aug 2019 22:16:48: 7000000 INFO @ Sat, 24 Aug 2019 22:16:49: 11000000 INFO @ Sat, 24 Aug 2019 22:16:51: 11000000 INFO @ Sat, 24 Aug 2019 22:16:57: 8000000 INFO @ Sat, 24 Aug 2019 22:16:57: 12000000 INFO @ Sat, 24 Aug 2019 22:17:02: 12000000 INFO @ Sat, 24 Aug 2019 22:17:05: 13000000 INFO @ Sat, 24 Aug 2019 22:17:06: 9000000 INFO @ Sat, 24 Aug 2019 22:17:13: 14000000 INFO @ Sat, 24 Aug 2019 22:17:13: 13000000 INFO @ Sat, 24 Aug 2019 22:17:14: 10000000 INFO @ Sat, 24 Aug 2019 22:17:21: 15000000 INFO @ Sat, 24 Aug 2019 22:17:22: 11000000 INFO @ Sat, 24 Aug 2019 22:17:24: 14000000 INFO @ Sat, 24 Aug 2019 22:17:29: 16000000 INFO @ Sat, 24 Aug 2019 22:17:31: 12000000 INFO @ Sat, 24 Aug 2019 22:17:35: 15000000 INFO @ Sat, 24 Aug 2019 22:17:37: 17000000 INFO @ Sat, 24 Aug 2019 22:17:39: 13000000 INFO @ Sat, 24 Aug 2019 22:17:45: 18000000 INFO @ Sat, 24 Aug 2019 22:17:46: 16000000 INFO @ Sat, 24 Aug 2019 22:17:47: 14000000 INFO @ Sat, 24 Aug 2019 22:17:53: 19000000 INFO @ Sat, 24 Aug 2019 22:17:56: 15000000 INFO @ Sat, 24 Aug 2019 22:17:57: 17000000 INFO @ Sat, 24 Aug 2019 22:18:01: 20000000 INFO @ Sat, 24 Aug 2019 22:18:04: 16000000 INFO @ Sat, 24 Aug 2019 22:18:08: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:18:08: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:18:08: #1 total tags in treatment: 2730425 INFO @ Sat, 24 Aug 2019 22:18:08: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:18:08: #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 22:18:08: #1 tags after filtering in treatment: 2500585 INFO @ Sat, 24 Aug 2019 22:18:08: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 24 Aug 2019 22:18:08: #1 finished! INFO @ Sat, 24 Aug 2019 22:18:08: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:18:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:18:08: #2 number of paired peaks: 37 WARNING @ Sat, 24 Aug 2019 22:18:08: Too few paired peaks (37) 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 22:18:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.10_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/SRX5546552/SRX5546552.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:18:09: 18000000 INFO @ Sat, 24 Aug 2019 22:18:13: 17000000 INFO @ Sat, 24 Aug 2019 22:18:20: 19000000 INFO @ Sat, 24 Aug 2019 22:18:21: 18000000 INFO @ Sat, 24 Aug 2019 22:18:30: 19000000 INFO @ Sat, 24 Aug 2019 22:18:31: 20000000 INFO @ Sat, 24 Aug 2019 22:18:38: 20000000 INFO @ Sat, 24 Aug 2019 22:18:40: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:18:40: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:18:40: #1 total tags in treatment: 2730425 INFO @ Sat, 24 Aug 2019 22:18:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:18:40: #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 22:18:40: #1 tags after filtering in treatment: 2500585 INFO @ Sat, 24 Aug 2019 22:18:40: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 24 Aug 2019 22:18:40: #1 finished! INFO @ Sat, 24 Aug 2019 22:18:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:18:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:18:40: #2 number of paired peaks: 37 WARNING @ Sat, 24 Aug 2019 22:18:40: Too few paired peaks (37) 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 22:18:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.05_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/SRX5546552/SRX5546552.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:18:45: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:18:45: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:18:45: #1 total tags in treatment: 2730425 INFO @ Sat, 24 Aug 2019 22:18:45: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:18:45: #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 22:18:45: #1 tags after filtering in treatment: 2500585 INFO @ Sat, 24 Aug 2019 22:18:45: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 24 Aug 2019 22:18:45: #1 finished! INFO @ Sat, 24 Aug 2019 22:18:45: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:18:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:18:45: #2 number of paired peaks: 37 WARNING @ Sat, 24 Aug 2019 22:18:45: Too few paired peaks (37) 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 22:18:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.20_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/SRX5546552/SRX5546552.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546552/SRX5546552.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。