Job ID = 2641153 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,791,485 reads read : 25,582,970 reads written : 25,582,970 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: 00:09:35 12791485 reads; of these: 12791485 (100.00%) were paired; of these: 7920456 (61.92%) aligned concordantly 0 times 4101837 (32.07%) aligned concordantly exactly 1 time 769192 (6.01%) aligned concordantly >1 times ---- 7920456 pairs aligned concordantly 0 times; of these: 2479566 (31.31%) aligned discordantly 1 time ---- 5440890 pairs aligned 0 times concordantly or discordantly; of these: 10881780 mates make up the pairs; of these: 6324484 (58.12%) aligned 0 times 3331244 (30.61%) aligned exactly 1 time 1226052 (11.27%) aligned >1 times 75.28% overall alignment rate Time searching: 00:09:35 Overall time: 00:09:35 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 8 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] 451507 / 5102740 = 0.0885 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:03:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.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 22:03:51: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:03:51: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:03:57: 1000000 INFO @ Sat, 24 Aug 2019 22:04:04: 2000000 INFO @ Sat, 24 Aug 2019 22:04:11: 3000000 INFO @ Sat, 24 Aug 2019 22:04:17: 4000000 INFO @ Sat, 24 Aug 2019 22:04:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.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 22:04:21: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:04:21: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:04:24: 5000000 INFO @ Sat, 24 Aug 2019 22:04:28: 1000000 INFO @ Sat, 24 Aug 2019 22:04:31: 6000000 INFO @ Sat, 24 Aug 2019 22:04:36: 2000000 INFO @ Sat, 24 Aug 2019 22:04:38: 7000000 INFO @ Sat, 24 Aug 2019 22:04:44: 3000000 INFO @ Sat, 24 Aug 2019 22:04:45: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:04:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.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 22:04:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:04:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:04:52: 9000000 INFO @ Sat, 24 Aug 2019 22:04:52: 4000000 INFO @ Sat, 24 Aug 2019 22:04:57: 1000000 INFO @ Sat, 24 Aug 2019 22:04:59: 10000000 INFO @ Sat, 24 Aug 2019 22:05:00: 5000000 INFO @ Sat, 24 Aug 2019 22:05:04: 2000000 INFO @ Sat, 24 Aug 2019 22:05:05: 11000000 INFO @ Sat, 24 Aug 2019 22:05:08: 6000000 INFO @ Sat, 24 Aug 2019 22:05:11: 3000000 INFO @ Sat, 24 Aug 2019 22:05:12: 12000000 INFO @ Sat, 24 Aug 2019 22:05:16: 7000000 INFO @ Sat, 24 Aug 2019 22:05:18: 4000000 INFO @ Sat, 24 Aug 2019 22:05:19: 13000000 INFO @ Sat, 24 Aug 2019 22:05:24: 8000000 INFO @ Sat, 24 Aug 2019 22:05:25: 5000000 INFO @ Sat, 24 Aug 2019 22:05:26: 14000000 INFO @ Sat, 24 Aug 2019 22:05:32: 9000000 INFO @ Sat, 24 Aug 2019 22:05:32: 6000000 INFO @ Sat, 24 Aug 2019 22:05:33: 15000000 INFO @ Sat, 24 Aug 2019 22:05:39: 7000000 INFO @ Sat, 24 Aug 2019 22:05:39: 10000000 INFO @ Sat, 24 Aug 2019 22:05:40: 16000000 INFO @ Sat, 24 Aug 2019 22:05:46: 8000000 INFO @ Sat, 24 Aug 2019 22:05:47: 17000000 INFO @ Sat, 24 Aug 2019 22:05:47: 11000000 INFO @ Sat, 24 Aug 2019 22:05:53: 9000000 INFO @ Sat, 24 Aug 2019 22:05:54: 18000000 INFO @ Sat, 24 Aug 2019 22:05:55: 12000000 INFO @ Sat, 24 Aug 2019 22:05:56: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:05:56: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:05:56: #1 total tags in treatment: 4422611 INFO @ Sat, 24 Aug 2019 22:05:56: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:05:56: #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 22:05:56: #1 tags after filtering in treatment: 2924507 INFO @ Sat, 24 Aug 2019 22:05:56: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 24 Aug 2019 22:05:56: #1 finished! INFO @ Sat, 24 Aug 2019 22:05:56: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:05:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:05:57: #2 number of paired peaks: 31 WARNING @ Sat, 24 Aug 2019 22:05:57: Too few paired peaks (31) 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 22:05:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.05_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/SRX5811105/SRX5811105.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:05:59: 10000000 INFO @ Sat, 24 Aug 2019 22:06:03: 13000000 INFO @ Sat, 24 Aug 2019 22:06:06: 11000000 INFO @ Sat, 24 Aug 2019 22:06:11: 14000000 INFO @ Sat, 24 Aug 2019 22:06:13: 12000000 INFO @ Sat, 24 Aug 2019 22:06:19: 15000000 INFO @ Sat, 24 Aug 2019 22:06:20: 13000000 INFO @ Sat, 24 Aug 2019 22:06:26: 16000000 INFO @ Sat, 24 Aug 2019 22:06:27: 14000000 INFO @ Sat, 24 Aug 2019 22:06:33: 15000000 INFO @ Sat, 24 Aug 2019 22:06:34: 17000000 INFO @ Sat, 24 Aug 2019 22:06:40: 16000000 INFO @ Sat, 24 Aug 2019 22:06:42: 18000000 INFO @ Sat, 24 Aug 2019 22:06:45: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:06:45: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:06:45: #1 total tags in treatment: 4422611 INFO @ Sat, 24 Aug 2019 22:06:45: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:06:45: #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 22:06:45: #1 tags after filtering in treatment: 2924507 INFO @ Sat, 24 Aug 2019 22:06:45: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 24 Aug 2019 22:06:45: #1 finished! INFO @ Sat, 24 Aug 2019 22:06:45: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:06:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:06:45: #2 number of paired peaks: 31 WARNING @ Sat, 24 Aug 2019 22:06:45: Too few paired peaks (31) 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 22:06:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.10_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/SRX5811105/SRX5811105.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:06:47: 17000000 INFO @ Sat, 24 Aug 2019 22:06:53: 18000000 INFO @ Sat, 24 Aug 2019 22:06:56: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:06:56: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:06:56: #1 total tags in treatment: 4422611 INFO @ Sat, 24 Aug 2019 22:06:56: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:06:56: #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 22:06:56: #1 tags after filtering in treatment: 2924507 INFO @ Sat, 24 Aug 2019 22:06:56: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 24 Aug 2019 22:06:56: #1 finished! INFO @ Sat, 24 Aug 2019 22:06:56: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:06:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:06:56: #2 number of paired peaks: 31 WARNING @ Sat, 24 Aug 2019 22:06:56: Too few paired peaks (31) 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 22:06:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.20_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/SRX5811105/SRX5811105.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811105/SRX5811105.20_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。