Job ID = 2641242 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,236,824 reads read : 6,473,648 reads written : 6,473,648 spots read : 3,183,440 reads read : 6,366,880 reads written : 6,366,880 spots read : 3,218,612 reads read : 6,437,224 reads written : 6,437,224 spots read : 3,180,612 reads read : 6,361,224 reads written : 6,361,224 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: 00:05:46 12819488 reads; of these: 12819488 (100.00%) were paired; of these: 5617999 (43.82%) aligned concordantly 0 times 6670557 (52.03%) aligned concordantly exactly 1 time 530932 (4.14%) aligned concordantly >1 times ---- 5617999 pairs aligned concordantly 0 times; of these: 466734 (8.31%) aligned discordantly 1 time ---- 5151265 pairs aligned 0 times concordantly or discordantly; of these: 10302530 mates make up the pairs; of these: 8172049 (79.32%) aligned 0 times 1903912 (18.48%) aligned exactly 1 time 226569 (2.20%) aligned >1 times 68.13% overall alignment rate Time searching: 00:05:46 Overall time: 00:05:46 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] 232586 / 7257178 = 0.0320 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:28:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.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 22:28:40: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:28:40: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:28:47: 1000000 INFO @ Sat, 24 Aug 2019 22:28:54: 2000000 INFO @ Sat, 24 Aug 2019 22:29:01: 3000000 INFO @ Sat, 24 Aug 2019 22:29:08: 4000000 INFO @ Sat, 24 Aug 2019 22:29:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.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 22:29:10: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:29:10: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:29:15: 5000000 INFO @ Sat, 24 Aug 2019 22:29:17: 1000000 INFO @ Sat, 24 Aug 2019 22:29:23: 6000000 INFO @ Sat, 24 Aug 2019 22:29:25: 2000000 INFO @ Sat, 24 Aug 2019 22:29:30: 7000000 INFO @ Sat, 24 Aug 2019 22:29:33: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:29:37: 8000000 INFO @ Sat, 24 Aug 2019 22:29:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.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 22:29:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:29:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:29:41: 4000000 INFO @ Sat, 24 Aug 2019 22:29:45: 9000000 INFO @ Sat, 24 Aug 2019 22:29:47: 1000000 INFO @ Sat, 24 Aug 2019 22:29:49: 5000000 INFO @ Sat, 24 Aug 2019 22:29:52: 10000000 INFO @ Sat, 24 Aug 2019 22:29:54: 2000000 INFO @ Sat, 24 Aug 2019 22:29:56: 6000000 INFO @ Sat, 24 Aug 2019 22:30:00: 11000000 INFO @ Sat, 24 Aug 2019 22:30:02: 3000000 INFO @ Sat, 24 Aug 2019 22:30:04: 7000000 INFO @ Sat, 24 Aug 2019 22:30:07: 12000000 INFO @ Sat, 24 Aug 2019 22:30:09: 4000000 INFO @ Sat, 24 Aug 2019 22:30:12: 8000000 INFO @ Sat, 24 Aug 2019 22:30:14: 13000000 INFO @ Sat, 24 Aug 2019 22:30:17: 5000000 INFO @ Sat, 24 Aug 2019 22:30:20: 9000000 INFO @ Sat, 24 Aug 2019 22:30:22: 14000000 INFO @ Sat, 24 Aug 2019 22:30:24: 6000000 INFO @ Sat, 24 Aug 2019 22:30:28: 10000000 INFO @ Sat, 24 Aug 2019 22:30:29: 15000000 INFO @ Sat, 24 Aug 2019 22:30:32: 7000000 INFO @ Sat, 24 Aug 2019 22:30:36: 11000000 INFO @ Sat, 24 Aug 2019 22:30:37: 16000000 INFO @ Sat, 24 Aug 2019 22:30:39: 8000000 INFO @ Sat, 24 Aug 2019 22:30:43: 12000000 INFO @ Sat, 24 Aug 2019 22:30:44: 17000000 INFO @ Sat, 24 Aug 2019 22:30:44: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:30:44: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:30:44: #1 total tags in treatment: 6970123 INFO @ Sat, 24 Aug 2019 22:30:44: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:30:44: #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 22:30:45: #1 tags after filtering in treatment: 5435766 INFO @ Sat, 24 Aug 2019 22:30:45: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 24 Aug 2019 22:30:45: #1 finished! INFO @ Sat, 24 Aug 2019 22:30:45: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:30:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:30:45: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:30:45: 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 22:30:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.05_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/SRX6403219/SRX6403219.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:30:47: 9000000 INFO @ Sat, 24 Aug 2019 22:30:53: 13000000 INFO @ Sat, 24 Aug 2019 22:30:57: 10000000 INFO @ Sat, 24 Aug 2019 22:31:02: 14000000 INFO @ Sat, 24 Aug 2019 22:31:05: 11000000 INFO @ Sat, 24 Aug 2019 22:31:09: 15000000 INFO @ Sat, 24 Aug 2019 22:31:13: 12000000 INFO @ Sat, 24 Aug 2019 22:31:17: 16000000 INFO @ Sat, 24 Aug 2019 22:31:20: 13000000 INFO @ Sat, 24 Aug 2019 22:31:25: 17000000 INFO @ Sat, 24 Aug 2019 22:31:25: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:31:25: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:31:25: #1 total tags in treatment: 6970123 INFO @ Sat, 24 Aug 2019 22:31:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:31:25: #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 22:31:25: #1 tags after filtering in treatment: 5435766 INFO @ Sat, 24 Aug 2019 22:31:25: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 24 Aug 2019 22:31:25: #1 finished! INFO @ Sat, 24 Aug 2019 22:31:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:31:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:31:25: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:31:25: 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 22:31:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.10_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/SRX6403219/SRX6403219.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:31:27: 14000000 INFO @ Sat, 24 Aug 2019 22:31:34: 15000000 INFO @ Sat, 24 Aug 2019 22:31:41: 16000000 INFO @ Sat, 24 Aug 2019 22:31:48: 17000000 INFO @ Sat, 24 Aug 2019 22:31:48: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:31:48: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:31:48: #1 total tags in treatment: 6970123 INFO @ Sat, 24 Aug 2019 22:31:48: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:31:48: #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 22:31:48: #1 tags after filtering in treatment: 5435766 INFO @ Sat, 24 Aug 2019 22:31:48: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 24 Aug 2019 22:31:48: #1 finished! INFO @ Sat, 24 Aug 2019 22:31:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:31:48: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:31:48: 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 22:31:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.20_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/SRX6403219/SRX6403219.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403219/SRX6403219.20_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。