Job ID = 2641252 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,252,764 reads read : 6,505,528 reads written : 6,505,528 spots read : 3,253,791 reads read : 6,507,582 reads written : 6,507,582 spots read : 3,368,629 reads read : 6,737,258 reads written : 6,737,258 spots read : 3,308,760 reads read : 6,617,520 reads written : 6,617,520 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: 00:06:03 13183944 reads; of these: 13183944 (100.00%) were paired; of these: 4692002 (35.59%) aligned concordantly 0 times 7489793 (56.81%) aligned concordantly exactly 1 time 1002149 (7.60%) aligned concordantly >1 times ---- 4692002 pairs aligned concordantly 0 times; of these: 14723 (0.31%) aligned discordantly 1 time ---- 4677279 pairs aligned 0 times concordantly or discordantly; of these: 9354558 mates make up the pairs; of these: 7728385 (82.62%) aligned 0 times 1396285 (14.93%) aligned exactly 1 time 229888 (2.46%) aligned >1 times 70.69% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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] 251298 / 8504273 = 0.0295 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:32:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.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 22:32:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:32:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:32:54: 1000000 INFO @ Sat, 24 Aug 2019 22:33:04: 2000000 INFO @ Sat, 24 Aug 2019 22:33:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.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 22:33:13: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:33:13: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:33:14: 3000000 INFO @ Sat, 24 Aug 2019 22:33:21: 1000000 INFO @ Sat, 24 Aug 2019 22:33:24: 4000000 INFO @ Sat, 24 Aug 2019 22:33:29: 2000000 INFO @ Sat, 24 Aug 2019 22:33:33: 5000000 INFO @ Sat, 24 Aug 2019 22:33:38: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:33:43: 6000000 INFO @ Sat, 24 Aug 2019 22:33:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.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 22:33:43: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:33:43: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:33:46: 4000000 INFO @ Sat, 24 Aug 2019 22:33:52: 1000000 INFO @ Sat, 24 Aug 2019 22:33:53: 7000000 INFO @ Sat, 24 Aug 2019 22:33:54: 5000000 INFO @ Sat, 24 Aug 2019 22:34:00: 2000000 INFO @ Sat, 24 Aug 2019 22:34:02: 6000000 INFO @ Sat, 24 Aug 2019 22:34:04: 8000000 INFO @ Sat, 24 Aug 2019 22:34:09: 3000000 INFO @ Sat, 24 Aug 2019 22:34:10: 7000000 INFO @ Sat, 24 Aug 2019 22:34:15: 9000000 INFO @ Sat, 24 Aug 2019 22:34:17: 4000000 INFO @ Sat, 24 Aug 2019 22:34:18: 8000000 INFO @ Sat, 24 Aug 2019 22:34:25: 5000000 INFO @ Sat, 24 Aug 2019 22:34:25: 10000000 INFO @ Sat, 24 Aug 2019 22:34:26: 9000000 INFO @ Sat, 24 Aug 2019 22:34:33: 6000000 INFO @ Sat, 24 Aug 2019 22:34:34: 10000000 INFO @ Sat, 24 Aug 2019 22:34:35: 11000000 INFO @ Sat, 24 Aug 2019 22:34:41: 7000000 INFO @ Sat, 24 Aug 2019 22:34:42: 11000000 INFO @ Sat, 24 Aug 2019 22:34:45: 12000000 INFO @ Sat, 24 Aug 2019 22:34:49: 8000000 INFO @ Sat, 24 Aug 2019 22:34:50: 12000000 INFO @ Sat, 24 Aug 2019 22:34:56: 13000000 INFO @ Sat, 24 Aug 2019 22:34:57: 9000000 INFO @ Sat, 24 Aug 2019 22:34:58: 13000000 INFO @ Sat, 24 Aug 2019 22:35:05: 10000000 INFO @ Sat, 24 Aug 2019 22:35:06: 14000000 INFO @ Sat, 24 Aug 2019 22:35:07: 14000000 INFO @ Sat, 24 Aug 2019 22:35:14: 11000000 INFO @ Sat, 24 Aug 2019 22:35:14: 15000000 INFO @ Sat, 24 Aug 2019 22:35:18: 15000000 INFO @ Sat, 24 Aug 2019 22:35:22: 16000000 INFO @ Sat, 24 Aug 2019 22:35:22: 12000000 INFO @ Sat, 24 Aug 2019 22:35:28: 16000000 INFO @ Sat, 24 Aug 2019 22:35:30: 17000000 INFO @ Sat, 24 Aug 2019 22:35:31: 13000000 INFO @ Sat, 24 Aug 2019 22:35:38: 18000000 INFO @ Sat, 24 Aug 2019 22:35:39: 17000000 INFO @ Sat, 24 Aug 2019 22:35:39: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:35:39: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:35:39: #1 total tags in treatment: 8240870 INFO @ Sat, 24 Aug 2019 22:35:39: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:35:39: #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 22:35:39: #1 tags after filtering in treatment: 6401939 INFO @ Sat, 24 Aug 2019 22:35:39: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 24 Aug 2019 22:35:39: #1 finished! INFO @ Sat, 24 Aug 2019 22:35:39: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:35:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:35:40: 14000000 INFO @ Sat, 24 Aug 2019 22:35:40: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:35:40: 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 22:35:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.10_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/SRX6403228/SRX6403228.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:35:48: 15000000 INFO @ Sat, 24 Aug 2019 22:35:49: 18000000 INFO @ Sat, 24 Aug 2019 22:35:50: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:35:50: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:35:50: #1 total tags in treatment: 8240870 INFO @ Sat, 24 Aug 2019 22:35:50: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:35:50: #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 22:35:51: #1 tags after filtering in treatment: 6401939 INFO @ Sat, 24 Aug 2019 22:35:51: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 24 Aug 2019 22:35:51: #1 finished! INFO @ Sat, 24 Aug 2019 22:35:51: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:35:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:35:51: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:35:51: 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 22:35:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.05_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/SRX6403228/SRX6403228.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:35:56: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:36:04: 17000000 INFO @ Sat, 24 Aug 2019 22:36:12: 18000000 INFO @ Sat, 24 Aug 2019 22:36:13: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:36:13: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:36:13: #1 total tags in treatment: 8240870 INFO @ Sat, 24 Aug 2019 22:36:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:36:13: #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 22:36:13: #1 tags after filtering in treatment: 6401939 INFO @ Sat, 24 Aug 2019 22:36:13: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 24 Aug 2019 22:36:13: #1 finished! INFO @ Sat, 24 Aug 2019 22:36:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:36:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:36:14: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:36:14: 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 22:36:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.20_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/SRX6403228/SRX6403228.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403228/SRX6403228.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。