Job ID = 2641106 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,668,284 reads read : 25,336,568 reads written : 25,336,568 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: 00:17:30 12668284 reads; of these: 12668284 (100.00%) were paired; of these: 8025400 (63.35%) aligned concordantly 0 times 4295719 (33.91%) aligned concordantly exactly 1 time 347165 (2.74%) aligned concordantly >1 times ---- 8025400 pairs aligned concordantly 0 times; of these: 5735566 (71.47%) aligned discordantly 1 time ---- 2289834 pairs aligned 0 times concordantly or discordantly; of these: 4579668 mates make up the pairs; of these: 2699842 (58.95%) aligned 0 times 770779 (16.83%) aligned exactly 1 time 1109047 (24.22%) aligned >1 times 89.34% overall alignment rate Time searching: 00:17:30 Overall time: 00:17:30 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] 1380821 / 10373159 = 0.1331 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:11:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.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 22:11:16: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:11:16: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:11:25: 1000000 INFO @ Sat, 24 Aug 2019 22:11:35: 2000000 INFO @ Sat, 24 Aug 2019 22:11:44: 3000000 INFO @ Sat, 24 Aug 2019 22:11:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.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 22:11:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:11:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:11:53: 4000000 INFO @ Sat, 24 Aug 2019 22:11:55: 1000000 INFO @ Sat, 24 Aug 2019 22:12:03: 5000000 INFO @ Sat, 24 Aug 2019 22:12:04: 2000000 INFO @ Sat, 24 Aug 2019 22:12:11: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:12:14: 3000000 INFO @ Sat, 24 Aug 2019 22:12:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.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 22:12:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:12:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:12:21: 7000000 INFO @ Sat, 24 Aug 2019 22:12:23: 4000000 INFO @ Sat, 24 Aug 2019 22:12:25: 1000000 INFO @ Sat, 24 Aug 2019 22:12:30: 8000000 INFO @ Sat, 24 Aug 2019 22:12:32: 5000000 INFO @ Sat, 24 Aug 2019 22:12:35: 2000000 INFO @ Sat, 24 Aug 2019 22:12:40: 9000000 INFO @ Sat, 24 Aug 2019 22:12:42: 6000000 INFO @ Sat, 24 Aug 2019 22:12:44: 3000000 INFO @ Sat, 24 Aug 2019 22:12:50: 10000000 INFO @ Sat, 24 Aug 2019 22:12:51: 7000000 INFO @ Sat, 24 Aug 2019 22:12:54: 4000000 INFO @ Sat, 24 Aug 2019 22:12:59: 11000000 INFO @ Sat, 24 Aug 2019 22:13:01: 8000000 INFO @ Sat, 24 Aug 2019 22:13:03: 5000000 INFO @ Sat, 24 Aug 2019 22:13:09: 12000000 INFO @ Sat, 24 Aug 2019 22:13:10: 9000000 INFO @ Sat, 24 Aug 2019 22:13:13: 6000000 INFO @ Sat, 24 Aug 2019 22:13:19: 13000000 INFO @ Sat, 24 Aug 2019 22:13:20: 10000000 INFO @ Sat, 24 Aug 2019 22:13:22: 7000000 INFO @ Sat, 24 Aug 2019 22:13:28: 14000000 INFO @ Sat, 24 Aug 2019 22:13:29: 11000000 INFO @ Sat, 24 Aug 2019 22:13:31: 8000000 INFO @ Sat, 24 Aug 2019 22:13:38: 15000000 INFO @ Sat, 24 Aug 2019 22:13:38: 12000000 INFO @ Sat, 24 Aug 2019 22:13:41: 9000000 INFO @ Sat, 24 Aug 2019 22:13:48: 13000000 INFO @ Sat, 24 Aug 2019 22:13:48: 16000000 INFO @ Sat, 24 Aug 2019 22:13:50: 10000000 INFO @ Sat, 24 Aug 2019 22:13:57: 14000000 INFO @ Sat, 24 Aug 2019 22:13:57: 17000000 INFO @ Sat, 24 Aug 2019 22:13:59: 11000000 INFO @ Sat, 24 Aug 2019 22:14:06: 15000000 INFO @ Sat, 24 Aug 2019 22:14:07: 18000000 INFO @ Sat, 24 Aug 2019 22:14:09: 12000000 INFO @ Sat, 24 Aug 2019 22:14:15: 16000000 INFO @ Sat, 24 Aug 2019 22:14:16: 19000000 INFO @ Sat, 24 Aug 2019 22:14:18: 13000000 INFO @ Sat, 24 Aug 2019 22:14:25: 17000000 INFO @ Sat, 24 Aug 2019 22:14:25: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:14:25: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:14:25: #1 total tags in treatment: 3971888 INFO @ Sat, 24 Aug 2019 22:14:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:14:25: #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 22:14:25: #1 tags after filtering in treatment: 3487338 INFO @ Sat, 24 Aug 2019 22:14:25: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 24 Aug 2019 22:14:25: #1 finished! INFO @ Sat, 24 Aug 2019 22:14:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:14:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:14:25: #2 number of paired peaks: 31 WARNING @ Sat, 24 Aug 2019 22:14:25: 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 22:14:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.05_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/SRX5546547/SRX5546547.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:14:28: 14000000 INFO @ Sat, 24 Aug 2019 22:14:34: 18000000 INFO @ Sat, 24 Aug 2019 22:14:37: 15000000 INFO @ Sat, 24 Aug 2019 22:14:43: 19000000 INFO @ Sat, 24 Aug 2019 22:14:46: 16000000 INFO @ Sat, 24 Aug 2019 22:14:51: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:14:51: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:14:51: #1 total tags in treatment: 3971888 INFO @ Sat, 24 Aug 2019 22:14:51: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:14:51: #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 22:14:51: #1 tags after filtering in treatment: 3487338 INFO @ Sat, 24 Aug 2019 22:14:51: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 24 Aug 2019 22:14:51: #1 finished! INFO @ Sat, 24 Aug 2019 22:14:51: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:14:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:14:52: #2 number of paired peaks: 31 WARNING @ Sat, 24 Aug 2019 22:14:52: 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 22:14:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.10_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/SRX5546547/SRX5546547.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:14:55: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:15:05: 18000000 INFO @ Sat, 24 Aug 2019 22:15:14: 19000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:15:22: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:15:22: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:15:22: #1 total tags in treatment: 3971888 INFO @ Sat, 24 Aug 2019 22:15:22: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:15:22: #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 22:15:22: #1 tags after filtering in treatment: 3487338 INFO @ Sat, 24 Aug 2019 22:15:22: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 24 Aug 2019 22:15:22: #1 finished! INFO @ Sat, 24 Aug 2019 22:15:22: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:15:22: #2 number of paired peaks: 31 WARNING @ Sat, 24 Aug 2019 22:15:22: 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 22:15:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.20_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/SRX5546547/SRX5546547.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546547/SRX5546547.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling