Job ID = 2641129 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,166,997 reads read : 20,333,994 reads written : 20,333,994 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: 00:14:40 10166997 reads; of these: 10166997 (100.00%) were paired; of these: 3639886 (35.80%) aligned concordantly 0 times 5373905 (52.86%) aligned concordantly exactly 1 time 1153206 (11.34%) aligned concordantly >1 times ---- 3639886 pairs aligned concordantly 0 times; of these: 2495830 (68.57%) aligned discordantly 1 time ---- 1144056 pairs aligned 0 times concordantly or discordantly; of these: 2288112 mates make up the pairs; of these: 1101883 (48.16%) aligned 0 times 226267 (9.89%) aligned exactly 1 time 959962 (41.95%) aligned >1 times 94.58% overall alignment rate Time searching: 00:14:40 Overall time: 00:14:40 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] 614675 / 9018047 = 0.0682 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:09:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.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 22:09:35: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:09:35: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:09:47: 1000000 INFO @ Sat, 24 Aug 2019 22:09:56: 2000000 INFO @ Sat, 24 Aug 2019 22:10:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.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 22:10:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:10:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:10:05: 3000000 INFO @ Sat, 24 Aug 2019 22:10:14: 1000000 INFO @ Sat, 24 Aug 2019 22:10:15: 4000000 INFO @ Sat, 24 Aug 2019 22:10:24: 2000000 INFO @ Sat, 24 Aug 2019 22:10:24: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:10:34: 6000000 INFO @ Sat, 24 Aug 2019 22:10:34: 3000000 INFO @ Sat, 24 Aug 2019 22:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.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 22:10:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:10:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:10:43: 7000000 INFO @ Sat, 24 Aug 2019 22:10:44: 4000000 INFO @ Sat, 24 Aug 2019 22:10:47: 1000000 INFO @ Sat, 24 Aug 2019 22:10:53: 8000000 INFO @ Sat, 24 Aug 2019 22:10:54: 5000000 INFO @ Sat, 24 Aug 2019 22:11:00: 2000000 INFO @ Sat, 24 Aug 2019 22:11:03: 9000000 INFO @ Sat, 24 Aug 2019 22:11:04: 6000000 INFO @ Sat, 24 Aug 2019 22:11:12: 3000000 INFO @ Sat, 24 Aug 2019 22:11:13: 10000000 INFO @ Sat, 24 Aug 2019 22:11:15: 7000000 INFO @ Sat, 24 Aug 2019 22:11:22: 11000000 INFO @ Sat, 24 Aug 2019 22:11:25: 8000000 INFO @ Sat, 24 Aug 2019 22:11:25: 4000000 INFO @ Sat, 24 Aug 2019 22:11:32: 12000000 INFO @ Sat, 24 Aug 2019 22:11:35: 9000000 INFO @ Sat, 24 Aug 2019 22:11:38: 5000000 INFO @ Sat, 24 Aug 2019 22:11:42: 13000000 INFO @ Sat, 24 Aug 2019 22:11:45: 10000000 INFO @ Sat, 24 Aug 2019 22:11:50: 6000000 INFO @ Sat, 24 Aug 2019 22:11:52: 14000000 INFO @ Sat, 24 Aug 2019 22:11:55: 11000000 INFO @ Sat, 24 Aug 2019 22:12:02: 15000000 INFO @ Sat, 24 Aug 2019 22:12:03: 7000000 INFO @ Sat, 24 Aug 2019 22:12:05: 12000000 INFO @ Sat, 24 Aug 2019 22:12:12: 16000000 INFO @ Sat, 24 Aug 2019 22:12:15: 13000000 INFO @ Sat, 24 Aug 2019 22:12:15: 8000000 INFO @ Sat, 24 Aug 2019 22:12:22: 17000000 INFO @ Sat, 24 Aug 2019 22:12:25: 14000000 INFO @ Sat, 24 Aug 2019 22:12:28: 9000000 INFO @ Sat, 24 Aug 2019 22:12:32: 18000000 INFO @ Sat, 24 Aug 2019 22:12:32: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:12:32: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:12:32: #1 total tags in treatment: 6057229 INFO @ Sat, 24 Aug 2019 22:12:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:12:32: #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 22:12:32: #1 tags after filtering in treatment: 4756834 INFO @ Sat, 24 Aug 2019 22:12:32: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 22:12:32: #1 finished! INFO @ Sat, 24 Aug 2019 22:12:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:12:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:12:32: #2 number of paired peaks: 27 WARNING @ Sat, 24 Aug 2019 22:12:32: Too few paired peaks (27) 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 22:12:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.05_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/SRX5546566/SRX5546566.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:12:35: 15000000 INFO @ Sat, 24 Aug 2019 22:12:40: 10000000 INFO @ Sat, 24 Aug 2019 22:12:45: 16000000 INFO @ Sat, 24 Aug 2019 22:12:52: 11000000 INFO @ Sat, 24 Aug 2019 22:12:55: 17000000 INFO @ Sat, 24 Aug 2019 22:13:04: 12000000 INFO @ Sat, 24 Aug 2019 22:13:05: 18000000 INFO @ Sat, 24 Aug 2019 22:13:05: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:13:05: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:13:05: #1 total tags in treatment: 6057229 INFO @ Sat, 24 Aug 2019 22:13:05: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:13:05: #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 22:13:05: #1 tags after filtering in treatment: 4756834 INFO @ Sat, 24 Aug 2019 22:13:05: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 22:13:05: #1 finished! INFO @ Sat, 24 Aug 2019 22:13:05: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:13:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:13:05: #2 number of paired peaks: 27 WARNING @ Sat, 24 Aug 2019 22:13:05: Too few paired peaks (27) 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 22:13:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.10_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/SRX5546566/SRX5546566.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:13:15: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:13:27: 14000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:13:38: 15000000 INFO @ Sat, 24 Aug 2019 22:13:50: 16000000 INFO @ Sat, 24 Aug 2019 22:14:02: 17000000 INFO @ Sat, 24 Aug 2019 22:14:13: 18000000 INFO @ Sat, 24 Aug 2019 22:14:13: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:14:13: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:14:13: #1 total tags in treatment: 6057229 INFO @ Sat, 24 Aug 2019 22:14:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:14:13: #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 22:14:13: #1 tags after filtering in treatment: 4756834 INFO @ Sat, 24 Aug 2019 22:14:13: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 22:14:13: #1 finished! INFO @ Sat, 24 Aug 2019 22:14:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:14:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:14:14: #2 number of paired peaks: 27 WARNING @ Sat, 24 Aug 2019 22:14:14: Too few paired peaks (27) 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 22:14:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.20_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/SRX5546566/SRX5546566.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546566/SRX5546566.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling