Job ID = 2641016 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,372,516 reads read : 2,745,032 reads written : 2,745,032 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: 00:00:50 1372516 reads; of these: 1372516 (100.00%) were paired; of these: 105608 (7.69%) aligned concordantly 0 times 1055426 (76.90%) aligned concordantly exactly 1 time 211482 (15.41%) aligned concordantly >1 times ---- 105608 pairs aligned concordantly 0 times; of these: 219 (0.21%) aligned discordantly 1 time ---- 105389 pairs aligned 0 times concordantly or discordantly; of these: 210778 mates make up the pairs; of these: 206012 (97.74%) aligned 0 times 3089 (1.47%) aligned exactly 1 time 1677 (0.80%) aligned >1 times 92.50% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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_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] 649858 / 1267077 = 0.5129 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:26:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.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 20:26:35: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:26:35: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:26:42: 1000000 INFO @ Sat, 24 Aug 2019 20:26:43: #1 tag size is determined as 32 bps INFO @ Sat, 24 Aug 2019 20:26:43: #1 tag size = 32 INFO @ Sat, 24 Aug 2019 20:26:43: #1 total tags in treatment: 617124 INFO @ Sat, 24 Aug 2019 20:26:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:26:43: #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 20:26:43: #1 tags after filtering in treatment: 538378 INFO @ Sat, 24 Aug 2019 20:26:43: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 24 Aug 2019 20:26:43: #1 finished! INFO @ Sat, 24 Aug 2019 20:26:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:26:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:26:44: #2 number of paired peaks: 33 WARNING @ Sat, 24 Aug 2019 20:26:44: Too few paired peaks (33) 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 20:26:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.05_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/SRX493936/SRX493936.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:27:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.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 20:27:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:27:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:27:10: 1000000 INFO @ Sat, 24 Aug 2019 20:27:12: #1 tag size is determined as 32 bps INFO @ Sat, 24 Aug 2019 20:27:12: #1 tag size = 32 INFO @ Sat, 24 Aug 2019 20:27:12: #1 total tags in treatment: 617124 INFO @ Sat, 24 Aug 2019 20:27:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:27:12: #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 20:27:12: #1 tags after filtering in treatment: 538378 INFO @ Sat, 24 Aug 2019 20:27:12: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 24 Aug 2019 20:27:12: #1 finished! INFO @ Sat, 24 Aug 2019 20:27:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:27:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:27:12: #2 number of paired peaks: 33 WARNING @ Sat, 24 Aug 2019 20:27:12: Too few paired peaks (33) 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 20:27:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.10_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/SRX493936/SRX493936.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:27:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.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 20:27:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:27:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:27:40: 1000000 INFO @ Sat, 24 Aug 2019 20:27:41: #1 tag size is determined as 32 bps INFO @ Sat, 24 Aug 2019 20:27:41: #1 tag size = 32 INFO @ Sat, 24 Aug 2019 20:27:41: #1 total tags in treatment: 617124 INFO @ Sat, 24 Aug 2019 20:27:41: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:27:41: #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 20:27:42: #1 tags after filtering in treatment: 538378 INFO @ Sat, 24 Aug 2019 20:27:42: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 24 Aug 2019 20:27:42: #1 finished! INFO @ Sat, 24 Aug 2019 20:27:42: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:27:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:27:42: #2 number of paired peaks: 33 WARNING @ Sat, 24 Aug 2019 20:27:42: Too few paired peaks (33) 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 20:27:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.20_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/SRX493936/SRX493936.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX493936/SRX493936.20_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。