Job ID = 2641149 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,875,462 reads read : 11,750,924 reads written : 11,750,924 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: 00:04:22 5875462 reads; of these: 5875462 (100.00%) were paired; of these: 4596400 (78.23%) aligned concordantly 0 times 1111299 (18.91%) aligned concordantly exactly 1 time 167763 (2.86%) aligned concordantly >1 times ---- 4596400 pairs aligned concordantly 0 times; of these: 1385463 (30.14%) aligned discordantly 1 time ---- 3210937 pairs aligned 0 times concordantly or discordantly; of these: 6421874 mates make up the pairs; of these: 3794173 (59.08%) aligned 0 times 2055767 (32.01%) aligned exactly 1 time 571934 (8.91%) aligned >1 times 67.71% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 45864 / 1406281 = 0.0326 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:46:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.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 21:46:55: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:46:55: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:47:02: 1000000 INFO @ Sat, 24 Aug 2019 21:47:08: 2000000 INFO @ Sat, 24 Aug 2019 21:47:15: 3000000 INFO @ Sat, 24 Aug 2019 21:47:21: 4000000 INFO @ Sat, 24 Aug 2019 21:47:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.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 21:47:24: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:47:24: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:47:28: 5000000 INFO @ Sat, 24 Aug 2019 21:47:33: 1000000 INFO @ Sat, 24 Aug 2019 21:47:34: 6000000 INFO @ Sat, 24 Aug 2019 21:47:41: 7000000 INFO @ Sat, 24 Aug 2019 21:47:42: 2000000 INFO @ Sat, 24 Aug 2019 21:47:47: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:47:47: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:47:47: #1 total tags in treatment: 1233818 INFO @ Sat, 24 Aug 2019 21:47:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:47:47: #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 21:47:47: #1 tags after filtering in treatment: 1047888 INFO @ Sat, 24 Aug 2019 21:47:47: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 24 Aug 2019 21:47:47: #1 finished! INFO @ Sat, 24 Aug 2019 21:47:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:47:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:47:47: #2 number of paired peaks: 34 WARNING @ Sat, 24 Aug 2019 21:47:47: Too few paired peaks (34) 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 21:47:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.05_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/SRX5811103/SRX5811103.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:47:51: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:47:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.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 21:47:55: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:47:55: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:48:02: 4000000 INFO @ Sat, 24 Aug 2019 21:48:05: 1000000 INFO @ Sat, 24 Aug 2019 21:48:13: 5000000 INFO @ Sat, 24 Aug 2019 21:48:16: 2000000 INFO @ Sat, 24 Aug 2019 21:48:24: 6000000 INFO @ Sat, 24 Aug 2019 21:48:27: 3000000 INFO @ Sat, 24 Aug 2019 21:48:34: 7000000 INFO @ Sat, 24 Aug 2019 21:48:38: 4000000 INFO @ Sat, 24 Aug 2019 21:48:43: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:48:44: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:48:44: #1 total tags in treatment: 1233818 INFO @ Sat, 24 Aug 2019 21:48:44: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:48:44: #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 21:48:44: #1 tags after filtering in treatment: 1047888 INFO @ Sat, 24 Aug 2019 21:48:44: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 24 Aug 2019 21:48:44: #1 finished! INFO @ Sat, 24 Aug 2019 21:48:44: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:48:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:48:44: #2 number of paired peaks: 34 WARNING @ Sat, 24 Aug 2019 21:48:44: Too few paired peaks (34) 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 21:48:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.10_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/SRX5811103/SRX5811103.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:48:47: 5000000 INFO @ Sat, 24 Aug 2019 21:48:56: 6000000 INFO @ Sat, 24 Aug 2019 21:49:05: 7000000 INFO @ Sat, 24 Aug 2019 21:49:13: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:49:13: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:49:13: #1 total tags in treatment: 1233818 INFO @ Sat, 24 Aug 2019 21:49:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:49:13: #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 21:49:13: #1 tags after filtering in treatment: 1047888 INFO @ Sat, 24 Aug 2019 21:49:13: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 24 Aug 2019 21:49:13: #1 finished! INFO @ Sat, 24 Aug 2019 21:49:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:49:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:49:13: #2 number of paired peaks: 34 WARNING @ Sat, 24 Aug 2019 21:49:13: Too few paired peaks (34) 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 21:49:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.20_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/SRX5811103/SRX5811103.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811103/SRX5811103.20_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。