Job ID = 2011899 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,331,867 reads read : 10,663,734 reads written : 10,663,734 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: 00:03:27 5331867 reads; of these: 5331867 (100.00%) were paired; of these: 508355 (9.53%) aligned concordantly 0 times 3710613 (69.59%) aligned concordantly exactly 1 time 1112899 (20.87%) aligned concordantly >1 times ---- 508355 pairs aligned concordantly 0 times; of these: 255940 (50.35%) aligned discordantly 1 time ---- 252415 pairs aligned 0 times concordantly or discordantly; of these: 504830 mates make up the pairs; of these: 270073 (53.50%) aligned 0 times 72132 (14.29%) aligned exactly 1 time 162625 (32.21%) aligned >1 times 97.47% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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] 324640 / 5077308 = 0.0639 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 06 Jul 2019 03:12:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.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, 06 Jul 2019 03:12:20: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:12:20: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:12:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.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, 06 Jul 2019 03:12:21: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:12:21: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:12:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.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, 06 Jul 2019 03:12:22: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:12:22: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:12:26: 1000000 INFO @ Sat, 06 Jul 2019 03:12:29: 1000000 INFO @ Sat, 06 Jul 2019 03:12:29: 1000000 INFO @ Sat, 06 Jul 2019 03:12:33: 2000000 INFO @ Sat, 06 Jul 2019 03:12:35: 2000000 INFO @ Sat, 06 Jul 2019 03:12:37: 2000000 INFO @ Sat, 06 Jul 2019 03:12:39: 3000000 INFO @ Sat, 06 Jul 2019 03:12:41: 3000000 INFO @ Sat, 06 Jul 2019 03:12:45: 4000000 INFO @ Sat, 06 Jul 2019 03:12:46: 3000000 INFO @ Sat, 06 Jul 2019 03:12:47: 4000000 INFO @ Sat, 06 Jul 2019 03:12:51: 5000000 INFO @ Sat, 06 Jul 2019 03:12:54: 4000000 INFO @ Sat, 06 Jul 2019 03:12:55: 5000000 INFO @ Sat, 06 Jul 2019 03:12:58: 6000000 INFO @ Sat, 06 Jul 2019 03:13:01: 5000000 INFO @ Sat, 06 Jul 2019 03:13:03: 6000000 INFO @ Sat, 06 Jul 2019 03:13:04: 7000000 INFO @ Sat, 06 Jul 2019 03:13:09: 6000000 INFO @ Sat, 06 Jul 2019 03:13:10: 8000000 INFO @ Sat, 06 Jul 2019 03:13:11: 7000000 INFO @ Sat, 06 Jul 2019 03:13:16: 9000000 INFO @ Sat, 06 Jul 2019 03:13:17: 7000000 INFO @ Sat, 06 Jul 2019 03:13:20: 8000000 INFO @ Sat, 06 Jul 2019 03:13:20: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:13:20: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:13:20: #1 total tags in treatment: 4506845 INFO @ Sat, 06 Jul 2019 03:13:20: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:13:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:13:21: #1 tags after filtering in treatment: 3320872 INFO @ Sat, 06 Jul 2019 03:13:21: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:13:21: #1 finished! INFO @ Sat, 06 Jul 2019 03:13:21: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:13:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:13:21: #2 number of paired peaks: 97 WARNING @ Sat, 06 Jul 2019 03:13:21: Too few paired peaks (97) 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, 06 Jul 2019 03:13:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.05_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/SRX5383672/SRX5383672.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:13:25: 8000000 INFO @ Sat, 06 Jul 2019 03:13:28: 9000000 INFO @ Sat, 06 Jul 2019 03:13:33: 9000000 INFO @ Sat, 06 Jul 2019 03:13:34: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:13:34: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:13:34: #1 total tags in treatment: 4506845 INFO @ Sat, 06 Jul 2019 03:13:34: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:13:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:13:34: #1 tags after filtering in treatment: 3320872 INFO @ Sat, 06 Jul 2019 03:13:34: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:13:34: #1 finished! INFO @ Sat, 06 Jul 2019 03:13:34: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:13:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:13:34: #2 number of paired peaks: 97 WARNING @ Sat, 06 Jul 2019 03:13:34: Too few paired peaks (97) 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, 06 Jul 2019 03:13:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.20_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/SRX5383672/SRX5383672.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:13:38: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:13:38: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:13:38: #1 total tags in treatment: 4506845 INFO @ Sat, 06 Jul 2019 03:13:38: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:13:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:13:38: #1 tags after filtering in treatment: 3320872 INFO @ Sat, 06 Jul 2019 03:13:38: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:13:38: #1 finished! INFO @ Sat, 06 Jul 2019 03:13:38: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:13:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:13:39: #2 number of paired peaks: 97 WARNING @ Sat, 06 Jul 2019 03:13:39: Too few paired peaks (97) 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, 06 Jul 2019 03:13:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.10_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/SRX5383672/SRX5383672.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383672/SRX5383672.10_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。