Job ID = 2641116 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,590,075 reads read : 23,180,150 reads written : 23,180,150 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: 00:16:15 11590075 reads; of these: 11590075 (100.00%) were paired; of these: 6130805 (52.90%) aligned concordantly 0 times 5073078 (43.77%) aligned concordantly exactly 1 time 386192 (3.33%) aligned concordantly >1 times ---- 6130805 pairs aligned concordantly 0 times; of these: 4195709 (68.44%) aligned discordantly 1 time ---- 1935096 pairs aligned 0 times concordantly or discordantly; of these: 3870192 mates make up the pairs; of these: 2522383 (65.17%) aligned 0 times 563123 (14.55%) aligned exactly 1 time 784686 (20.28%) aligned >1 times 89.12% overall alignment rate Time searching: 00:16:15 Overall time: 00:16:15 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] 1560570 / 9651889 = 0.1617 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:08:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.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 22:08:48: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:08:48: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:08:57: 1000000 INFO @ Sat, 24 Aug 2019 22:09:05: 2000000 INFO @ Sat, 24 Aug 2019 22:09:14: 3000000 INFO @ Sat, 24 Aug 2019 22:09:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.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 22:09:18: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:09:18: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:09:22: 4000000 INFO @ Sat, 24 Aug 2019 22:09:27: 1000000 INFO @ Sat, 24 Aug 2019 22:09:31: 5000000 INFO @ Sat, 24 Aug 2019 22:09:35: 2000000 INFO @ Sat, 24 Aug 2019 22:09:39: 6000000 INFO @ Sat, 24 Aug 2019 22:09:44: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:09:48: 7000000 INFO @ Sat, 24 Aug 2019 22:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.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 22:09:48: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:09:48: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:09:52: 4000000 INFO @ Sat, 24 Aug 2019 22:09:56: 8000000 INFO @ Sat, 24 Aug 2019 22:09:57: 1000000 INFO @ Sat, 24 Aug 2019 22:10:01: 5000000 INFO @ Sat, 24 Aug 2019 22:10:05: 9000000 INFO @ Sat, 24 Aug 2019 22:10:05: 2000000 INFO @ Sat, 24 Aug 2019 22:10:09: 6000000 INFO @ Sat, 24 Aug 2019 22:10:13: 10000000 INFO @ Sat, 24 Aug 2019 22:10:14: 3000000 INFO @ Sat, 24 Aug 2019 22:10:18: 7000000 INFO @ Sat, 24 Aug 2019 22:10:22: 11000000 INFO @ Sat, 24 Aug 2019 22:10:22: 4000000 INFO @ Sat, 24 Aug 2019 22:10:26: 8000000 INFO @ Sat, 24 Aug 2019 22:10:30: 12000000 INFO @ Sat, 24 Aug 2019 22:10:31: 5000000 INFO @ Sat, 24 Aug 2019 22:10:35: 9000000 INFO @ Sat, 24 Aug 2019 22:10:39: 13000000 INFO @ Sat, 24 Aug 2019 22:10:39: 6000000 INFO @ Sat, 24 Aug 2019 22:10:43: 10000000 INFO @ Sat, 24 Aug 2019 22:10:47: 14000000 INFO @ Sat, 24 Aug 2019 22:10:48: 7000000 INFO @ Sat, 24 Aug 2019 22:10:52: 11000000 INFO @ Sat, 24 Aug 2019 22:10:56: 15000000 INFO @ Sat, 24 Aug 2019 22:10:56: 8000000 INFO @ Sat, 24 Aug 2019 22:11:00: 12000000 INFO @ Sat, 24 Aug 2019 22:11:04: 16000000 INFO @ Sat, 24 Aug 2019 22:11:05: 9000000 INFO @ Sat, 24 Aug 2019 22:11:09: 13000000 INFO @ Sat, 24 Aug 2019 22:11:13: 10000000 INFO @ Sat, 24 Aug 2019 22:11:13: 17000000 INFO @ Sat, 24 Aug 2019 22:11:17: 14000000 INFO @ Sat, 24 Aug 2019 22:11:19: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:11:19: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:11:19: #1 total tags in treatment: 4578829 INFO @ Sat, 24 Aug 2019 22:11:19: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:11:19: #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 22:11:19: #1 tags after filtering in treatment: 3941610 INFO @ Sat, 24 Aug 2019 22:11:19: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 24 Aug 2019 22:11:19: #1 finished! INFO @ Sat, 24 Aug 2019 22:11:19: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:11:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:11:19: #2 number of paired peaks: 19 WARNING @ Sat, 24 Aug 2019 22:11:19: Too few paired peaks (19) 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 22:11:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.05_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/SRX5546555/SRX5546555.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:11:22: 11000000 INFO @ Sat, 24 Aug 2019 22:11:26: 15000000 INFO @ Sat, 24 Aug 2019 22:11:30: 12000000 INFO @ Sat, 24 Aug 2019 22:11:34: 16000000 INFO @ Sat, 24 Aug 2019 22:11:38: 13000000 INFO @ Sat, 24 Aug 2019 22:11:43: 17000000 INFO @ Sat, 24 Aug 2019 22:11:47: 14000000 INFO @ Sat, 24 Aug 2019 22:11:47: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:11:47: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:11:47: #1 total tags in treatment: 4578829 INFO @ Sat, 24 Aug 2019 22:11:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:11:47: #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 22:11:47: #1 tags after filtering in treatment: 3941610 INFO @ Sat, 24 Aug 2019 22:11:47: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 24 Aug 2019 22:11:47: #1 finished! INFO @ Sat, 24 Aug 2019 22:11:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:11:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:11:47: #2 number of paired peaks: 19 WARNING @ Sat, 24 Aug 2019 22:11:47: Too few paired peaks (19) 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 22:11:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.10_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/SRX5546555/SRX5546555.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:11:55: 15000000 INFO @ Sat, 24 Aug 2019 22:12:03: 16000000 INFO @ Sat, 24 Aug 2019 22:12:11: 17000000 INFO @ Sat, 24 Aug 2019 22:12:16: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:12:16: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:12:16: #1 total tags in treatment: 4578829 INFO @ Sat, 24 Aug 2019 22:12:16: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:12:16: #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 22:12:16: #1 tags after filtering in treatment: 3941610 INFO @ Sat, 24 Aug 2019 22:12:16: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 24 Aug 2019 22:12:16: #1 finished! INFO @ Sat, 24 Aug 2019 22:12:16: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:12:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:12:16: #2 number of paired peaks: 19 WARNING @ Sat, 24 Aug 2019 22:12:16: Too few paired peaks (19) 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 22:12:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.20_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/SRX5546555/SRX5546555.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546555/SRX5546555.20_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。