Job ID = 4289014 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,833,441 reads read : 13,666,882 reads written : 13,666,882 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: 00:07:23 6833441 reads; of these: 6833441 (100.00%) were paired; of these: 555885 (8.13%) aligned concordantly 0 times 5695362 (83.35%) aligned concordantly exactly 1 time 582194 (8.52%) aligned concordantly >1 times ---- 555885 pairs aligned concordantly 0 times; of these: 136010 (24.47%) aligned discordantly 1 time ---- 419875 pairs aligned 0 times concordantly or discordantly; of these: 839750 mates make up the pairs; of these: 710260 (84.58%) aligned 0 times 91599 (10.91%) aligned exactly 1 time 37891 (4.51%) aligned >1 times 94.80% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 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] 395225 / 6411040 = 0.0616 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:30:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.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 @ Tue, 10 Dec 2019 13:30:25: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:30:25: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:30:36: 1000000 INFO @ Tue, 10 Dec 2019 13:30:47: 2000000 INFO @ Tue, 10 Dec 2019 13:30:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.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 @ Tue, 10 Dec 2019 13:30:54: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:30:54: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:30:59: 3000000 INFO @ Tue, 10 Dec 2019 13:31:03: 1000000 INFO @ Tue, 10 Dec 2019 13:31:11: 4000000 INFO @ Tue, 10 Dec 2019 13:31:12: 2000000 INFO @ Tue, 10 Dec 2019 13:31:20: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:31:23: 5000000 INFO @ Tue, 10 Dec 2019 13:31:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.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 @ Tue, 10 Dec 2019 13:31:25: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:31:25: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:31:29: 4000000 INFO @ Tue, 10 Dec 2019 13:31:35: 1000000 INFO @ Tue, 10 Dec 2019 13:31:35: 6000000 INFO @ Tue, 10 Dec 2019 13:31:39: 5000000 INFO @ Tue, 10 Dec 2019 13:31:45: 2000000 INFO @ Tue, 10 Dec 2019 13:31:48: 7000000 INFO @ Tue, 10 Dec 2019 13:31:49: 6000000 INFO @ Tue, 10 Dec 2019 13:31:55: 3000000 INFO @ Tue, 10 Dec 2019 13:31:59: 7000000 INFO @ Tue, 10 Dec 2019 13:32:00: 8000000 INFO @ Tue, 10 Dec 2019 13:32:05: 4000000 INFO @ Tue, 10 Dec 2019 13:32:09: 8000000 INFO @ Tue, 10 Dec 2019 13:32:13: 9000000 INFO @ Tue, 10 Dec 2019 13:32:14: 5000000 INFO @ Tue, 10 Dec 2019 13:32:18: 9000000 INFO @ Tue, 10 Dec 2019 13:32:23: 6000000 INFO @ Tue, 10 Dec 2019 13:32:25: 10000000 INFO @ Tue, 10 Dec 2019 13:32:26: 10000000 INFO @ Tue, 10 Dec 2019 13:32:31: 7000000 INFO @ Tue, 10 Dec 2019 13:32:35: 11000000 INFO @ Tue, 10 Dec 2019 13:32:37: 11000000 INFO @ Tue, 10 Dec 2019 13:32:40: 8000000 INFO @ Tue, 10 Dec 2019 13:32:44: 12000000 INFO @ Tue, 10 Dec 2019 13:32:45: #1 tag size is determined as 75 bps INFO @ Tue, 10 Dec 2019 13:32:45: #1 tag size = 75 INFO @ Tue, 10 Dec 2019 13:32:45: #1 total tags in treatment: 5883477 INFO @ Tue, 10 Dec 2019 13:32:45: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:32:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:32:46: #1 tags after filtering in treatment: 4748790 INFO @ Tue, 10 Dec 2019 13:32:46: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 10 Dec 2019 13:32:46: #1 finished! INFO @ Tue, 10 Dec 2019 13:32:46: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:32:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:32:46: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 13:32:46: Too few paired peaks (0) 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 @ Tue, 10 Dec 2019 13:32:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.10_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/SRX3205550/SRX3205550.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:32:49: 9000000 INFO @ Tue, 10 Dec 2019 13:32:49: 12000000 INFO @ Tue, 10 Dec 2019 13:32:51: #1 tag size is determined as 75 bps INFO @ Tue, 10 Dec 2019 13:32:51: #1 tag size = 75 INFO @ Tue, 10 Dec 2019 13:32:51: #1 total tags in treatment: 5883477 INFO @ Tue, 10 Dec 2019 13:32:51: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:32:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:32:51: #1 tags after filtering in treatment: 4748790 INFO @ Tue, 10 Dec 2019 13:32:51: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 10 Dec 2019 13:32:51: #1 finished! INFO @ Tue, 10 Dec 2019 13:32:51: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:32:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:32:52: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 13:32:52: Too few paired peaks (0) 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 @ Tue, 10 Dec 2019 13:32:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.05_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/SRX3205550/SRX3205550.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:32:57: 10000000 INFO @ Tue, 10 Dec 2019 13:33:04: 11000000 INFO @ Tue, 10 Dec 2019 13:33:12: 12000000 INFO @ Tue, 10 Dec 2019 13:33:14: #1 tag size is determined as 75 bps INFO @ Tue, 10 Dec 2019 13:33:14: #1 tag size = 75 INFO @ Tue, 10 Dec 2019 13:33:14: #1 total tags in treatment: 5883477 INFO @ Tue, 10 Dec 2019 13:33:14: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:33:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:33:14: #1 tags after filtering in treatment: 4748790 INFO @ Tue, 10 Dec 2019 13:33:14: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 10 Dec 2019 13:33:14: #1 finished! INFO @ Tue, 10 Dec 2019 13:33:14: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:33:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:33:14: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 13:33:14: Too few paired peaks (0) 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 @ Tue, 10 Dec 2019 13:33:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.20_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/SRX3205550/SRX3205550.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205550/SRX3205550.20_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。