Job ID = 4289519 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,248,253 reads read : 24,496,506 reads written : 24,496,506 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: 00:11:34 12248253 reads; of these: 12248253 (100.00%) were paired; of these: 1285116 (10.49%) aligned concordantly 0 times 9635830 (78.67%) aligned concordantly exactly 1 time 1327307 (10.84%) aligned concordantly >1 times ---- 1285116 pairs aligned concordantly 0 times; of these: 213845 (16.64%) aligned discordantly 1 time ---- 1071271 pairs aligned 0 times concordantly or discordantly; of these: 2142542 mates make up the pairs; of these: 1847053 (86.21%) aligned 0 times 190035 (8.87%) aligned exactly 1 time 105454 (4.92%) aligned >1 times 92.46% overall alignment rate Time searching: 00:11:34 Overall time: 00:11:34 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] 497909 / 11091289 = 0.0449 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:57:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.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 14:57:05: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:57:05: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:57:12: 1000000 INFO @ Tue, 10 Dec 2019 14:57:19: 2000000 INFO @ Tue, 10 Dec 2019 14:57:26: 3000000 INFO @ Tue, 10 Dec 2019 14:57:33: 4000000 INFO @ Tue, 10 Dec 2019 14:57:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.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 14:57:35: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:57:35: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:57:40: 5000000 INFO @ Tue, 10 Dec 2019 14:57:45: 1000000 INFO @ Tue, 10 Dec 2019 14:57:48: 6000000 INFO @ Tue, 10 Dec 2019 14:57:55: 2000000 INFO @ Tue, 10 Dec 2019 14:57:55: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:58:03: 8000000 INFO @ Tue, 10 Dec 2019 14:58:03: 3000000 INFO @ Tue, 10 Dec 2019 14:58:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.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 14:58:06: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:58:06: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:58:12: 9000000 INFO @ Tue, 10 Dec 2019 14:58:13: 4000000 INFO @ Tue, 10 Dec 2019 14:58:15: 1000000 INFO @ Tue, 10 Dec 2019 14:58:21: 10000000 INFO @ Tue, 10 Dec 2019 14:58:22: 5000000 INFO @ Tue, 10 Dec 2019 14:58:24: 2000000 INFO @ Tue, 10 Dec 2019 14:58:30: 11000000 INFO @ Tue, 10 Dec 2019 14:58:30: 6000000 INFO @ Tue, 10 Dec 2019 14:58:33: 3000000 INFO @ Tue, 10 Dec 2019 14:58:39: 12000000 INFO @ Tue, 10 Dec 2019 14:58:39: 7000000 INFO @ Tue, 10 Dec 2019 14:58:42: 4000000 INFO @ Tue, 10 Dec 2019 14:58:47: 13000000 INFO @ Tue, 10 Dec 2019 14:58:48: 8000000 INFO @ Tue, 10 Dec 2019 14:58:52: 5000000 INFO @ Tue, 10 Dec 2019 14:58:55: 14000000 INFO @ Tue, 10 Dec 2019 14:58:57: 9000000 INFO @ Tue, 10 Dec 2019 14:59:02: 6000000 INFO @ Tue, 10 Dec 2019 14:59:04: 15000000 INFO @ Tue, 10 Dec 2019 14:59:07: 10000000 INFO @ Tue, 10 Dec 2019 14:59:11: 7000000 INFO @ Tue, 10 Dec 2019 14:59:14: 16000000 INFO @ Tue, 10 Dec 2019 14:59:15: 11000000 INFO @ Tue, 10 Dec 2019 14:59:20: 8000000 INFO @ Tue, 10 Dec 2019 14:59:23: 12000000 INFO @ Tue, 10 Dec 2019 14:59:24: 17000000 INFO @ Tue, 10 Dec 2019 14:59:31: 9000000 INFO @ Tue, 10 Dec 2019 14:59:31: 13000000 INFO @ Tue, 10 Dec 2019 14:59:32: 18000000 INFO @ Tue, 10 Dec 2019 14:59:40: 14000000 INFO @ Tue, 10 Dec 2019 14:59:40: 19000000 INFO @ Tue, 10 Dec 2019 14:59:40: 10000000 INFO @ Tue, 10 Dec 2019 14:59:47: 20000000 INFO @ Tue, 10 Dec 2019 14:59:48: 15000000 INFO @ Tue, 10 Dec 2019 14:59:49: 11000000 INFO @ Tue, 10 Dec 2019 14:59:55: 21000000 INFO @ Tue, 10 Dec 2019 14:59:57: 16000000 INFO @ Tue, 10 Dec 2019 14:59:58: 12000000 INFO @ Tue, 10 Dec 2019 15:00:00: #1 tag size is determined as 42 bps INFO @ Tue, 10 Dec 2019 15:00:00: #1 tag size = 42 INFO @ Tue, 10 Dec 2019 15:00:00: #1 total tags in treatment: 10470008 INFO @ Tue, 10 Dec 2019 15:00:00: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:00:00: #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 15:00:00: #1 tags after filtering in treatment: 6609145 INFO @ Tue, 10 Dec 2019 15:00:00: #1 Redundant rate of treatment: 0.37 INFO @ Tue, 10 Dec 2019 15:00:00: #1 finished! INFO @ Tue, 10 Dec 2019 15:00:00: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:00:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:00:01: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:00:01: 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 15:00:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.05_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/SRX6742722/SRX6742722.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:00:04: 17000000 INFO @ Tue, 10 Dec 2019 15:00:06: 13000000 INFO @ Tue, 10 Dec 2019 15:00:12: 18000000 INFO @ Tue, 10 Dec 2019 15:00:15: 14000000 INFO @ Tue, 10 Dec 2019 15:00:19: 19000000 INFO @ Tue, 10 Dec 2019 15:00:23: 15000000 INFO @ Tue, 10 Dec 2019 15:00:26: 20000000 INFO @ Tue, 10 Dec 2019 15:00:32: 16000000 INFO @ Tue, 10 Dec 2019 15:00:33: 21000000 INFO @ Tue, 10 Dec 2019 15:00:39: #1 tag size is determined as 42 bps INFO @ Tue, 10 Dec 2019 15:00:39: #1 tag size = 42 INFO @ Tue, 10 Dec 2019 15:00:39: #1 total tags in treatment: 10470008 INFO @ Tue, 10 Dec 2019 15:00:39: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:00:39: #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 15:00:39: #1 tags after filtering in treatment: 6609145 INFO @ Tue, 10 Dec 2019 15:00:39: #1 Redundant rate of treatment: 0.37 INFO @ Tue, 10 Dec 2019 15:00:39: #1 finished! INFO @ Tue, 10 Dec 2019 15:00:39: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:00:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:00:40: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:00:40: 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 15:00:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.10_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/SRX6742722/SRX6742722.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:00:40: 17000000 INFO @ Tue, 10 Dec 2019 15:00:48: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 15:00:57: 19000000 INFO @ Tue, 10 Dec 2019 15:01:05: 20000000 BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 15:01:13: 21000000 INFO @ Tue, 10 Dec 2019 15:01:18: #1 tag size is determined as 42 bps INFO @ Tue, 10 Dec 2019 15:01:18: #1 tag size = 42 INFO @ Tue, 10 Dec 2019 15:01:18: #1 total tags in treatment: 10470008 INFO @ Tue, 10 Dec 2019 15:01:18: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:01:18: #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 15:01:19: #1 tags after filtering in treatment: 6609145 INFO @ Tue, 10 Dec 2019 15:01:19: #1 Redundant rate of treatment: 0.37 INFO @ Tue, 10 Dec 2019 15:01:19: #1 finished! INFO @ Tue, 10 Dec 2019 15:01:19: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:01:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:01:19: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:01:19: 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 15:01:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.20_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/SRX6742722/SRX6742722.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742722/SRX6742722.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling