Job ID = 4289520 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 15,469,503 reads read : 30,939,006 reads written : 30,939,006 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: 00:12:24 15469503 reads; of these: 15469503 (100.00%) were paired; of these: 1710447 (11.06%) aligned concordantly 0 times 11935933 (77.16%) aligned concordantly exactly 1 time 1823123 (11.79%) aligned concordantly >1 times ---- 1710447 pairs aligned concordantly 0 times; of these: 238324 (13.93%) aligned discordantly 1 time ---- 1472123 pairs aligned 0 times concordantly or discordantly; of these: 2944246 mates make up the pairs; of these: 2584163 (87.77%) aligned 0 times 230107 (7.82%) aligned exactly 1 time 129976 (4.41%) aligned >1 times 91.65% overall alignment rate Time searching: 00:12:24 Overall time: 00:12:24 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] 624420 / 13856940 = 0.0451 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 15:00:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.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 15:00:27: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:00:27: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:00:35: 1000000 INFO @ Tue, 10 Dec 2019 15:00:42: 2000000 INFO @ Tue, 10 Dec 2019 15:00:50: 3000000 INFO @ Tue, 10 Dec 2019 15:00:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.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 15:00:57: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:00:57: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:00:57: 4000000 INFO @ Tue, 10 Dec 2019 15:01:05: 1000000 INFO @ Tue, 10 Dec 2019 15:01:06: 5000000 INFO @ Tue, 10 Dec 2019 15:01:12: 2000000 INFO @ Tue, 10 Dec 2019 15:01:14: 6000000 INFO @ Tue, 10 Dec 2019 15:01:20: 3000000 INFO @ Tue, 10 Dec 2019 15:01:23: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 15:01:27: 4000000 INFO @ Tue, 10 Dec 2019 15:01:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.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 15:01:27: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:01:27: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:01:31: 8000000 INFO @ Tue, 10 Dec 2019 15:01:34: 1000000 INFO @ Tue, 10 Dec 2019 15:01:35: 5000000 INFO @ Tue, 10 Dec 2019 15:01:40: 9000000 INFO @ Tue, 10 Dec 2019 15:01:41: 2000000 INFO @ Tue, 10 Dec 2019 15:01:42: 6000000 INFO @ Tue, 10 Dec 2019 15:01:47: 3000000 INFO @ Tue, 10 Dec 2019 15:01:48: 10000000 INFO @ Tue, 10 Dec 2019 15:01:50: 7000000 INFO @ Tue, 10 Dec 2019 15:01:54: 4000000 INFO @ Tue, 10 Dec 2019 15:01:57: 11000000 INFO @ Tue, 10 Dec 2019 15:01:57: 8000000 INFO @ Tue, 10 Dec 2019 15:02:01: 5000000 INFO @ Tue, 10 Dec 2019 15:02:05: 12000000 INFO @ Tue, 10 Dec 2019 15:02:05: 9000000 INFO @ Tue, 10 Dec 2019 15:02:08: 6000000 INFO @ Tue, 10 Dec 2019 15:02:13: 10000000 INFO @ Tue, 10 Dec 2019 15:02:13: 13000000 INFO @ Tue, 10 Dec 2019 15:02:14: 7000000 INFO @ Tue, 10 Dec 2019 15:02:20: 11000000 INFO @ Tue, 10 Dec 2019 15:02:21: 14000000 INFO @ Tue, 10 Dec 2019 15:02:21: 8000000 INFO @ Tue, 10 Dec 2019 15:02:27: 12000000 INFO @ Tue, 10 Dec 2019 15:02:29: 9000000 INFO @ Tue, 10 Dec 2019 15:02:29: 15000000 INFO @ Tue, 10 Dec 2019 15:02:35: 13000000 INFO @ Tue, 10 Dec 2019 15:02:36: 10000000 INFO @ Tue, 10 Dec 2019 15:02:36: 16000000 INFO @ Tue, 10 Dec 2019 15:02:43: 14000000 INFO @ Tue, 10 Dec 2019 15:02:43: 11000000 INFO @ Tue, 10 Dec 2019 15:02:44: 17000000 INFO @ Tue, 10 Dec 2019 15:02:50: 12000000 INFO @ Tue, 10 Dec 2019 15:02:50: 15000000 INFO @ Tue, 10 Dec 2019 15:02:52: 18000000 INFO @ Tue, 10 Dec 2019 15:02:57: 13000000 INFO @ Tue, 10 Dec 2019 15:02:58: 16000000 INFO @ Tue, 10 Dec 2019 15:03:00: 19000000 INFO @ Tue, 10 Dec 2019 15:03:04: 14000000 INFO @ Tue, 10 Dec 2019 15:03:06: 17000000 INFO @ Tue, 10 Dec 2019 15:03:07: 20000000 INFO @ Tue, 10 Dec 2019 15:03:11: 15000000 INFO @ Tue, 10 Dec 2019 15:03:13: 18000000 INFO @ Tue, 10 Dec 2019 15:03:15: 21000000 INFO @ Tue, 10 Dec 2019 15:03:18: 16000000 INFO @ Tue, 10 Dec 2019 15:03:21: 19000000 INFO @ Tue, 10 Dec 2019 15:03:22: 22000000 INFO @ Tue, 10 Dec 2019 15:03:25: 17000000 INFO @ Tue, 10 Dec 2019 15:03:28: 20000000 INFO @ Tue, 10 Dec 2019 15:03:29: 23000000 INFO @ Tue, 10 Dec 2019 15:03:31: 18000000 INFO @ Tue, 10 Dec 2019 15:03:36: 21000000 INFO @ Tue, 10 Dec 2019 15:03:37: 24000000 INFO @ Tue, 10 Dec 2019 15:03:38: 19000000 INFO @ Tue, 10 Dec 2019 15:03:43: 22000000 INFO @ Tue, 10 Dec 2019 15:03:45: 25000000 INFO @ Tue, 10 Dec 2019 15:03:45: 20000000 INFO @ Tue, 10 Dec 2019 15:03:50: 23000000 INFO @ Tue, 10 Dec 2019 15:03:52: 21000000 INFO @ Tue, 10 Dec 2019 15:03:52: 26000000 INFO @ Tue, 10 Dec 2019 15:03:58: 24000000 INFO @ Tue, 10 Dec 2019 15:03:58: 22000000 INFO @ Tue, 10 Dec 2019 15:04:00: 27000000 INFO @ Tue, 10 Dec 2019 15:04:00: #1 tag size is determined as 42 bps INFO @ Tue, 10 Dec 2019 15:04:00: #1 tag size = 42 INFO @ Tue, 10 Dec 2019 15:04:00: #1 total tags in treatment: 13137845 INFO @ Tue, 10 Dec 2019 15:04:00: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:04:00: #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 15:04:01: #1 tags after filtering in treatment: 7492709 INFO @ Tue, 10 Dec 2019 15:04:01: #1 Redundant rate of treatment: 0.43 INFO @ Tue, 10 Dec 2019 15:04:01: #1 finished! INFO @ Tue, 10 Dec 2019 15:04:01: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:04:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:04:01: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:04:01: 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 15:04:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.05_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/SRX6742723/SRX6742723.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:04:05: 23000000 INFO @ Tue, 10 Dec 2019 15:04:05: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 15:04:11: 24000000 INFO @ Tue, 10 Dec 2019 15:04:13: 26000000 INFO @ Tue, 10 Dec 2019 15:04:18: 25000000 INFO @ Tue, 10 Dec 2019 15:04:20: 27000000 INFO @ Tue, 10 Dec 2019 15:04:21: #1 tag size is determined as 42 bps INFO @ Tue, 10 Dec 2019 15:04:21: #1 tag size = 42 INFO @ Tue, 10 Dec 2019 15:04:21: #1 total tags in treatment: 13137845 INFO @ Tue, 10 Dec 2019 15:04:21: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:04:21: #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 15:04:21: #1 tags after filtering in treatment: 7492709 INFO @ Tue, 10 Dec 2019 15:04:21: #1 Redundant rate of treatment: 0.43 INFO @ Tue, 10 Dec 2019 15:04:21: #1 finished! INFO @ Tue, 10 Dec 2019 15:04:21: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:04:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:04:22: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:04:22: 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 15:04:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.10_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/SRX6742723/SRX6742723.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:04:24: 26000000 BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 15:04:31: 27000000 INFO @ Tue, 10 Dec 2019 15:04:31: #1 tag size is determined as 42 bps INFO @ Tue, 10 Dec 2019 15:04:31: #1 tag size = 42 INFO @ Tue, 10 Dec 2019 15:04:31: #1 total tags in treatment: 13137845 INFO @ Tue, 10 Dec 2019 15:04:31: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:04:31: #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 15:04:32: #1 tags after filtering in treatment: 7492709 INFO @ Tue, 10 Dec 2019 15:04:32: #1 Redundant rate of treatment: 0.43 INFO @ Tue, 10 Dec 2019 15:04:32: #1 finished! INFO @ Tue, 10 Dec 2019 15:04:32: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:04:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:04:32: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:04:32: 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 15:04:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.20_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/SRX6742723/SRX6742723.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742723/SRX6742723.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling