Job ID = 2640988 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,314,416 reads read : 20,628,832 reads written : 20,628,832 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: 00:12:43 10314416 reads; of these: 10314416 (100.00%) were paired; of these: 1102423 (10.69%) aligned concordantly 0 times 8461624 (82.04%) aligned concordantly exactly 1 time 750369 (7.27%) aligned concordantly >1 times ---- 1102423 pairs aligned concordantly 0 times; of these: 182105 (16.52%) aligned discordantly 1 time ---- 920318 pairs aligned 0 times concordantly or discordantly; of these: 1840636 mates make up the pairs; of these: 1763580 (95.81%) aligned 0 times 36977 (2.01%) aligned exactly 1 time 40079 (2.18%) aligned >1 times 91.45% overall alignment rate Time searching: 00:12:43 Overall time: 00:12:43 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] 92193 / 9392124 = 0.0098 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:56:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.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 20:56:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:56:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:56:27: 1000000 INFO @ Sat, 24 Aug 2019 20:56:37: 2000000 INFO @ Sat, 24 Aug 2019 20:56:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.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 20:56:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:56:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:56:47: 3000000 INFO @ Sat, 24 Aug 2019 20:56:55: 1000000 INFO @ Sat, 24 Aug 2019 20:56:58: 4000000 INFO @ Sat, 24 Aug 2019 20:57:07: 2000000 INFO @ Sat, 24 Aug 2019 20:57:08: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:57:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.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 20:57:13: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:57:13: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:57:18: 3000000 INFO @ Sat, 24 Aug 2019 20:57:19: 6000000 INFO @ Sat, 24 Aug 2019 20:57:24: 1000000 INFO @ Sat, 24 Aug 2019 20:57:29: 4000000 INFO @ Sat, 24 Aug 2019 20:57:29: 7000000 INFO @ Sat, 24 Aug 2019 20:57:35: 2000000 INFO @ Sat, 24 Aug 2019 20:57:40: 5000000 INFO @ Sat, 24 Aug 2019 20:57:40: 8000000 INFO @ Sat, 24 Aug 2019 20:57:46: 3000000 INFO @ Sat, 24 Aug 2019 20:57:51: 6000000 INFO @ Sat, 24 Aug 2019 20:57:51: 9000000 INFO @ Sat, 24 Aug 2019 20:57:56: 4000000 INFO @ Sat, 24 Aug 2019 20:58:02: 10000000 INFO @ Sat, 24 Aug 2019 20:58:02: 7000000 INFO @ Sat, 24 Aug 2019 20:58:10: 5000000 INFO @ Sat, 24 Aug 2019 20:58:13: 11000000 INFO @ Sat, 24 Aug 2019 20:58:13: 8000000 INFO @ Sat, 24 Aug 2019 20:58:20: 6000000 INFO @ Sat, 24 Aug 2019 20:58:24: 9000000 INFO @ Sat, 24 Aug 2019 20:58:24: 12000000 INFO @ Sat, 24 Aug 2019 20:58:31: 7000000 INFO @ Sat, 24 Aug 2019 20:58:35: 10000000 INFO @ Sat, 24 Aug 2019 20:58:36: 13000000 INFO @ Sat, 24 Aug 2019 20:58:41: 8000000 INFO @ Sat, 24 Aug 2019 20:58:47: 11000000 INFO @ Sat, 24 Aug 2019 20:58:48: 14000000 INFO @ Sat, 24 Aug 2019 20:58:51: 9000000 INFO @ Sat, 24 Aug 2019 20:58:58: 12000000 INFO @ Sat, 24 Aug 2019 20:58:59: 15000000 INFO @ Sat, 24 Aug 2019 20:59:02: 10000000 INFO @ Sat, 24 Aug 2019 20:59:10: 13000000 INFO @ Sat, 24 Aug 2019 20:59:11: 16000000 INFO @ Sat, 24 Aug 2019 20:59:13: 11000000 INFO @ Sat, 24 Aug 2019 20:59:21: 14000000 INFO @ Sat, 24 Aug 2019 20:59:23: 17000000 INFO @ Sat, 24 Aug 2019 20:59:24: 12000000 INFO @ Sat, 24 Aug 2019 20:59:33: 15000000 INFO @ Sat, 24 Aug 2019 20:59:34: 13000000 INFO @ Sat, 24 Aug 2019 20:59:35: 18000000 INFO @ Sat, 24 Aug 2019 20:59:43: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:59:43: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:59:43: #1 total tags in treatment: 9121273 INFO @ Sat, 24 Aug 2019 20:59:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:59:43: #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 20:59:43: #1 tags after filtering in treatment: 7231119 INFO @ Sat, 24 Aug 2019 20:59:43: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 20:59:43: #1 finished! INFO @ Sat, 24 Aug 2019 20:59:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:59:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:59:43: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:59:43: 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 @ Sat, 24 Aug 2019 20:59:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.05_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/SRX4936094/SRX4936094.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:59:44: 14000000 INFO @ Sat, 24 Aug 2019 20:59:44: 16000000 INFO @ Sat, 24 Aug 2019 20:59:54: 15000000 INFO @ Sat, 24 Aug 2019 20:59:56: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:00:04: 16000000 INFO @ Sat, 24 Aug 2019 21:00:07: 18000000 INFO @ Sat, 24 Aug 2019 21:00:14: 17000000 INFO @ Sat, 24 Aug 2019 21:00:15: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:00:15: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:00:15: #1 total tags in treatment: 9121273 INFO @ Sat, 24 Aug 2019 21:00:15: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:00:15: #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 21:00:15: #1 tags after filtering in treatment: 7231119 INFO @ Sat, 24 Aug 2019 21:00:15: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 21:00:15: #1 finished! INFO @ Sat, 24 Aug 2019 21:00:15: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:00:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:00:16: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:00:16: 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 @ Sat, 24 Aug 2019 21:00:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.10_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/SRX4936094/SRX4936094.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:00:23: 18000000 INFO @ Sat, 24 Aug 2019 21:00:29: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:00:29: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:00:29: #1 total tags in treatment: 9121273 INFO @ Sat, 24 Aug 2019 21:00:29: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:00:29: #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 21:00:30: #1 tags after filtering in treatment: 7231119 INFO @ Sat, 24 Aug 2019 21:00:30: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 21:00:30: #1 finished! INFO @ Sat, 24 Aug 2019 21:00:30: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:00:30: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:00:30: 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 @ Sat, 24 Aug 2019 21:00:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.20_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/SRX4936094/SRX4936094.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936094/SRX4936094.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling