Job ID = 2641216 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 25,745,109 reads read : 51,490,218 reads written : 51,490,218 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: 00:22:07 25745109 reads; of these: 25745109 (100.00%) were paired; of these: 15386811 (59.77%) aligned concordantly 0 times 8043594 (31.24%) aligned concordantly exactly 1 time 2314704 (8.99%) aligned concordantly >1 times ---- 15386811 pairs aligned concordantly 0 times; of these: 5766532 (37.48%) aligned discordantly 1 time ---- 9620279 pairs aligned 0 times concordantly or discordantly; of these: 19240558 mates make up the pairs; of these: 8870866 (46.11%) aligned 0 times 6554221 (34.06%) aligned exactly 1 time 3815471 (19.83%) aligned >1 times 82.77% overall alignment rate Time searching: 00:22:07 Overall time: 00:22:07 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 20 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] 1920861 / 10912949 = 0.1760 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:43:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.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 22:43:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:43:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:43:47: 1000000 INFO @ Sat, 24 Aug 2019 22:43:56: 2000000 INFO @ Sat, 24 Aug 2019 22:44:06: 3000000 INFO @ Sat, 24 Aug 2019 22:44:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.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 22:44:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:44:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:44:15: 1000000 INFO @ Sat, 24 Aug 2019 22:44:15: 4000000 INFO @ Sat, 24 Aug 2019 22:44:23: 2000000 INFO @ Sat, 24 Aug 2019 22:44:25: 5000000 INFO @ Sat, 24 Aug 2019 22:44:32: 3000000 INFO @ Sat, 24 Aug 2019 22:44:34: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:44:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.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 22:44:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:44:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:44:40: 4000000 INFO @ Sat, 24 Aug 2019 22:44:44: 7000000 INFO @ Sat, 24 Aug 2019 22:44:47: 1000000 INFO @ Sat, 24 Aug 2019 22:44:48: 5000000 INFO @ Sat, 24 Aug 2019 22:44:53: 8000000 INFO @ Sat, 24 Aug 2019 22:44:56: 2000000 INFO @ Sat, 24 Aug 2019 22:44:57: 6000000 INFO @ Sat, 24 Aug 2019 22:45:03: 9000000 INFO @ Sat, 24 Aug 2019 22:45:06: 3000000 INFO @ Sat, 24 Aug 2019 22:45:06: 7000000 INFO @ Sat, 24 Aug 2019 22:45:11: 10000000 INFO @ Sat, 24 Aug 2019 22:45:15: 8000000 INFO @ Sat, 24 Aug 2019 22:45:16: 4000000 INFO @ Sat, 24 Aug 2019 22:45:20: 11000000 INFO @ Sat, 24 Aug 2019 22:45:24: 9000000 INFO @ Sat, 24 Aug 2019 22:45:26: 5000000 INFO @ Sat, 24 Aug 2019 22:45:30: 12000000 INFO @ Sat, 24 Aug 2019 22:45:34: 10000000 INFO @ Sat, 24 Aug 2019 22:45:35: 6000000 INFO @ Sat, 24 Aug 2019 22:45:39: 13000000 INFO @ Sat, 24 Aug 2019 22:45:44: 11000000 INFO @ Sat, 24 Aug 2019 22:45:45: 7000000 INFO @ Sat, 24 Aug 2019 22:45:49: 14000000 INFO @ Sat, 24 Aug 2019 22:45:54: 12000000 INFO @ Sat, 24 Aug 2019 22:45:54: 8000000 INFO @ Sat, 24 Aug 2019 22:45:59: 15000000 INFO @ Sat, 24 Aug 2019 22:46:03: 13000000 INFO @ Sat, 24 Aug 2019 22:46:04: 9000000 INFO @ Sat, 24 Aug 2019 22:46:09: 16000000 INFO @ Sat, 24 Aug 2019 22:46:12: 14000000 INFO @ Sat, 24 Aug 2019 22:46:13: 10000000 INFO @ Sat, 24 Aug 2019 22:46:19: 17000000 INFO @ Sat, 24 Aug 2019 22:46:20: 15000000 INFO @ Sat, 24 Aug 2019 22:46:21: 11000000 INFO @ Sat, 24 Aug 2019 22:46:29: 18000000 INFO @ Sat, 24 Aug 2019 22:46:29: 16000000 INFO @ Sat, 24 Aug 2019 22:46:30: 12000000 INFO @ Sat, 24 Aug 2019 22:46:38: 17000000 INFO @ Sat, 24 Aug 2019 22:46:39: 19000000 INFO @ Sat, 24 Aug 2019 22:46:40: 13000000 INFO @ Sat, 24 Aug 2019 22:46:47: 18000000 INFO @ Sat, 24 Aug 2019 22:46:49: 20000000 INFO @ Sat, 24 Aug 2019 22:46:50: 14000000 INFO @ Sat, 24 Aug 2019 22:46:55: 19000000 INFO @ Sat, 24 Aug 2019 22:46:59: 21000000 INFO @ Sat, 24 Aug 2019 22:47:00: 15000000 INFO @ Sat, 24 Aug 2019 22:47:04: 20000000 INFO @ Sat, 24 Aug 2019 22:47:08: 22000000 INFO @ Sat, 24 Aug 2019 22:47:09: 16000000 INFO @ Sat, 24 Aug 2019 22:47:13: 21000000 INFO @ Sat, 24 Aug 2019 22:47:18: 23000000 INFO @ Sat, 24 Aug 2019 22:47:19: 17000000 INFO @ Sat, 24 Aug 2019 22:47:22: 22000000 INFO @ Sat, 24 Aug 2019 22:47:28: 24000000 INFO @ Sat, 24 Aug 2019 22:47:29: 18000000 INFO @ Sat, 24 Aug 2019 22:47:30: 23000000 INFO @ Sat, 24 Aug 2019 22:47:37: 25000000 INFO @ Sat, 24 Aug 2019 22:47:38: 24000000 INFO @ Sat, 24 Aug 2019 22:47:39: 19000000 INFO @ Sat, 24 Aug 2019 22:47:47: 26000000 INFO @ Sat, 24 Aug 2019 22:47:47: 25000000 INFO @ Sat, 24 Aug 2019 22:47:49: 20000000 INFO @ Sat, 24 Aug 2019 22:47:55: 26000000 INFO @ Sat, 24 Aug 2019 22:47:57: 27000000 INFO @ Sat, 24 Aug 2019 22:47:58: 21000000 INFO @ Sat, 24 Aug 2019 22:48:04: 27000000 INFO @ Sat, 24 Aug 2019 22:48:06: 28000000 INFO @ Sat, 24 Aug 2019 22:48:08: 22000000 INFO @ Sat, 24 Aug 2019 22:48:13: 28000000 INFO @ Sat, 24 Aug 2019 22:48:16: 29000000 INFO @ Sat, 24 Aug 2019 22:48:18: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:48:21: 29000000 INFO @ Sat, 24 Aug 2019 22:48:26: 30000000 INFO @ Sat, 24 Aug 2019 22:48:27: 24000000 INFO @ Sat, 24 Aug 2019 22:48:30: 30000000 INFO @ Sat, 24 Aug 2019 22:48:36: 31000000 INFO @ Sat, 24 Aug 2019 22:48:37: 25000000 INFO @ Sat, 24 Aug 2019 22:48:39: 31000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:48:46: 32000000 INFO @ Sat, 24 Aug 2019 22:48:47: 26000000 INFO @ Sat, 24 Aug 2019 22:48:48: 32000000 INFO @ Sat, 24 Aug 2019 22:48:56: 33000000 INFO @ Sat, 24 Aug 2019 22:48:56: 33000000 INFO @ Sat, 24 Aug 2019 22:48:56: 27000000 INFO @ Sat, 24 Aug 2019 22:49:06: 34000000 INFO @ Sat, 24 Aug 2019 22:49:06: 28000000 INFO @ Sat, 24 Aug 2019 22:49:06: 34000000 INFO @ Sat, 24 Aug 2019 22:49:15: 35000000 INFO @ Sat, 24 Aug 2019 22:49:16: 29000000 INFO @ Sat, 24 Aug 2019 22:49:16: 35000000 INFO @ Sat, 24 Aug 2019 22:49:24: 36000000 INFO @ Sat, 24 Aug 2019 22:49:25: 30000000 INFO @ Sat, 24 Aug 2019 22:49:26: 36000000 INFO @ Sat, 24 Aug 2019 22:49:32: 37000000 INFO @ Sat, 24 Aug 2019 22:49:35: 31000000 INFO @ Sat, 24 Aug 2019 22:49:36: 37000000 INFO @ Sat, 24 Aug 2019 22:49:41: 38000000 INFO @ Sat, 24 Aug 2019 22:49:45: 32000000 INFO @ Sat, 24 Aug 2019 22:49:45: 38000000 INFO @ Sat, 24 Aug 2019 22:49:47: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:49:47: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:49:47: #1 total tags in treatment: 8449737 INFO @ Sat, 24 Aug 2019 22:49:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:49:47: #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 22:49:48: #1 tags after filtering in treatment: 4567418 INFO @ Sat, 24 Aug 2019 22:49:48: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 24 Aug 2019 22:49:48: #1 finished! INFO @ Sat, 24 Aug 2019 22:49:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:49:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:49:48: #2 number of paired peaks: 18 WARNING @ Sat, 24 Aug 2019 22:49:48: Too few paired peaks (18) 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 22:49:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.10_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/SRX5811113/SRX5811113.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:49:53: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:49:53: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:49:53: #1 total tags in treatment: 8449737 INFO @ Sat, 24 Aug 2019 22:49:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:49:53: #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 22:49:53: #1 tags after filtering in treatment: 4567418 INFO @ Sat, 24 Aug 2019 22:49:53: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 24 Aug 2019 22:49:53: #1 finished! INFO @ Sat, 24 Aug 2019 22:49:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:49:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:49:53: #2 number of paired peaks: 18 WARNING @ Sat, 24 Aug 2019 22:49:53: Too few paired peaks (18) 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 22:49:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.05_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/SRX5811113/SRX5811113.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:49:55: 33000000 INFO @ Sat, 24 Aug 2019 22:50:04: 34000000 INFO @ Sat, 24 Aug 2019 22:50:13: 35000000 INFO @ Sat, 24 Aug 2019 22:50:23: 36000000 INFO @ Sat, 24 Aug 2019 22:50:32: 37000000 INFO @ Sat, 24 Aug 2019 22:50:41: 38000000 INFO @ Sat, 24 Aug 2019 22:50:49: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:50:49: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:50:49: #1 total tags in treatment: 8449737 INFO @ Sat, 24 Aug 2019 22:50:49: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:50:49: #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 22:50:49: #1 tags after filtering in treatment: 4567418 INFO @ Sat, 24 Aug 2019 22:50:49: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 24 Aug 2019 22:50:49: #1 finished! INFO @ Sat, 24 Aug 2019 22:50:49: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:50:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:50:49: #2 number of paired peaks: 18 WARNING @ Sat, 24 Aug 2019 22:50:49: Too few paired peaks (18) 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 22:50:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.20_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/SRX5811113/SRX5811113.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811113/SRX5811113.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling