Job ID = 2641213 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 32,619,470 reads read : 65,238,940 reads written : 65,238,940 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: 00:22:32 32619470 reads; of these: 32619470 (100.00%) were paired; of these: 4851604 (14.87%) aligned concordantly 0 times 24106026 (73.90%) aligned concordantly exactly 1 time 3661840 (11.23%) aligned concordantly >1 times ---- 4851604 pairs aligned concordantly 0 times; of these: 444711 (9.17%) aligned discordantly 1 time ---- 4406893 pairs aligned 0 times concordantly or discordantly; of these: 8813786 mates make up the pairs; of these: 8025023 (91.05%) aligned 0 times 529749 (6.01%) aligned exactly 1 time 259014 (2.94%) aligned >1 times 87.70% overall alignment rate Time searching: 00:22:32 Overall time: 00:22:32 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 24 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] 6517951 / 27899350 = 0.2336 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:36:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.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 22:36:29: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:36:29: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:36:37: 1000000 INFO @ Sat, 24 Aug 2019 22:36:44: 2000000 INFO @ Sat, 24 Aug 2019 22:36:52: 3000000 INFO @ Sat, 24 Aug 2019 22:36:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.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 22:36:58: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:36:58: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:37:00: 4000000 INFO @ Sat, 24 Aug 2019 22:37:06: 1000000 INFO @ Sat, 24 Aug 2019 22:37:08: 5000000 INFO @ Sat, 24 Aug 2019 22:37:13: 2000000 INFO @ Sat, 24 Aug 2019 22:37:16: 6000000 INFO @ Sat, 24 Aug 2019 22:37:19: 3000000 INFO @ Sat, 24 Aug 2019 22:37:24: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:37:26: 4000000 INFO @ Sat, 24 Aug 2019 22:37:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.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 22:37:28: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:37:28: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:37:32: 8000000 INFO @ Sat, 24 Aug 2019 22:37:34: 5000000 INFO @ Sat, 24 Aug 2019 22:37:39: 1000000 INFO @ Sat, 24 Aug 2019 22:37:41: 9000000 INFO @ Sat, 24 Aug 2019 22:37:41: 6000000 INFO @ Sat, 24 Aug 2019 22:37:48: 7000000 INFO @ Sat, 24 Aug 2019 22:37:49: 10000000 INFO @ Sat, 24 Aug 2019 22:37:50: 2000000 INFO @ Sat, 24 Aug 2019 22:37:55: 8000000 INFO @ Sat, 24 Aug 2019 22:37:57: 11000000 INFO @ Sat, 24 Aug 2019 22:38:01: 3000000 INFO @ Sat, 24 Aug 2019 22:38:02: 9000000 INFO @ Sat, 24 Aug 2019 22:38:05: 12000000 INFO @ Sat, 24 Aug 2019 22:38:09: 10000000 INFO @ Sat, 24 Aug 2019 22:38:11: 4000000 INFO @ Sat, 24 Aug 2019 22:38:13: 13000000 INFO @ Sat, 24 Aug 2019 22:38:17: 11000000 INFO @ Sat, 24 Aug 2019 22:38:22: 14000000 INFO @ Sat, 24 Aug 2019 22:38:22: 5000000 INFO @ Sat, 24 Aug 2019 22:38:24: 12000000 INFO @ Sat, 24 Aug 2019 22:38:30: 15000000 INFO @ Sat, 24 Aug 2019 22:38:31: 13000000 INFO @ Sat, 24 Aug 2019 22:38:33: 6000000 INFO @ Sat, 24 Aug 2019 22:38:38: 14000000 INFO @ Sat, 24 Aug 2019 22:38:38: 16000000 INFO @ Sat, 24 Aug 2019 22:38:44: 7000000 INFO @ Sat, 24 Aug 2019 22:38:45: 15000000 INFO @ Sat, 24 Aug 2019 22:38:46: 17000000 INFO @ Sat, 24 Aug 2019 22:38:52: 16000000 INFO @ Sat, 24 Aug 2019 22:38:55: 18000000 INFO @ Sat, 24 Aug 2019 22:38:55: 8000000 INFO @ Sat, 24 Aug 2019 22:39:00: 17000000 INFO @ Sat, 24 Aug 2019 22:39:03: 19000000 INFO @ Sat, 24 Aug 2019 22:39:05: 9000000 INFO @ Sat, 24 Aug 2019 22:39:07: 18000000 INFO @ Sat, 24 Aug 2019 22:39:11: 20000000 INFO @ Sat, 24 Aug 2019 22:39:14: 19000000 INFO @ Sat, 24 Aug 2019 22:39:16: 10000000 INFO @ Sat, 24 Aug 2019 22:39:19: 21000000 INFO @ Sat, 24 Aug 2019 22:39:21: 20000000 INFO @ Sat, 24 Aug 2019 22:39:26: 11000000 INFO @ Sat, 24 Aug 2019 22:39:27: 22000000 INFO @ Sat, 24 Aug 2019 22:39:29: 21000000 INFO @ Sat, 24 Aug 2019 22:39:35: 23000000 INFO @ Sat, 24 Aug 2019 22:39:36: 22000000 INFO @ Sat, 24 Aug 2019 22:39:36: 12000000 INFO @ Sat, 24 Aug 2019 22:39:43: 23000000 INFO @ Sat, 24 Aug 2019 22:39:44: 24000000 INFO @ Sat, 24 Aug 2019 22:39:46: 13000000 INFO @ Sat, 24 Aug 2019 22:39:50: 24000000 INFO @ Sat, 24 Aug 2019 22:39:52: 25000000 INFO @ Sat, 24 Aug 2019 22:39:57: 14000000 INFO @ Sat, 24 Aug 2019 22:39:57: 25000000 INFO @ Sat, 24 Aug 2019 22:40:00: 26000000 INFO @ Sat, 24 Aug 2019 22:40:04: 26000000 INFO @ Sat, 24 Aug 2019 22:40:07: 15000000 INFO @ Sat, 24 Aug 2019 22:40:08: 27000000 INFO @ Sat, 24 Aug 2019 22:40:11: 27000000 INFO @ Sat, 24 Aug 2019 22:40:16: 28000000 INFO @ Sat, 24 Aug 2019 22:40:17: 16000000 INFO @ Sat, 24 Aug 2019 22:40:18: 28000000 INFO @ Sat, 24 Aug 2019 22:40:24: 29000000 INFO @ Sat, 24 Aug 2019 22:40:25: 29000000 INFO @ Sat, 24 Aug 2019 22:40:27: 17000000 INFO @ Sat, 24 Aug 2019 22:40:32: 30000000 INFO @ Sat, 24 Aug 2019 22:40:33: 30000000 INFO @ Sat, 24 Aug 2019 22:40:38: 18000000 INFO @ Sat, 24 Aug 2019 22:40:40: 31000000 INFO @ Sat, 24 Aug 2019 22:40:41: 31000000 INFO @ Sat, 24 Aug 2019 22:40:47: 32000000 INFO @ Sat, 24 Aug 2019 22:40:48: 19000000 INFO @ Sat, 24 Aug 2019 22:40:49: 32000000 INFO @ Sat, 24 Aug 2019 22:40:54: 33000000 INFO @ Sat, 24 Aug 2019 22:40:57: 33000000 INFO @ Sat, 24 Aug 2019 22:40:58: 20000000 INFO @ Sat, 24 Aug 2019 22:41:01: 34000000 INFO @ Sat, 24 Aug 2019 22:41:05: 34000000 INFO @ Sat, 24 Aug 2019 22:41:08: 35000000 INFO @ Sat, 24 Aug 2019 22:41:08: 21000000 INFO @ Sat, 24 Aug 2019 22:41:13: 35000000 INFO @ Sat, 24 Aug 2019 22:41:15: 36000000 INFO @ Sat, 24 Aug 2019 22:41:18: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:41:21: 36000000 INFO @ Sat, 24 Aug 2019 22:41:22: 37000000 INFO @ Sat, 24 Aug 2019 22:41:28: 23000000 INFO @ Sat, 24 Aug 2019 22:41:29: 37000000 INFO @ Sat, 24 Aug 2019 22:41:29: 38000000 INFO @ Sat, 24 Aug 2019 22:41:36: 39000000 INFO @ Sat, 24 Aug 2019 22:41:37: 38000000 INFO @ Sat, 24 Aug 2019 22:41:38: 24000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:41:43: 40000000 INFO @ Sat, 24 Aug 2019 22:41:45: 39000000 INFO @ Sat, 24 Aug 2019 22:41:48: 25000000 INFO @ Sat, 24 Aug 2019 22:41:50: 41000000 INFO @ Sat, 24 Aug 2019 22:41:53: 40000000 INFO @ Sat, 24 Aug 2019 22:41:57: 42000000 INFO @ Sat, 24 Aug 2019 22:41:58: 26000000 INFO @ Sat, 24 Aug 2019 22:42:01: 41000000 INFO @ Sat, 24 Aug 2019 22:42:05: 43000000 INFO @ Sat, 24 Aug 2019 22:42:08: 27000000 INFO @ Sat, 24 Aug 2019 22:42:09: 42000000 INFO @ Sat, 24 Aug 2019 22:42:12: 44000000 INFO @ Sat, 24 Aug 2019 22:42:13: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:42:13: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:42:13: #1 total tags in treatment: 21258204 INFO @ Sat, 24 Aug 2019 22:42:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:42:13: #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 22:42:14: #1 tags after filtering in treatment: 8231747 INFO @ Sat, 24 Aug 2019 22:42:14: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 24 Aug 2019 22:42:14: #1 finished! INFO @ Sat, 24 Aug 2019 22:42:14: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:42:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:42:14: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:42:14: 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 @ Sat, 24 Aug 2019 22:42:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.10_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/SRX5811110/SRX5811110.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:42:17: 43000000 INFO @ Sat, 24 Aug 2019 22:42:18: 28000000 INFO @ Sat, 24 Aug 2019 22:42:25: 44000000 INFO @ Sat, 24 Aug 2019 22:42:27: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:42:27: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:42:27: #1 total tags in treatment: 21258204 INFO @ Sat, 24 Aug 2019 22:42:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:42:27: #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 22:42:28: #1 tags after filtering in treatment: 8231747 INFO @ Sat, 24 Aug 2019 22:42:28: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 24 Aug 2019 22:42:28: #1 finished! INFO @ Sat, 24 Aug 2019 22:42:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:42:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:42:28: 29000000 INFO @ Sat, 24 Aug 2019 22:42:28: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:42:28: 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 22:42:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.05_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/SRX5811110/SRX5811110.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:42:38: 30000000 INFO @ Sat, 24 Aug 2019 22:42:47: 31000000 INFO @ Sat, 24 Aug 2019 22:42:56: 32000000 INFO @ Sat, 24 Aug 2019 22:43:05: 33000000 INFO @ Sat, 24 Aug 2019 22:43:14: 34000000 INFO @ Sat, 24 Aug 2019 22:43:23: 35000000 INFO @ Sat, 24 Aug 2019 22:43:32: 36000000 INFO @ Sat, 24 Aug 2019 22:43:41: 37000000 INFO @ Sat, 24 Aug 2019 22:43:51: 38000000 INFO @ Sat, 24 Aug 2019 22:44:00: 39000000 INFO @ Sat, 24 Aug 2019 22:44:09: 40000000 INFO @ Sat, 24 Aug 2019 22:44:18: 41000000 INFO @ Sat, 24 Aug 2019 22:44:28: 42000000 INFO @ Sat, 24 Aug 2019 22:44:37: 43000000 INFO @ Sat, 24 Aug 2019 22:44:46: 44000000 INFO @ Sat, 24 Aug 2019 22:44:48: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:44:48: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:44:48: #1 total tags in treatment: 21258204 INFO @ Sat, 24 Aug 2019 22:44:48: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:44:48: #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 22:44:48: #1 tags after filtering in treatment: 8231747 INFO @ Sat, 24 Aug 2019 22:44:48: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 24 Aug 2019 22:44:48: #1 finished! INFO @ Sat, 24 Aug 2019 22:44:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:44:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:44:49: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:44:49: 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 22:44:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.20_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/SRX5811110/SRX5811110.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811110/SRX5811110.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling