Job ID = 2641142 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 35,207,862 reads read : 70,415,724 reads written : 70,415,724 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: 00:43:02 35207862 reads; of these: 35207862 (100.00%) were paired; of these: 3154757 (8.96%) aligned concordantly 0 times 26436146 (75.09%) aligned concordantly exactly 1 time 5616959 (15.95%) aligned concordantly >1 times ---- 3154757 pairs aligned concordantly 0 times; of these: 249938 (7.92%) aligned discordantly 1 time ---- 2904819 pairs aligned 0 times concordantly or discordantly; of these: 5809638 mates make up the pairs; of these: 5462627 (94.03%) aligned 0 times 169215 (2.91%) aligned exactly 1 time 177796 (3.06%) aligned >1 times 92.24% overall alignment rate Time searching: 00:43:02 Overall time: 00:43:02 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 28 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] 9756652 / 32275354 = 0.3023 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 23:06:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.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 23:06:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 23:06:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 23:06:21: 1000000 INFO @ Sat, 24 Aug 2019 23:06:28: 2000000 INFO @ Sat, 24 Aug 2019 23:06:35: 3000000 INFO @ Sat, 24 Aug 2019 23:06:42: 4000000 INFO @ Sat, 24 Aug 2019 23:06:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.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 23:06:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 23:06:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 23:06:50: 5000000 INFO @ Sat, 24 Aug 2019 23:06:55: 1000000 INFO @ Sat, 24 Aug 2019 23:06:57: 6000000 INFO @ Sat, 24 Aug 2019 23:07:04: 7000000 INFO @ Sat, 24 Aug 2019 23:07:05: 2000000 INFO @ Sat, 24 Aug 2019 23:07:11: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 23:07:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.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 23:07:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 23:07:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 23:07:17: 3000000 INFO @ Sat, 24 Aug 2019 23:07:18: 9000000 INFO @ Sat, 24 Aug 2019 23:07:25: 10000000 INFO @ Sat, 24 Aug 2019 23:07:26: 1000000 INFO @ Sat, 24 Aug 2019 23:07:28: 4000000 INFO @ Sat, 24 Aug 2019 23:07:32: 11000000 INFO @ Sat, 24 Aug 2019 23:07:38: 2000000 INFO @ Sat, 24 Aug 2019 23:07:39: 12000000 INFO @ Sat, 24 Aug 2019 23:07:40: 5000000 INFO @ Sat, 24 Aug 2019 23:07:46: 13000000 INFO @ Sat, 24 Aug 2019 23:07:49: 3000000 INFO @ Sat, 24 Aug 2019 23:07:51: 6000000 INFO @ Sat, 24 Aug 2019 23:07:53: 14000000 INFO @ Sat, 24 Aug 2019 23:08:00: 4000000 INFO @ Sat, 24 Aug 2019 23:08:00: 15000000 INFO @ Sat, 24 Aug 2019 23:08:02: 7000000 INFO @ Sat, 24 Aug 2019 23:08:07: 16000000 INFO @ Sat, 24 Aug 2019 23:08:11: 5000000 INFO @ Sat, 24 Aug 2019 23:08:14: 8000000 INFO @ Sat, 24 Aug 2019 23:08:14: 17000000 INFO @ Sat, 24 Aug 2019 23:08:21: 6000000 INFO @ Sat, 24 Aug 2019 23:08:21: 18000000 INFO @ Sat, 24 Aug 2019 23:08:25: 9000000 INFO @ Sat, 24 Aug 2019 23:08:28: 19000000 INFO @ Sat, 24 Aug 2019 23:08:31: 7000000 INFO @ Sat, 24 Aug 2019 23:08:35: 20000000 INFO @ Sat, 24 Aug 2019 23:08:36: 10000000 INFO @ Sat, 24 Aug 2019 23:08:42: 8000000 INFO @ Sat, 24 Aug 2019 23:08:42: 21000000 INFO @ Sat, 24 Aug 2019 23:08:47: 11000000 INFO @ Sat, 24 Aug 2019 23:08:50: 22000000 INFO @ Sat, 24 Aug 2019 23:08:52: 9000000 INFO @ Sat, 24 Aug 2019 23:08:57: 23000000 INFO @ Sat, 24 Aug 2019 23:08:58: 12000000 INFO @ Sat, 24 Aug 2019 23:09:02: 10000000 INFO @ Sat, 24 Aug 2019 23:09:04: 24000000 INFO @ Sat, 24 Aug 2019 23:09:09: 13000000 INFO @ Sat, 24 Aug 2019 23:09:12: 25000000 INFO @ Sat, 24 Aug 2019 23:09:13: 11000000 INFO @ Sat, 24 Aug 2019 23:09:20: 14000000 INFO @ Sat, 24 Aug 2019 23:09:20: 26000000 INFO @ Sat, 24 Aug 2019 23:09:23: 12000000 INFO @ Sat, 24 Aug 2019 23:09:27: 27000000 INFO @ Sat, 24 Aug 2019 23:09:30: 15000000 INFO @ Sat, 24 Aug 2019 23:09:33: 13000000 INFO @ Sat, 24 Aug 2019 23:09:34: 28000000 INFO @ Sat, 24 Aug 2019 23:09:41: 16000000 INFO @ Sat, 24 Aug 2019 23:09:41: 29000000 INFO @ Sat, 24 Aug 2019 23:09:43: 14000000 INFO @ Sat, 24 Aug 2019 23:09:48: 30000000 INFO @ Sat, 24 Aug 2019 23:09:51: 17000000 INFO @ Sat, 24 Aug 2019 23:09:53: 15000000 INFO @ Sat, 24 Aug 2019 23:09:55: 31000000 INFO @ Sat, 24 Aug 2019 23:10:02: 18000000 INFO @ Sat, 24 Aug 2019 23:10:02: 32000000 INFO @ Sat, 24 Aug 2019 23:10:03: 16000000 INFO @ Sat, 24 Aug 2019 23:10:09: 33000000 INFO @ Sat, 24 Aug 2019 23:10:13: 19000000 INFO @ Sat, 24 Aug 2019 23:10:13: 17000000 INFO @ Sat, 24 Aug 2019 23:10:16: 34000000 INFO @ Sat, 24 Aug 2019 23:10:23: 18000000 INFO @ Sat, 24 Aug 2019 23:10:23: 20000000 INFO @ Sat, 24 Aug 2019 23:10:23: 35000000 INFO @ Sat, 24 Aug 2019 23:10:30: 36000000 INFO @ Sat, 24 Aug 2019 23:10:33: 19000000 INFO @ Sat, 24 Aug 2019 23:10:34: 21000000 INFO @ Sat, 24 Aug 2019 23:10:37: 37000000 INFO @ Sat, 24 Aug 2019 23:10:43: 20000000 INFO @ Sat, 24 Aug 2019 23:10:44: 22000000 INFO @ Sat, 24 Aug 2019 23:10:45: 38000000 INFO @ Sat, 24 Aug 2019 23:10:52: 39000000 INFO @ Sat, 24 Aug 2019 23:10:53: 21000000 INFO @ Sat, 24 Aug 2019 23:10:55: 23000000 INFO @ Sat, 24 Aug 2019 23:10:59: 40000000 INFO @ Sat, 24 Aug 2019 23:11:03: 22000000 INFO @ Sat, 24 Aug 2019 23:11:05: 24000000 INFO @ Sat, 24 Aug 2019 23:11:06: 41000000 INFO @ Sat, 24 Aug 2019 23:11:13: 42000000 INFO @ Sat, 24 Aug 2019 23:11:13: 23000000 INFO @ Sat, 24 Aug 2019 23:11:15: 25000000 INFO @ Sat, 24 Aug 2019 23:11:20: 43000000 INFO @ Sat, 24 Aug 2019 23:11:22: 24000000 INFO @ Sat, 24 Aug 2019 23:11:25: 26000000 INFO @ Sat, 24 Aug 2019 23:11:27: 44000000 INFO @ Sat, 24 Aug 2019 23:11:32: 25000000 INFO @ Sat, 24 Aug 2019 23:11:33: 45000000 INFO @ Sat, 24 Aug 2019 23:11:35: 27000000 INFO @ Sat, 24 Aug 2019 23:11:37: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 23:11:37: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 23:11:37: #1 total tags in treatment: 22349202 INFO @ Sat, 24 Aug 2019 23:11:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 23:11:37: #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 23:11:37: #1 tags after filtering in treatment: 13015937 INFO @ Sat, 24 Aug 2019 23:11:37: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 24 Aug 2019 23:11:37: #1 finished! INFO @ Sat, 24 Aug 2019 23:11:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 23:11:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 23:11:38: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 23:11:38: 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 23:11:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.05_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/SRX5781920/SRX5781920.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 23:11:40: 26000000 INFO @ Sat, 24 Aug 2019 23:11:45: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 23:11:50: 27000000 INFO @ Sat, 24 Aug 2019 23:11:55: 29000000 INFO @ Sat, 24 Aug 2019 23:12:00: 28000000 INFO @ Sat, 24 Aug 2019 23:12:05: 30000000 INFO @ Sat, 24 Aug 2019 23:12:10: 29000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 23:12:16: 31000000 INFO @ Sat, 24 Aug 2019 23:12:20: 30000000 INFO @ Sat, 24 Aug 2019 23:12:26: 32000000 INFO @ Sat, 24 Aug 2019 23:12:30: 31000000 INFO @ Sat, 24 Aug 2019 23:12:37: 33000000 INFO @ Sat, 24 Aug 2019 23:12:40: 32000000 INFO @ Sat, 24 Aug 2019 23:12:47: 34000000 INFO @ Sat, 24 Aug 2019 23:12:50: 33000000 INFO @ Sat, 24 Aug 2019 23:12:57: 35000000 INFO @ Sat, 24 Aug 2019 23:12:59: 34000000 INFO @ Sat, 24 Aug 2019 23:13:08: 36000000 INFO @ Sat, 24 Aug 2019 23:13:09: 35000000 INFO @ Sat, 24 Aug 2019 23:13:18: 37000000 INFO @ Sat, 24 Aug 2019 23:13:19: 36000000 INFO @ Sat, 24 Aug 2019 23:13:28: 38000000 INFO @ Sat, 24 Aug 2019 23:13:29: 37000000 INFO @ Sat, 24 Aug 2019 23:13:38: 39000000 INFO @ Sat, 24 Aug 2019 23:13:38: 38000000 INFO @ Sat, 24 Aug 2019 23:13:48: 39000000 INFO @ Sat, 24 Aug 2019 23:13:49: 40000000 INFO @ Sat, 24 Aug 2019 23:13:58: 40000000 INFO @ Sat, 24 Aug 2019 23:13:59: 41000000 INFO @ Sat, 24 Aug 2019 23:14:08: 41000000 INFO @ Sat, 24 Aug 2019 23:14:09: 42000000 INFO @ Sat, 24 Aug 2019 23:14:18: 42000000 INFO @ Sat, 24 Aug 2019 23:14:20: 43000000 INFO @ Sat, 24 Aug 2019 23:14:28: 43000000 INFO @ Sat, 24 Aug 2019 23:14:30: 44000000 INFO @ Sat, 24 Aug 2019 23:14:38: 44000000 INFO @ Sat, 24 Aug 2019 23:14:40: 45000000 INFO @ Sat, 24 Aug 2019 23:14:45: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 23:14:45: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 23:14:45: #1 total tags in treatment: 22349202 INFO @ Sat, 24 Aug 2019 23:14:45: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 23:14:45: #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 23:14:45: #1 tags after filtering in treatment: 13015937 INFO @ Sat, 24 Aug 2019 23:14:45: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 24 Aug 2019 23:14:45: #1 finished! INFO @ Sat, 24 Aug 2019 23:14:45: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 23:14:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 23:14:46: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 23:14:46: 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 23:14:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.10_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/SRX5781920/SRX5781920.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 23:14:47: 45000000 INFO @ Sat, 24 Aug 2019 23:14:51: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 23:14:51: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 23:14:51: #1 total tags in treatment: 22349202 INFO @ Sat, 24 Aug 2019 23:14:51: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 23:14:51: #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 23:14:52: #1 tags after filtering in treatment: 13015937 INFO @ Sat, 24 Aug 2019 23:14:52: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 24 Aug 2019 23:14:52: #1 finished! INFO @ Sat, 24 Aug 2019 23:14:52: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 23:14:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 23:14:53: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 23:14:53: 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 23:14:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.20_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/SRX5781920/SRX5781920.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5781920/SRX5781920.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling