Job ID = 2010542 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,628,738 reads read : 27,257,476 reads written : 27,257,476 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: 00:11:18 13628738 reads; of these: 13628738 (100.00%) were paired; of these: 860001 (6.31%) aligned concordantly 0 times 10633422 (78.02%) aligned concordantly exactly 1 time 2135315 (15.67%) aligned concordantly >1 times ---- 860001 pairs aligned concordantly 0 times; of these: 282377 (32.83%) aligned discordantly 1 time ---- 577624 pairs aligned 0 times concordantly or discordantly; of these: 1155248 mates make up the pairs; of these: 804222 (69.61%) aligned 0 times 199946 (17.31%) aligned exactly 1 time 151080 (13.08%) aligned >1 times 97.05% overall alignment rate Time searching: 00:11:18 Overall time: 00:11:18 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] 416007 / 13008793 = 0.0320 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 23:29:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.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 @ Fri, 05 Jul 2019 23:29:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:29:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:29:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.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 @ Fri, 05 Jul 2019 23:29:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:29:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:29:24: 1000000 INFO @ Fri, 05 Jul 2019 23:29:25: 1000000 INFO @ Fri, 05 Jul 2019 23:29:33: 2000000 INFO @ Fri, 05 Jul 2019 23:29:34: 2000000 INFO @ Fri, 05 Jul 2019 23:29:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.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 @ Fri, 05 Jul 2019 23:29:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:29:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:29:42: 3000000 INFO @ Fri, 05 Jul 2019 23:29:43: 3000000 INFO @ Fri, 05 Jul 2019 23:29:47: 1000000 INFO @ Fri, 05 Jul 2019 23:29:52: 4000000 INFO @ Fri, 05 Jul 2019 23:29:54: 4000000 INFO @ Fri, 05 Jul 2019 23:29:57: 2000000 INFO @ Fri, 05 Jul 2019 23:30:01: 5000000 INFO @ Fri, 05 Jul 2019 23:30:04: 5000000 INFO @ Fri, 05 Jul 2019 23:30:07: 3000000 INFO @ Fri, 05 Jul 2019 23:30:10: 6000000 INFO @ Fri, 05 Jul 2019 23:30:14: 6000000 INFO @ Fri, 05 Jul 2019 23:30:17: 4000000 INFO @ Fri, 05 Jul 2019 23:30:19: 7000000 INFO @ Fri, 05 Jul 2019 23:30:24: 7000000 INFO @ Fri, 05 Jul 2019 23:30:27: 5000000 INFO @ Fri, 05 Jul 2019 23:30:28: 8000000 INFO @ Fri, 05 Jul 2019 23:30:34: 8000000 INFO @ Fri, 05 Jul 2019 23:30:37: 9000000 INFO @ Fri, 05 Jul 2019 23:30:37: 6000000 INFO @ Fri, 05 Jul 2019 23:30:44: 9000000 INFO @ Fri, 05 Jul 2019 23:30:46: 10000000 INFO @ Fri, 05 Jul 2019 23:30:47: 7000000 INFO @ Fri, 05 Jul 2019 23:30:54: 10000000 INFO @ Fri, 05 Jul 2019 23:30:55: 11000000 INFO @ Fri, 05 Jul 2019 23:30:57: 8000000 INFO @ Fri, 05 Jul 2019 23:31:04: 11000000 INFO @ Fri, 05 Jul 2019 23:31:04: 12000000 INFO @ Fri, 05 Jul 2019 23:31:07: 9000000 INFO @ Fri, 05 Jul 2019 23:31:13: 13000000 INFO @ Fri, 05 Jul 2019 23:31:14: 12000000 INFO @ Fri, 05 Jul 2019 23:31:17: 10000000 INFO @ Fri, 05 Jul 2019 23:31:22: 14000000 INFO @ Fri, 05 Jul 2019 23:31:24: 13000000 INFO @ Fri, 05 Jul 2019 23:31:27: 11000000 INFO @ Fri, 05 Jul 2019 23:31:31: 15000000 INFO @ Fri, 05 Jul 2019 23:31:33: 14000000 INFO @ Fri, 05 Jul 2019 23:31:38: 12000000 INFO @ Fri, 05 Jul 2019 23:31:40: 16000000 INFO @ Fri, 05 Jul 2019 23:31:42: 15000000 INFO @ Fri, 05 Jul 2019 23:31:48: 13000000 INFO @ Fri, 05 Jul 2019 23:31:49: 17000000 INFO @ Fri, 05 Jul 2019 23:31:51: 16000000 INFO @ Fri, 05 Jul 2019 23:31:58: 18000000 INFO @ Fri, 05 Jul 2019 23:31:58: 14000000 INFO @ Fri, 05 Jul 2019 23:32:00: 17000000 INFO @ Fri, 05 Jul 2019 23:32:07: 19000000 INFO @ Fri, 05 Jul 2019 23:32:09: 15000000 INFO @ Fri, 05 Jul 2019 23:32:09: 18000000 INFO @ Fri, 05 Jul 2019 23:32:16: 20000000 INFO @ Fri, 05 Jul 2019 23:32:18: 19000000 INFO @ Fri, 05 Jul 2019 23:32:19: 16000000 INFO @ Fri, 05 Jul 2019 23:32:25: 21000000 INFO @ Fri, 05 Jul 2019 23:32:27: 20000000 INFO @ Fri, 05 Jul 2019 23:32:29: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:32:32: 22000000 INFO @ Fri, 05 Jul 2019 23:32:36: 21000000 INFO @ Fri, 05 Jul 2019 23:32:39: 18000000 INFO @ Fri, 05 Jul 2019 23:32:41: 23000000 INFO @ Fri, 05 Jul 2019 23:32:44: 22000000 INFO @ Fri, 05 Jul 2019 23:32:48: 19000000 INFO @ Fri, 05 Jul 2019 23:32:50: 24000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:32:53: 23000000 INFO @ Fri, 05 Jul 2019 23:32:58: 20000000 INFO @ Fri, 05 Jul 2019 23:32:59: 25000000 INFO @ Fri, 05 Jul 2019 23:33:02: 24000000 INFO @ Fri, 05 Jul 2019 23:33:04: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:33:04: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:33:04: #1 total tags in treatment: 12354209 INFO @ Fri, 05 Jul 2019 23:33:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:33:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:33:04: #1 tags after filtering in treatment: 8128166 INFO @ Fri, 05 Jul 2019 23:33:04: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 05 Jul 2019 23:33:04: #1 finished! INFO @ Fri, 05 Jul 2019 23:33:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:33:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:33:05: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:33:05: 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 @ Fri, 05 Jul 2019 23:33:05: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:33:08: 21000000 INFO @ Fri, 05 Jul 2019 23:33:10: 25000000 INFO @ Fri, 05 Jul 2019 23:33:16: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:33:16: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:33:16: #1 total tags in treatment: 12354209 INFO @ Fri, 05 Jul 2019 23:33:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:33:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:33:16: #1 tags after filtering in treatment: 8128166 INFO @ Fri, 05 Jul 2019 23:33:16: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 05 Jul 2019 23:33:16: #1 finished! INFO @ Fri, 05 Jul 2019 23:33:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:33:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:33:17: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:33:17: 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 @ Fri, 05 Jul 2019 23:33:17: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:33:17: 22000000 INFO @ Fri, 05 Jul 2019 23:33:26: 23000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.05_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.10_model.r’: No such file or directory CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:33:35: 24000000 INFO @ Fri, 05 Jul 2019 23:33:45: 25000000 INFO @ Fri, 05 Jul 2019 23:33:51: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:33:51: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:33:51: #1 total tags in treatment: 12354209 INFO @ Fri, 05 Jul 2019 23:33:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:33:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:33:51: #1 tags after filtering in treatment: 8128166 INFO @ Fri, 05 Jul 2019 23:33:51: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 05 Jul 2019 23:33:51: #1 finished! INFO @ Fri, 05 Jul 2019 23:33:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:33:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:33:52: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:33:52: 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 @ Fri, 05 Jul 2019 23:33:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.20_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/SRX381244/SRX381244.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381244/SRX381244.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling