Job ID = 2010555 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,480,103 reads read : 26,960,206 reads written : 26,960,206 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: 00:10:25 13480103 reads; of these: 13480103 (100.00%) were paired; of these: 2219794 (16.47%) aligned concordantly 0 times 8853635 (65.68%) aligned concordantly exactly 1 time 2406674 (17.85%) aligned concordantly >1 times ---- 2219794 pairs aligned concordantly 0 times; of these: 396987 (17.88%) aligned discordantly 1 time ---- 1822807 pairs aligned 0 times concordantly or discordantly; of these: 3645614 mates make up the pairs; of these: 3231396 (88.64%) aligned 0 times 187374 (5.14%) aligned exactly 1 time 226844 (6.22%) aligned >1 times 88.01% overall alignment rate Time searching: 00:10:25 Overall time: 00:10:25 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] 689993 / 11645601 = 0.0592 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 23:26:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.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 23:26:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:26:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:26:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.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 23:26:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:26:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:27:05: 1000000 INFO @ Fri, 05 Jul 2019 23:27:06: 1000000 INFO @ Fri, 05 Jul 2019 23:27:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.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 23:27:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:27:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:27:14: 2000000 INFO @ Fri, 05 Jul 2019 23:27:16: 2000000 INFO @ Fri, 05 Jul 2019 23:27:20: 1000000 INFO @ Fri, 05 Jul 2019 23:27:22: 3000000 INFO @ Fri, 05 Jul 2019 23:27:26: 3000000 INFO @ Fri, 05 Jul 2019 23:27:30: 2000000 INFO @ Fri, 05 Jul 2019 23:27:31: 4000000 INFO @ Fri, 05 Jul 2019 23:27:35: 4000000 INFO @ Fri, 05 Jul 2019 23:27:40: 3000000 INFO @ Fri, 05 Jul 2019 23:27:40: 5000000 INFO @ Fri, 05 Jul 2019 23:27:45: 5000000 INFO @ Fri, 05 Jul 2019 23:27:48: 6000000 INFO @ Fri, 05 Jul 2019 23:27:49: 4000000 INFO @ Fri, 05 Jul 2019 23:27:54: 6000000 INFO @ Fri, 05 Jul 2019 23:27:57: 7000000 INFO @ Fri, 05 Jul 2019 23:27:59: 5000000 INFO @ Fri, 05 Jul 2019 23:28:04: 7000000 INFO @ Fri, 05 Jul 2019 23:28:05: 8000000 INFO @ Fri, 05 Jul 2019 23:28:08: 6000000 INFO @ Fri, 05 Jul 2019 23:28:13: 8000000 INFO @ Fri, 05 Jul 2019 23:28:14: 9000000 INFO @ Fri, 05 Jul 2019 23:28:18: 7000000 INFO @ Fri, 05 Jul 2019 23:28:22: 10000000 INFO @ Fri, 05 Jul 2019 23:28:23: 9000000 INFO @ Fri, 05 Jul 2019 23:28:27: 8000000 INFO @ Fri, 05 Jul 2019 23:28:30: 11000000 INFO @ Fri, 05 Jul 2019 23:28:32: 10000000 INFO @ Fri, 05 Jul 2019 23:28:37: 9000000 INFO @ Fri, 05 Jul 2019 23:28:38: 12000000 INFO @ Fri, 05 Jul 2019 23:28:42: 11000000 INFO @ Fri, 05 Jul 2019 23:28:46: 13000000 INFO @ Fri, 05 Jul 2019 23:28:47: 10000000 INFO @ Fri, 05 Jul 2019 23:28:52: 12000000 INFO @ Fri, 05 Jul 2019 23:28:54: 14000000 INFO @ Fri, 05 Jul 2019 23:28:56: 11000000 INFO @ Fri, 05 Jul 2019 23:29:01: 13000000 INFO @ Fri, 05 Jul 2019 23:29:03: 15000000 INFO @ Fri, 05 Jul 2019 23:29:06: 12000000 INFO @ Fri, 05 Jul 2019 23:29:11: 14000000 INFO @ Fri, 05 Jul 2019 23:29:11: 16000000 INFO @ Fri, 05 Jul 2019 23:29:15: 13000000 INFO @ Fri, 05 Jul 2019 23:29:19: 17000000 INFO @ Fri, 05 Jul 2019 23:29:20: 15000000 INFO @ Fri, 05 Jul 2019 23:29:25: 14000000 INFO @ Fri, 05 Jul 2019 23:29:28: 18000000 INFO @ Fri, 05 Jul 2019 23:29:29: 16000000 INFO @ Fri, 05 Jul 2019 23:29:35: 15000000 INFO @ Fri, 05 Jul 2019 23:29:36: 19000000 INFO @ Fri, 05 Jul 2019 23:29:39: 17000000 INFO @ Fri, 05 Jul 2019 23:29:44: 16000000 INFO @ Fri, 05 Jul 2019 23:29:44: 20000000 INFO @ Fri, 05 Jul 2019 23:29:48: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:29:53: 21000000 INFO @ Fri, 05 Jul 2019 23:29:53: 17000000 INFO @ Fri, 05 Jul 2019 23:29:58: 19000000 INFO @ Fri, 05 Jul 2019 23:30:01: 22000000 INFO @ Fri, 05 Jul 2019 23:30:03: 18000000 INFO @ Fri, 05 Jul 2019 23:30:04: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:30:04: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:30:04: #1 total tags in treatment: 10585359 INFO @ Fri, 05 Jul 2019 23:30:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:30:04: #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 23:30:04: #1 tags after filtering in treatment: 7108394 INFO @ Fri, 05 Jul 2019 23:30:04: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 23:30:04: #1 finished! INFO @ Fri, 05 Jul 2019 23:30:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:30:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:30:05: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:30:05: 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 23:30:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.05_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/SRX381256/SRX381256.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:30:07: 20000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:30:12: 19000000 INFO @ Fri, 05 Jul 2019 23:30:16: 21000000 INFO @ Fri, 05 Jul 2019 23:30:22: 20000000 INFO @ Fri, 05 Jul 2019 23:30:26: 22000000 INFO @ Fri, 05 Jul 2019 23:30:29: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:30:29: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:30:29: #1 total tags in treatment: 10585359 INFO @ Fri, 05 Jul 2019 23:30:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:30:29: #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 23:30:29: #1 tags after filtering in treatment: 7108394 INFO @ Fri, 05 Jul 2019 23:30:29: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 23:30:29: #1 finished! INFO @ Fri, 05 Jul 2019 23:30:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:30:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:30:30: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:30:30: 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 @ Fri, 05 Jul 2019 23:30:30: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:30:31: 21000000 INFO @ Fri, 05 Jul 2019 23:30:40: 22000000 INFO @ Fri, 05 Jul 2019 23:30:43: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:30:43: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:30:43: #1 total tags in treatment: 10585359 INFO @ Fri, 05 Jul 2019 23:30:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:30:43: #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 23:30:43: #1 tags after filtering in treatment: 7108394 INFO @ Fri, 05 Jul 2019 23:30:43: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 23:30:43: #1 finished! INFO @ Fri, 05 Jul 2019 23:30:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:30:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:30:44: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:30:44: 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 23:30:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 9 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 2 millis rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.20_*.xls’: No such file or directory needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381256/SRX381256.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling