Job ID = 2010651 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,083,027 reads read : 10,166,054 reads written : 10,166,054 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: 00:03:52 5083027 reads; of these: 5083027 (100.00%) were paired; of these: 655014 (12.89%) aligned concordantly 0 times 3956203 (77.83%) aligned concordantly exactly 1 time 471810 (9.28%) aligned concordantly >1 times ---- 655014 pairs aligned concordantly 0 times; of these: 311761 (47.60%) aligned discordantly 1 time ---- 343253 pairs aligned 0 times concordantly or discordantly; of these: 686506 mates make up the pairs; of these: 408795 (59.55%) aligned 0 times 171156 (24.93%) aligned exactly 1 time 106555 (15.52%) aligned >1 times 95.98% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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_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] 187010 / 4554122 = 0.0411 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 23:55:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.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 23:55:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:55:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:55:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.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 23:55:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:55:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:55:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.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 23:55:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:55:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:55:25: 1000000 INFO @ Fri, 05 Jul 2019 23:55:26: 1000000 INFO @ Fri, 05 Jul 2019 23:55:26: 1000000 INFO @ Fri, 05 Jul 2019 23:55:33: 2000000 INFO @ Fri, 05 Jul 2019 23:55:33: 2000000 INFO @ Fri, 05 Jul 2019 23:55:34: 2000000 INFO @ Fri, 05 Jul 2019 23:55:41: 3000000 INFO @ Fri, 05 Jul 2019 23:55:42: 3000000 INFO @ Fri, 05 Jul 2019 23:55:43: 3000000 INFO @ Fri, 05 Jul 2019 23:55:48: 4000000 INFO @ Fri, 05 Jul 2019 23:55:50: 4000000 INFO @ Fri, 05 Jul 2019 23:55:51: 4000000 INFO @ Fri, 05 Jul 2019 23:55:55: 5000000 INFO @ Fri, 05 Jul 2019 23:55:59: 5000000 INFO @ Fri, 05 Jul 2019 23:56:00: 5000000 INFO @ Fri, 05 Jul 2019 23:56:02: 6000000 INFO @ Fri, 05 Jul 2019 23:56:07: 6000000 INFO @ Fri, 05 Jul 2019 23:56:08: 6000000 INFO @ Fri, 05 Jul 2019 23:56:10: 7000000 INFO @ Fri, 05 Jul 2019 23:56:16: 7000000 INFO @ Fri, 05 Jul 2019 23:56:17: 7000000 INFO @ Fri, 05 Jul 2019 23:56:17: 8000000 INFO @ Fri, 05 Jul 2019 23:56:24: 9000000 INFO @ Fri, 05 Jul 2019 23:56:25: 8000000 INFO @ Fri, 05 Jul 2019 23:56:27: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:56:27: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:56:27: #1 total tags in treatment: 4241559 INFO @ Fri, 05 Jul 2019 23:56:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:56:27: #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 23:56:27: #1 tags after filtering in treatment: 3071870 INFO @ Fri, 05 Jul 2019 23:56:27: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 05 Jul 2019 23:56:27: #1 finished! INFO @ Fri, 05 Jul 2019 23:56:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:56:27: #2 number of paired peaks: 29 WARNING @ Fri, 05 Jul 2019 23:56:27: Too few paired peaks (29) 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 23:56:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.20_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/SRX3865841/SRX3865841.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:56:27: 8000000 INFO @ Fri, 05 Jul 2019 23:56:33: 9000000 INFO @ Fri, 05 Jul 2019 23:56:36: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:56:36: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:56:36: #1 total tags in treatment: 4241559 INFO @ Fri, 05 Jul 2019 23:56:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:56:36: #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 23:56:36: #1 tags after filtering in treatment: 3071870 INFO @ Fri, 05 Jul 2019 23:56:36: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 05 Jul 2019 23:56:36: #1 finished! INFO @ Fri, 05 Jul 2019 23:56:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:56:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:56:37: #2 number of paired peaks: 29 WARNING @ Fri, 05 Jul 2019 23:56:37: Too few paired peaks (29) 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 23:56:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.10_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/SRX3865841/SRX3865841.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:56:38: 9000000 INFO @ Fri, 05 Jul 2019 23:56:42: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:56:42: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:56:42: #1 total tags in treatment: 4241559 INFO @ Fri, 05 Jul 2019 23:56:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:56:42: #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 23:56:42: #1 tags after filtering in treatment: 3071870 INFO @ Fri, 05 Jul 2019 23:56:42: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 05 Jul 2019 23:56:42: #1 finished! INFO @ Fri, 05 Jul 2019 23:56:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:56:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:56:43: #2 number of paired peaks: 29 WARNING @ Fri, 05 Jul 2019 23:56:43: Too few paired peaks (29) 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 23:56:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.05_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/SRX3865841/SRX3865841.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865841/SRX3865841.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。