Job ID = 2008187 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,178,499 reads read : 14,356,998 reads written : 14,356,998 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628933.sra.cache’: 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: 00:09:02 7178499 reads; of these: 7178499 (100.00%) were paired; of these: 364668 (5.08%) aligned concordantly 0 times 5834434 (81.28%) aligned concordantly exactly 1 time 979397 (13.64%) aligned concordantly >1 times ---- 364668 pairs aligned concordantly 0 times; of these: 170135 (46.65%) aligned discordantly 1 time ---- 194533 pairs aligned 0 times concordantly or discordantly; of these: 389066 mates make up the pairs; of these: 246017 (63.23%) aligned 0 times 76478 (19.66%) aligned exactly 1 time 66571 (17.11%) aligned >1 times 98.29% overall alignment rate Time searching: 00:09:02 Overall time: 00:09:02 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 8 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] 985212 / 6959383 = 0.1416 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 17:53:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.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 17:53:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:53:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:53:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.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 17:53:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:53:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:53:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.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 17:53:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:53:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:53:35: 1000000 INFO @ Fri, 05 Jul 2019 17:53:36: 1000000 INFO @ Fri, 05 Jul 2019 17:53:38: 1000000 INFO @ Fri, 05 Jul 2019 17:53:43: 2000000 INFO @ Fri, 05 Jul 2019 17:53:43: 2000000 INFO @ Fri, 05 Jul 2019 17:53:46: 2000000 INFO @ Fri, 05 Jul 2019 17:53:50: 3000000 INFO @ Fri, 05 Jul 2019 17:53:51: 3000000 INFO @ Fri, 05 Jul 2019 17:53:54: 3000000 INFO @ Fri, 05 Jul 2019 17:53:57: 4000000 INFO @ Fri, 05 Jul 2019 17:53:58: 4000000 INFO @ Fri, 05 Jul 2019 17:54:03: 4000000 INFO @ Fri, 05 Jul 2019 17:54:06: 5000000 INFO @ Fri, 05 Jul 2019 17:54:06: 5000000 INFO @ Fri, 05 Jul 2019 17:54:11: 5000000 INFO @ Fri, 05 Jul 2019 17:54:14: 6000000 INFO @ Fri, 05 Jul 2019 17:54:14: 6000000 INFO @ Fri, 05 Jul 2019 17:54:19: 6000000 INFO @ Fri, 05 Jul 2019 17:54:21: 7000000 INFO @ Fri, 05 Jul 2019 17:54:21: 7000000 INFO @ Fri, 05 Jul 2019 17:54:27: 7000000 INFO @ Fri, 05 Jul 2019 17:54:29: 8000000 INFO @ Fri, 05 Jul 2019 17:54:29: 8000000 INFO @ Fri, 05 Jul 2019 17:54:35: 8000000 INFO @ Fri, 05 Jul 2019 17:54:36: 9000000 INFO @ Fri, 05 Jul 2019 17:54:36: 9000000 INFO @ Fri, 05 Jul 2019 17:54:44: 9000000 INFO @ Fri, 05 Jul 2019 17:54:44: 10000000 INFO @ Fri, 05 Jul 2019 17:54:44: 10000000 INFO @ Fri, 05 Jul 2019 17:54:51: 11000000 INFO @ Fri, 05 Jul 2019 17:54:52: 11000000 INFO @ Fri, 05 Jul 2019 17:54:52: 10000000 INFO @ Fri, 05 Jul 2019 17:54:59: 12000000 INFO @ Fri, 05 Jul 2019 17:54:59: 12000000 INFO @ Fri, 05 Jul 2019 17:55:00: 11000000 INFO @ Fri, 05 Jul 2019 17:55:00: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 17:55:00: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 17:55:00: #1 total tags in treatment: 5831969 INFO @ Fri, 05 Jul 2019 17:55:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:55:00: #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 17:55:00: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 17:55:00: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 17:55:00: #1 total tags in treatment: 5831969 INFO @ Fri, 05 Jul 2019 17:55:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:55:00: #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 17:55:00: #1 tags after filtering in treatment: 3547538 INFO @ Fri, 05 Jul 2019 17:55:00: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 05 Jul 2019 17:55:00: #1 finished! INFO @ Fri, 05 Jul 2019 17:55:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:55:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:55:00: #1 tags after filtering in treatment: 3547538 INFO @ Fri, 05 Jul 2019 17:55:00: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 05 Jul 2019 17:55:00: #1 finished! INFO @ Fri, 05 Jul 2019 17:55:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:55:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:55:01: #2 number of paired peaks: 1 WARNING @ Fri, 05 Jul 2019 17:55:01: Too few paired peaks (1) 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 17:55:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.10_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/ERX585722/ERX585722.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:55:01: #2 number of paired peaks: 1 WARNING @ Fri, 05 Jul 2019 17:55:01: Too few paired peaks (1) 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 17:55:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.05_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/ERX585722/ERX585722.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:55:08: 12000000 INFO @ Fri, 05 Jul 2019 17:55:09: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 17:55:09: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 17:55:09: #1 total tags in treatment: 5831969 INFO @ Fri, 05 Jul 2019 17:55:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:55:09: #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 17:55:09: #1 tags after filtering in treatment: 3547538 INFO @ Fri, 05 Jul 2019 17:55:09: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 05 Jul 2019 17:55:09: #1 finished! INFO @ Fri, 05 Jul 2019 17:55:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:55:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:55:10: #2 number of paired peaks: 1 WARNING @ Fri, 05 Jul 2019 17:55:10: Too few paired peaks (1) 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 17:55:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.20_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/ERX585722/ERX585722.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585722/ERX585722.20_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。