Job ID = 2010695 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,337,170 reads read : 8,674,340 reads written : 8,674,340 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: 00:02:16 4337170 reads; of these: 4337170 (100.00%) were paired; of these: 2272578 (52.40%) aligned concordantly 0 times 1908023 (43.99%) aligned concordantly exactly 1 time 156569 (3.61%) aligned concordantly >1 times ---- 2272578 pairs aligned concordantly 0 times; of these: 152196 (6.70%) aligned discordantly 1 time ---- 2120382 pairs aligned 0 times concordantly or discordantly; of these: 4240764 mates make up the pairs; of these: 2367163 (55.82%) aligned 0 times 1704630 (40.20%) aligned exactly 1 time 168971 (3.98%) aligned >1 times 72.71% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 186273 / 2216183 = 0.0841 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 23:59:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.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 23:59:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:59:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:59:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.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 23:59:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:59:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:59:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.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 23:59:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:59:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:59:51: 1000000 INFO @ Fri, 05 Jul 2019 23:59:52: 1000000 INFO @ Fri, 05 Jul 2019 23:59:53: 1000000 INFO @ Sat, 06 Jul 2019 00:00:01: 2000000 INFO @ Sat, 06 Jul 2019 00:00:03: 2000000 INFO @ Sat, 06 Jul 2019 00:00:03: 2000000 INFO @ Sat, 06 Jul 2019 00:00:11: 3000000 INFO @ Sat, 06 Jul 2019 00:00:13: 3000000 INFO @ Sat, 06 Jul 2019 00:00:14: 3000000 INFO @ Sat, 06 Jul 2019 00:00:21: 4000000 INFO @ Sat, 06 Jul 2019 00:00:23: 4000000 INFO @ Sat, 06 Jul 2019 00:00:24: 4000000 INFO @ Sat, 06 Jul 2019 00:00:31: 5000000 INFO @ Sat, 06 Jul 2019 00:00:34: 5000000 INFO @ Sat, 06 Jul 2019 00:00:34: 5000000 INFO @ Sat, 06 Jul 2019 00:00:40: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:00:40: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:00:40: #1 total tags in treatment: 1887868 INFO @ Sat, 06 Jul 2019 00:00:40: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:00:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:00:40: #1 tags after filtering in treatment: 1295713 INFO @ Sat, 06 Jul 2019 00:00:40: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 06 Jul 2019 00:00:40: #1 finished! INFO @ Sat, 06 Jul 2019 00:00:40: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:00:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:00:40: #2 number of paired peaks: 41 WARNING @ Sat, 06 Jul 2019 00:00:40: Too few paired peaks (41) 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, 06 Jul 2019 00:00:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.05_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/SRX3865927/SRX3865927.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:00:43: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:00:43: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:00:43: #1 total tags in treatment: 1887868 INFO @ Sat, 06 Jul 2019 00:00:43: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:00:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:00:43: #1 tags after filtering in treatment: 1295713 INFO @ Sat, 06 Jul 2019 00:00:43: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 06 Jul 2019 00:00:43: #1 finished! INFO @ Sat, 06 Jul 2019 00:00:43: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:00:43: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:00:43: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:00:43: #1 total tags in treatment: 1887868 INFO @ Sat, 06 Jul 2019 00:00:43: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:00:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:00:43: #2 number of paired peaks: 41 WARNING @ Sat, 06 Jul 2019 00:00:43: Too few paired peaks (41) 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, 06 Jul 2019 00:00:43: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:00:43: #1 tags after filtering in treatment: 1295713 INFO @ Sat, 06 Jul 2019 00:00:43: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 06 Jul 2019 00:00:43: #1 finished! INFO @ Sat, 06 Jul 2019 00:00:43: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:00:43: #2 looking for paired plus/minus strand peaks... cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.10_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/SRX3865927/SRX3865927.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:00:43: #2 number of paired peaks: 41 WARNING @ Sat, 06 Jul 2019 00:00:43: Too few paired peaks (41) 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, 06 Jul 2019 00:00:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.20_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/SRX3865927/SRX3865927.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865927/SRX3865927.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。