Job ID = 2010633 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,540,912 reads read : 5,081,824 reads written : 5,081,824 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: 00:01:29 2540912 reads; of these: 2540912 (100.00%) were paired; of these: 1319019 (51.91%) aligned concordantly 0 times 534968 (21.05%) aligned concordantly exactly 1 time 686925 (27.03%) aligned concordantly >1 times ---- 1319019 pairs aligned concordantly 0 times; of these: 1393 (0.11%) aligned discordantly 1 time ---- 1317626 pairs aligned 0 times concordantly or discordantly; of these: 2635252 mates make up the pairs; of these: 2576766 (97.78%) aligned 0 times 28704 (1.09%) aligned exactly 1 time 29782 (1.13%) aligned >1 times 49.29% overall alignment rate Time searching: 00:01:29 Overall time: 00:01:29 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] 189907 / 1222726 = 0.1553 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 23:44:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.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 23:44:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:44:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:44:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.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 23:44:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:44:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:44:49: 1000000 INFO @ Fri, 05 Jul 2019 23:44:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.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 23:44:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:44:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:44:51: 1000000 INFO @ Fri, 05 Jul 2019 23:44:57: 2000000 INFO @ Fri, 05 Jul 2019 23:44:58: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 23:44:58: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 23:44:58: #1 total tags in treatment: 1032067 INFO @ Fri, 05 Jul 2019 23:44:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:44:58: #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 23:44:58: #1 tags after filtering in treatment: 497194 INFO @ Fri, 05 Jul 2019 23:44:58: #1 Redundant rate of treatment: 0.52 INFO @ Fri, 05 Jul 2019 23:44:58: #1 finished! INFO @ Fri, 05 Jul 2019 23:44:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:44:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:44:58: #2 number of paired peaks: 54 WARNING @ Fri, 05 Jul 2019 23:44:58: Too few paired peaks (54) 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 23:44:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.10_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/SRX3829149/SRX3829149.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:45:02: 1000000 INFO @ Fri, 05 Jul 2019 23:45:03: 2000000 INFO @ Fri, 05 Jul 2019 23:45:05: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 23:45:05: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 23:45:05: #1 total tags in treatment: 1032067 INFO @ Fri, 05 Jul 2019 23:45:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:45:05: #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 23:45:05: #1 tags after filtering in treatment: 497194 INFO @ Fri, 05 Jul 2019 23:45:05: #1 Redundant rate of treatment: 0.52 INFO @ Fri, 05 Jul 2019 23:45:05: #1 finished! INFO @ Fri, 05 Jul 2019 23:45:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:45:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:45:05: #2 number of paired peaks: 54 WARNING @ Fri, 05 Jul 2019 23:45:05: Too few paired peaks (54) 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 23:45:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.05_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/SRX3829149/SRX3829149.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:45:13: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:45:14: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 23:45:14: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 23:45:14: #1 total tags in treatment: 1032067 INFO @ Fri, 05 Jul 2019 23:45:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:45:14: #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 23:45:14: #1 tags after filtering in treatment: 497194 INFO @ Fri, 05 Jul 2019 23:45:14: #1 Redundant rate of treatment: 0.52 INFO @ Fri, 05 Jul 2019 23:45:14: #1 finished! INFO @ Fri, 05 Jul 2019 23:45:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:45:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:45:14: #2 number of paired peaks: 54 WARNING @ Fri, 05 Jul 2019 23:45:14: Too few paired peaks (54) 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 23:45:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.20_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/SRX3829149/SRX3829149.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3829149/SRX3829149.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。