Job ID = 2008294 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,287,410 reads read : 4,574,820 reads written : 4,574,820 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: 00:01:45 2287410 reads; of these: 2287410 (100.00%) were paired; of these: 255274 (11.16%) aligned concordantly 0 times 1745612 (76.31%) aligned concordantly exactly 1 time 286524 (12.53%) aligned concordantly >1 times ---- 255274 pairs aligned concordantly 0 times; of these: 32388 (12.69%) aligned discordantly 1 time ---- 222886 pairs aligned 0 times concordantly or discordantly; of these: 445772 mates make up the pairs; of these: 397698 (89.22%) aligned 0 times 13711 (3.08%) aligned exactly 1 time 34363 (7.71%) aligned >1 times 91.31% overall alignment rate Time searching: 00:01:45 Overall time: 00:01:45 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] 960959 / 2055822 = 0.4674 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 18:24:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.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 18:24:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:24:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:24:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.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 18:24:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:24:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:24:50: 1000000 INFO @ Fri, 05 Jul 2019 18:24:51: 1000000 INFO @ Fri, 05 Jul 2019 18:24:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.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 18:24:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:24:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:24:58: 2000000 INFO @ Fri, 05 Jul 2019 18:24:59: 2000000 INFO @ Fri, 05 Jul 2019 18:25:00: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:25:00: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:25:00: #1 total tags in treatment: 1076617 INFO @ Fri, 05 Jul 2019 18:25:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:25:00: #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 18:25:00: #1 tags after filtering in treatment: 899579 INFO @ Fri, 05 Jul 2019 18:25:00: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 05 Jul 2019 18:25:00: #1 finished! INFO @ Fri, 05 Jul 2019 18:25:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:25:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:25:00: #2 number of paired peaks: 29 WARNING @ Fri, 05 Jul 2019 18:25:00: 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 18:25:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.05_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/ERX585806/ERX585806.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:25:01: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:25:01: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:25:01: #1 total tags in treatment: 1076617 INFO @ Fri, 05 Jul 2019 18:25:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:25:01: #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 18:25:01: #1 tags after filtering in treatment: 899579 INFO @ Fri, 05 Jul 2019 18:25:01: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 05 Jul 2019 18:25:01: #1 finished! INFO @ Fri, 05 Jul 2019 18:25:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:25:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:25:01: #2 number of paired peaks: 29 WARNING @ Fri, 05 Jul 2019 18:25:01: 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 18:25:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.10_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/ERX585806/ERX585806.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:25:07: 1000000 INFO @ Fri, 05 Jul 2019 18:25:16: 2000000 INFO @ Fri, 05 Jul 2019 18:25:18: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:25:18: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:25:18: #1 total tags in treatment: 1076617 INFO @ Fri, 05 Jul 2019 18:25:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:25:18: #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 18:25:18: #1 tags after filtering in treatment: 899579 INFO @ Fri, 05 Jul 2019 18:25:18: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 05 Jul 2019 18:25:18: #1 finished! INFO @ Fri, 05 Jul 2019 18:25:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:25:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:25:18: #2 number of paired peaks: 29 WARNING @ Fri, 05 Jul 2019 18:25:18: 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 18:25:18: Process for pairing-model is terminated! BedGraph に変換しました。 cut: /home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.20_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585806/ERX585806.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。