Job ID = 2641245 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,542,476 reads read : 3,084,952 reads written : 3,084,952 spots read : 1,518,317 reads read : 3,036,634 reads written : 3,036,634 spots read : 1,532,555 reads read : 3,065,110 reads written : 3,065,110 spots read : 1,521,875 reads read : 3,043,750 reads written : 3,043,750 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: 00:02:50 6115223 reads; of these: 6115223 (100.00%) were paired; of these: 2094163 (34.25%) aligned concordantly 0 times 3520729 (57.57%) aligned concordantly exactly 1 time 500331 (8.18%) aligned concordantly >1 times ---- 2094163 pairs aligned concordantly 0 times; of these: 4298 (0.21%) aligned discordantly 1 time ---- 2089865 pairs aligned 0 times concordantly or discordantly; of these: 4179730 mates make up the pairs; of these: 3411272 (81.61%) aligned 0 times 654838 (15.67%) aligned exactly 1 time 113620 (2.72%) aligned >1 times 72.11% overall alignment rate Time searching: 00:02:50 Overall time: 00:02:50 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] 87240 / 4023759 = 0.0217 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:22:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.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 @ Sat, 24 Aug 2019 22:22:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:22:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:22:41: 1000000 INFO @ Sat, 24 Aug 2019 22:22:47: 2000000 INFO @ Sat, 24 Aug 2019 22:22:54: 3000000 INFO @ Sat, 24 Aug 2019 22:23:00: 4000000 INFO @ Sat, 24 Aug 2019 22:23:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.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 @ Sat, 24 Aug 2019 22:23:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:23:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:23:07: 5000000 INFO @ Sat, 24 Aug 2019 22:23:11: 1000000 INFO @ Sat, 24 Aug 2019 22:23:13: 6000000 INFO @ Sat, 24 Aug 2019 22:23:17: 2000000 INFO @ Sat, 24 Aug 2019 22:23:20: 7000000 INFO @ Sat, 24 Aug 2019 22:23:24: 3000000 INFO @ Sat, 24 Aug 2019 22:23:26: 8000000 INFO @ Sat, 24 Aug 2019 22:23:30: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:23:30: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:23:30: #1 total tags in treatment: 3933870 INFO @ Sat, 24 Aug 2019 22:23:30: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:23:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:23:30: #1 tags after filtering in treatment: 3360845 INFO @ Sat, 24 Aug 2019 22:23:30: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 24 Aug 2019 22:23:30: #1 finished! INFO @ Sat, 24 Aug 2019 22:23:30: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:23:31: 4000000 INFO @ Sat, 24 Aug 2019 22:23:31: #2 number of paired peaks: 44 WARNING @ Sat, 24 Aug 2019 22:23:31: Too few paired peaks (44) 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, 24 Aug 2019 22:23:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.05_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/SRX6403222/SRX6403222.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:23:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.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 @ Sat, 24 Aug 2019 22:23:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:23:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:23:37: 5000000 INFO @ Sat, 24 Aug 2019 22:23:42: 1000000 INFO @ Sat, 24 Aug 2019 22:23:44: 6000000 INFO @ Sat, 24 Aug 2019 22:23:50: 2000000 INFO @ Sat, 24 Aug 2019 22:23:50: 7000000 INFO @ Sat, 24 Aug 2019 22:23:57: 8000000 INFO @ Sat, 24 Aug 2019 22:23:58: 3000000 INFO @ Sat, 24 Aug 2019 22:24:01: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:24:01: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:24:01: #1 total tags in treatment: 3933870 INFO @ Sat, 24 Aug 2019 22:24:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:24:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:24:01: #1 tags after filtering in treatment: 3360845 INFO @ Sat, 24 Aug 2019 22:24:01: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 24 Aug 2019 22:24:01: #1 finished! INFO @ Sat, 24 Aug 2019 22:24:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:24:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:24:02: #2 number of paired peaks: 44 WARNING @ Sat, 24 Aug 2019 22:24:02: Too few paired peaks (44) 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, 24 Aug 2019 22:24:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.10_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/SRX6403222/SRX6403222.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:24:05: 4000000 INFO @ Sat, 24 Aug 2019 22:24:13: 5000000 INFO @ Sat, 24 Aug 2019 22:24:20: 6000000 INFO @ Sat, 24 Aug 2019 22:24:28: 7000000 INFO @ Sat, 24 Aug 2019 22:24:35: 8000000 INFO @ Sat, 24 Aug 2019 22:24:40: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:24:40: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:24:40: #1 total tags in treatment: 3933870 INFO @ Sat, 24 Aug 2019 22:24:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:24:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:24:40: #1 tags after filtering in treatment: 3360845 INFO @ Sat, 24 Aug 2019 22:24:40: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 24 Aug 2019 22:24:40: #1 finished! INFO @ Sat, 24 Aug 2019 22:24:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:24:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:24:40: #2 number of paired peaks: 44 WARNING @ Sat, 24 Aug 2019 22:24:40: Too few paired peaks (44) 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, 24 Aug 2019 22:24:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.20_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/SRX6403222/SRX6403222.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403222/SRX6403222.20_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。