Job ID = 2011894 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,511,793 reads read : 7,023,586 reads written : 7,023,586 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: 00:02:15 3511793 reads; of these: 3511793 (100.00%) were paired; of these: 397048 (11.31%) aligned concordantly 0 times 2543944 (72.44%) aligned concordantly exactly 1 time 570801 (16.25%) aligned concordantly >1 times ---- 397048 pairs aligned concordantly 0 times; of these: 209224 (52.69%) aligned discordantly 1 time ---- 187824 pairs aligned 0 times concordantly or discordantly; of these: 375648 mates make up the pairs; of these: 220193 (58.62%) aligned 0 times 57849 (15.40%) aligned exactly 1 time 97606 (25.98%) aligned >1 times 96.86% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 130055 / 3323144 = 0.0391 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 @ Sat, 06 Jul 2019 03:07:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.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, 06 Jul 2019 03:07:19: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:07:19: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:07:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.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, 06 Jul 2019 03:07:20: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:07:20: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:07:25: 1000000 INFO @ Sat, 06 Jul 2019 03:07:27: 1000000 INFO @ Sat, 06 Jul 2019 03:07:31: 2000000 INFO @ Sat, 06 Jul 2019 03:07:34: 2000000 INFO @ Sat, 06 Jul 2019 03:07:37: 3000000 INFO @ Sat, 06 Jul 2019 03:07:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.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, 06 Jul 2019 03:07:41: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:07:41: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:07:41: 3000000 INFO @ Sat, 06 Jul 2019 03:07:43: 4000000 INFO @ Sat, 06 Jul 2019 03:07:47: 1000000 INFO @ Sat, 06 Jul 2019 03:07:48: 4000000 INFO @ Sat, 06 Jul 2019 03:07:49: 5000000 INFO @ Sat, 06 Jul 2019 03:07:53: 2000000 INFO @ Sat, 06 Jul 2019 03:07:55: 6000000 INFO @ Sat, 06 Jul 2019 03:07:56: 5000000 INFO @ Sat, 06 Jul 2019 03:07:58: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:07:58: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:07:58: #1 total tags in treatment: 2989354 INFO @ Sat, 06 Jul 2019 03:07:58: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:07:58: #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 03:07:58: #1 tags after filtering in treatment: 2443690 INFO @ Sat, 06 Jul 2019 03:07:58: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 06 Jul 2019 03:07:58: #1 finished! INFO @ Sat, 06 Jul 2019 03:07:58: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:07:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:07:59: #2 number of paired peaks: 57 WARNING @ Sat, 06 Jul 2019 03:07:59: Too few paired peaks (57) 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 03:07:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:07:59: 3000000 INFO @ Sat, 06 Jul 2019 03:08:03: 6000000 INFO @ Sat, 06 Jul 2019 03:08:05: 4000000 INFO @ Sat, 06 Jul 2019 03:08:06: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:08:06: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:08:06: #1 total tags in treatment: 2989354 INFO @ Sat, 06 Jul 2019 03:08:06: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:08:06: #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 03:08:06: #1 tags after filtering in treatment: 2443690 INFO @ Sat, 06 Jul 2019 03:08:06: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 06 Jul 2019 03:08:06: #1 finished! INFO @ Sat, 06 Jul 2019 03:08:06: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:08:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:08:07: #2 number of paired peaks: 57 WARNING @ Sat, 06 Jul 2019 03:08:07: Too few paired peaks (57) 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 03:08:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:08:11: 5000000 INFO @ Sat, 06 Jul 2019 03:08:17: 6000000 INFO @ Sat, 06 Jul 2019 03:08:20: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:08:20: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:08:20: #1 total tags in treatment: 2989354 INFO @ Sat, 06 Jul 2019 03:08:20: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:08:20: #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 03:08:20: #1 tags after filtering in treatment: 2443690 INFO @ Sat, 06 Jul 2019 03:08:20: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 06 Jul 2019 03:08:20: #1 finished! INFO @ Sat, 06 Jul 2019 03:08:20: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:08:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:08:21: #2 number of paired peaks: 57 WARNING @ Sat, 06 Jul 2019 03:08:21: Too few paired peaks (57) 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 03:08:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383670/SRX5383670.20_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。