Job ID = 2010671 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,794,678 reads read : 11,589,356 reads written : 11,589,356 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: 00:03:07 5794678 reads; of these: 5794678 (100.00%) were paired; of these: 592774 (10.23%) aligned concordantly 0 times 4941047 (85.27%) aligned concordantly exactly 1 time 260857 (4.50%) aligned concordantly >1 times ---- 592774 pairs aligned concordantly 0 times; of these: 51508 (8.69%) aligned discordantly 1 time ---- 541266 pairs aligned 0 times concordantly or discordantly; of these: 1082532 mates make up the pairs; of these: 829785 (76.65%) aligned 0 times 231012 (21.34%) aligned exactly 1 time 21735 (2.01%) aligned >1 times 92.84% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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] 222371 / 5238993 = 0.0424 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 23:58:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.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 23:58:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:58:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:58:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.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 23:58:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:58:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:58:31: 1000000 INFO @ Fri, 05 Jul 2019 23:58:32: 1000000 INFO @ Fri, 05 Jul 2019 23:58:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.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 23:58:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:58:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:58:36: 2000000 INFO @ Fri, 05 Jul 2019 23:58:38: 2000000 INFO @ Fri, 05 Jul 2019 23:58:41: 1000000 INFO @ Fri, 05 Jul 2019 23:58:42: 3000000 INFO @ Fri, 05 Jul 2019 23:58:44: 3000000 INFO @ Fri, 05 Jul 2019 23:58:47: 2000000 INFO @ Fri, 05 Jul 2019 23:58:48: 4000000 INFO @ Fri, 05 Jul 2019 23:58:50: 4000000 INFO @ Fri, 05 Jul 2019 23:58:53: 3000000 INFO @ Fri, 05 Jul 2019 23:58:53: 5000000 INFO @ Fri, 05 Jul 2019 23:58:57: 5000000 INFO @ Fri, 05 Jul 2019 23:58:58: 4000000 INFO @ Fri, 05 Jul 2019 23:58:59: 6000000 INFO @ Fri, 05 Jul 2019 23:59:03: 6000000 INFO @ Fri, 05 Jul 2019 23:59:04: 5000000 INFO @ Fri, 05 Jul 2019 23:59:04: 7000000 INFO @ Fri, 05 Jul 2019 23:59:09: 7000000 INFO @ Fri, 05 Jul 2019 23:59:10: 6000000 INFO @ Fri, 05 Jul 2019 23:59:10: 8000000 INFO @ Fri, 05 Jul 2019 23:59:15: 8000000 INFO @ Fri, 05 Jul 2019 23:59:15: 7000000 INFO @ Fri, 05 Jul 2019 23:59:16: 9000000 INFO @ Fri, 05 Jul 2019 23:59:21: 9000000 INFO @ Fri, 05 Jul 2019 23:59:21: 8000000 INFO @ Fri, 05 Jul 2019 23:59:21: 10000000 INFO @ Fri, 05 Jul 2019 23:59:23: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 23:59:23: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 23:59:23: #1 total tags in treatment: 4979947 INFO @ Fri, 05 Jul 2019 23:59:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:59:23: #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 23:59:23: #1 tags after filtering in treatment: 3201311 INFO @ Fri, 05 Jul 2019 23:59:23: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 05 Jul 2019 23:59:23: #1 finished! INFO @ Fri, 05 Jul 2019 23:59:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:59:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:59:23: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:59:23: Too few paired peaks (0) 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 23:59:23: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:59:27: 9000000 INFO @ Fri, 05 Jul 2019 23:59:27: 10000000 INFO @ Fri, 05 Jul 2019 23:59:29: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 23:59:29: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 23:59:29: #1 total tags in treatment: 4979947 INFO @ Fri, 05 Jul 2019 23:59:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:59:29: #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 23:59:29: #1 tags after filtering in treatment: 3201311 INFO @ Fri, 05 Jul 2019 23:59:29: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 05 Jul 2019 23:59:29: #1 finished! INFO @ Fri, 05 Jul 2019 23:59:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:59:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:59:29: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:59:29: Too few paired peaks (0) 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 23:59:29: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:59:32: 10000000 INFO @ Fri, 05 Jul 2019 23:59:34: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 23:59:34: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 23:59:34: #1 total tags in treatment: 4979947 INFO @ Fri, 05 Jul 2019 23:59:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:59:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.10_peaks.narrowPeak: No such file or directory INFO @ Fri, 05 Jul 2019 23:59:34: #1 tags after filtering in treatment: 3201311 INFO @ Fri, 05 Jul 2019 23:59:34: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 05 Jul 2019 23:59:34: #1 finished! INFO @ Fri, 05 Jul 2019 23:59:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:59:34: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:59:34: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:59:34: Too few paired peaks (0) 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 23:59:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.20_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/SRX3865874/SRX3865874.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865874/SRX3865874.20_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。