Job ID = 2010666 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,140,548 reads read : 10,281,096 reads written : 10,281,096 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: 00:03:11 5140548 reads; of these: 5140548 (100.00%) were paired; of these: 705012 (13.71%) aligned concordantly 0 times 3783717 (73.61%) aligned concordantly exactly 1 time 651819 (12.68%) aligned concordantly >1 times ---- 705012 pairs aligned concordantly 0 times; of these: 22094 (3.13%) aligned discordantly 1 time ---- 682918 pairs aligned 0 times concordantly or discordantly; of these: 1365836 mates make up the pairs; of these: 1151031 (84.27%) aligned 0 times 171684 (12.57%) aligned exactly 1 time 43121 (3.16%) aligned >1 times 88.80% overall alignment rate Time searching: 00:03:11 Overall time: 00:03:11 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] 282471 / 4454376 = 0.0634 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 23:55:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.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 23:55:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:55:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:55:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.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 23:55:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:55:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:55:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.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 23:55:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:55:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:55:34: 1000000 INFO @ Fri, 05 Jul 2019 23:55:35: 1000000 INFO @ Fri, 05 Jul 2019 23:55:36: 1000000 INFO @ Fri, 05 Jul 2019 23:55:42: 2000000 INFO @ Fri, 05 Jul 2019 23:55:43: 2000000 INFO @ Fri, 05 Jul 2019 23:55:44: 2000000 INFO @ Fri, 05 Jul 2019 23:55:49: 3000000 INFO @ Fri, 05 Jul 2019 23:55:50: 3000000 INFO @ Fri, 05 Jul 2019 23:55:51: 3000000 INFO @ Fri, 05 Jul 2019 23:55:56: 4000000 INFO @ Fri, 05 Jul 2019 23:55:58: 4000000 INFO @ Fri, 05 Jul 2019 23:55:59: 4000000 INFO @ Fri, 05 Jul 2019 23:56:04: 5000000 INFO @ Fri, 05 Jul 2019 23:56:05: 5000000 INFO @ Fri, 05 Jul 2019 23:56:06: 5000000 INFO @ Fri, 05 Jul 2019 23:56:11: 6000000 INFO @ Fri, 05 Jul 2019 23:56:12: 6000000 INFO @ Fri, 05 Jul 2019 23:56:13: 6000000 INFO @ Fri, 05 Jul 2019 23:56:18: 7000000 INFO @ Fri, 05 Jul 2019 23:56:20: 7000000 INFO @ Fri, 05 Jul 2019 23:56:21: 7000000 INFO @ Fri, 05 Jul 2019 23:56:26: 8000000 INFO @ Fri, 05 Jul 2019 23:56:27: 8000000 INFO @ Fri, 05 Jul 2019 23:56:28: 8000000 INFO @ Fri, 05 Jul 2019 23:56:30: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 23:56:30: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 23:56:30: #1 total tags in treatment: 4153373 INFO @ Fri, 05 Jul 2019 23:56:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:56:30: #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 23:56:30: #1 tags after filtering in treatment: 2819878 INFO @ Fri, 05 Jul 2019 23:56:30: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 23:56:30: #1 finished! INFO @ Fri, 05 Jul 2019 23:56:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:56:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:56:30: #2 number of paired peaks: 28 WARNING @ Fri, 05 Jul 2019 23:56:30: Too few paired peaks (28) 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 23:56:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.05_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/SRX3865870/SRX3865870.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:56:31: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 23:56:31: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 23:56:31: #1 total tags in treatment: 4153373 INFO @ Fri, 05 Jul 2019 23:56:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:56:31: #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 23:56:31: #1 tags after filtering in treatment: 2819878 INFO @ Fri, 05 Jul 2019 23:56:31: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 23:56:31: #1 finished! INFO @ Fri, 05 Jul 2019 23:56:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:56:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:56:31: #2 number of paired peaks: 28 WARNING @ Fri, 05 Jul 2019 23:56:31: Too few paired peaks (28) 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 23:56:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.10_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/SRX3865870/SRX3865870.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:56:32: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 23:56:32: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 23:56:32: #1 total tags in treatment: 4153373 INFO @ Fri, 05 Jul 2019 23:56:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:56:32: #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 23:56:32: #1 tags after filtering in treatment: 2819878 INFO @ Fri, 05 Jul 2019 23:56:32: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 23:56:32: #1 finished! INFO @ Fri, 05 Jul 2019 23:56:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:56:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:56:32: #2 number of paired peaks: 28 WARNING @ Fri, 05 Jul 2019 23:56:32: Too few paired peaks (28) 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 23:56:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.20_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/SRX3865870/SRX3865870.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865870/SRX3865870.20_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。