Job ID = 4288986 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,907,455 reads read : 9,814,910 reads written : 9,814,910 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: 00:04:43 4907455 reads; of these: 4907455 (100.00%) were paired; of these: 904642 (18.43%) aligned concordantly 0 times 3682977 (75.05%) aligned concordantly exactly 1 time 319836 (6.52%) aligned concordantly >1 times ---- 904642 pairs aligned concordantly 0 times; of these: 134957 (14.92%) aligned discordantly 1 time ---- 769685 pairs aligned 0 times concordantly or discordantly; of these: 1539370 mates make up the pairs; of these: 1251329 (81.29%) aligned 0 times 241055 (15.66%) aligned exactly 1 time 46986 (3.05%) aligned >1 times 87.25% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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] 1178183 / 4135239 = 0.2849 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:16:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.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 @ Tue, 10 Dec 2019 13:16:31: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:16:31: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:16:39: 1000000 INFO @ Tue, 10 Dec 2019 13:16:46: 2000000 INFO @ Tue, 10 Dec 2019 13:16:54: 3000000 INFO @ Tue, 10 Dec 2019 13:17:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.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 @ Tue, 10 Dec 2019 13:17:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:17:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:17:02: 4000000 INFO @ Tue, 10 Dec 2019 13:17:10: 1000000 INFO @ Tue, 10 Dec 2019 13:17:11: 5000000 INFO @ Tue, 10 Dec 2019 13:17:20: 2000000 INFO @ Tue, 10 Dec 2019 13:17:21: 6000000 INFO @ Tue, 10 Dec 2019 13:17:22: #1 tag size is determined as 75 bps INFO @ Tue, 10 Dec 2019 13:17:22: #1 tag size = 75 INFO @ Tue, 10 Dec 2019 13:17:22: #1 total tags in treatment: 2828000 INFO @ Tue, 10 Dec 2019 13:17:22: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:17:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:17:23: #1 tags after filtering in treatment: 2564584 INFO @ Tue, 10 Dec 2019 13:17:23: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 10 Dec 2019 13:17:23: #1 finished! INFO @ Tue, 10 Dec 2019 13:17:23: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:17:23: #2 number of paired peaks: 32 WARNING @ Tue, 10 Dec 2019 13:17:23: Too few paired peaks (32) 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 @ Tue, 10 Dec 2019 13:17:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.05_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/SRX3205543/SRX3205543.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:17:28: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:17:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.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 @ Tue, 10 Dec 2019 13:17:31: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:17:31: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:17:36: 4000000 INFO @ Tue, 10 Dec 2019 13:17:40: 1000000 INFO @ Tue, 10 Dec 2019 13:17:46: 5000000 INFO @ Tue, 10 Dec 2019 13:17:49: 2000000 INFO @ Tue, 10 Dec 2019 13:17:55: 6000000 INFO @ Tue, 10 Dec 2019 13:17:57: #1 tag size is determined as 75 bps INFO @ Tue, 10 Dec 2019 13:17:57: #1 tag size = 75 INFO @ Tue, 10 Dec 2019 13:17:57: #1 total tags in treatment: 2828000 INFO @ Tue, 10 Dec 2019 13:17:57: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:17:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:17:57: #1 tags after filtering in treatment: 2564584 INFO @ Tue, 10 Dec 2019 13:17:57: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 10 Dec 2019 13:17:57: #1 finished! INFO @ Tue, 10 Dec 2019 13:17:57: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:17:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:17:57: #2 number of paired peaks: 32 WARNING @ Tue, 10 Dec 2019 13:17:57: Too few paired peaks (32) 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 @ Tue, 10 Dec 2019 13:17:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.10_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/SRX3205543/SRX3205543.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:17:58: 3000000 INFO @ Tue, 10 Dec 2019 13:18:06: 4000000 INFO @ Tue, 10 Dec 2019 13:18:14: 5000000 INFO @ Tue, 10 Dec 2019 13:18:22: 6000000 INFO @ Tue, 10 Dec 2019 13:18:23: #1 tag size is determined as 75 bps INFO @ Tue, 10 Dec 2019 13:18:23: #1 tag size = 75 INFO @ Tue, 10 Dec 2019 13:18:23: #1 total tags in treatment: 2828000 INFO @ Tue, 10 Dec 2019 13:18:23: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:18:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:18:23: #1 tags after filtering in treatment: 2564584 INFO @ Tue, 10 Dec 2019 13:18:23: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 10 Dec 2019 13:18:23: #1 finished! INFO @ Tue, 10 Dec 2019 13:18:23: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:18:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:18:23: #2 number of paired peaks: 32 WARNING @ Tue, 10 Dec 2019 13:18:23: Too few paired peaks (32) 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 @ Tue, 10 Dec 2019 13:18:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.20_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/SRX3205543/SRX3205543.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205543/SRX3205543.20_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。