Job ID = 2008301 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,082,801 reads read : 22,165,602 reads written : 22,165,602 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: 00:09:38 11082801 reads; of these: 11082801 (100.00%) were paired; of these: 4021375 (36.28%) aligned concordantly 0 times 6187362 (55.83%) aligned concordantly exactly 1 time 874064 (7.89%) aligned concordantly >1 times ---- 4021375 pairs aligned concordantly 0 times; of these: 48568 (1.21%) aligned discordantly 1 time ---- 3972807 pairs aligned 0 times concordantly or discordantly; of these: 7945614 mates make up the pairs; of these: 7876822 (99.13%) aligned 0 times 46851 (0.59%) aligned exactly 1 time 21941 (0.28%) aligned >1 times 64.46% overall alignment rate Time searching: 00:09:38 Overall time: 00:09:38 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_sort_core] merging from 8 files... [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] 5090891 / 7100250 = 0.7170 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 19:00:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.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 19:00:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:00:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:00:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.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 19:00:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:00:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:00:57: 1000000 INFO @ Fri, 05 Jul 2019 19:00:57: 1000000 INFO @ Fri, 05 Jul 2019 19:01:08: 2000000 INFO @ Fri, 05 Jul 2019 19:01:09: 2000000 INFO @ Fri, 05 Jul 2019 19:01:19: 3000000 INFO @ Fri, 05 Jul 2019 19:01:20: 3000000 INFO @ Fri, 05 Jul 2019 19:01:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.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 19:01:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:01:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:01:31: 4000000 INFO @ Fri, 05 Jul 2019 19:01:32: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 19:01:32: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 19:01:32: #1 total tags in treatment: 1989147 INFO @ Fri, 05 Jul 2019 19:01:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:01:32: #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 19:01:32: #1 tags after filtering in treatment: 1437702 INFO @ Fri, 05 Jul 2019 19:01:32: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 05 Jul 2019 19:01:32: #1 finished! INFO @ Fri, 05 Jul 2019 19:01:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:01:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:01:32: #2 number of paired peaks: 28 WARNING @ Fri, 05 Jul 2019 19:01:32: 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 19:01:32: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 19:01:32: 4000000 INFO @ Fri, 05 Jul 2019 19:01:33: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 19:01:33: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 19:01:33: #1 total tags in treatment: 1989147 INFO @ Fri, 05 Jul 2019 19:01:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:01:33: #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 19:01:33: #1 tags after filtering in treatment: 1437702 INFO @ Fri, 05 Jul 2019 19:01:33: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 05 Jul 2019 19:01:33: #1 finished! INFO @ Fri, 05 Jul 2019 19:01:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:01:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:01:33: #2 number of paired peaks: 28 WARNING @ Fri, 05 Jul 2019 19:01:33: 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 19:01:33: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 19:01:34: 1000000 cut: /home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:01:45: 2000000 INFO @ Fri, 05 Jul 2019 19:01:56: 3000000 INFO @ Fri, 05 Jul 2019 19:02:07: 4000000 INFO @ Fri, 05 Jul 2019 19:02:08: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 19:02:08: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 19:02:08: #1 total tags in treatment: 1989147 INFO @ Fri, 05 Jul 2019 19:02:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:02:08: #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 19:02:08: #1 tags after filtering in treatment: 1437702 INFO @ Fri, 05 Jul 2019 19:02:08: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 05 Jul 2019 19:02:08: #1 finished! INFO @ Fri, 05 Jul 2019 19:02:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:02:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:02:08: #2 number of paired peaks: 28 WARNING @ Fri, 05 Jul 2019 19:02:08: 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 19:02:08: Process for pairing-model is terminated! BedGraph に変換しました。 cut: /home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.20_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585811/ERX585811.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。