Job ID = 2640768 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,312,504 reads read : 22,625,008 reads written : 22,625,008 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: 00:07:00 11312504 reads; of these: 11312504 (100.00%) were paired; of these: 2073714 (18.33%) aligned concordantly 0 times 6779072 (59.93%) aligned concordantly exactly 1 time 2459718 (21.74%) aligned concordantly >1 times ---- 2073714 pairs aligned concordantly 0 times; of these: 16476 (0.79%) aligned discordantly 1 time ---- 2057238 pairs aligned 0 times concordantly or discordantly; of these: 4114476 mates make up the pairs; of these: 4023116 (97.78%) aligned 0 times 39411 (0.96%) aligned exactly 1 time 51949 (1.26%) aligned >1 times 82.22% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 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] 1965180 / 9250132 = 0.2124 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:19:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.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, 24 Aug 2019 19:19:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:19:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:19:39: 1000000 INFO @ Sat, 24 Aug 2019 19:19:46: 2000000 INFO @ Sat, 24 Aug 2019 19:19:54: 3000000 INFO @ Sat, 24 Aug 2019 19:20:01: 4000000 INFO @ Sat, 24 Aug 2019 19:20:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.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, 24 Aug 2019 19:20:01: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:20:01: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:20:10: 5000000 INFO @ Sat, 24 Aug 2019 19:20:10: 1000000 INFO @ Sat, 24 Aug 2019 19:20:18: 6000000 INFO @ Sat, 24 Aug 2019 19:20:19: 2000000 INFO @ Sat, 24 Aug 2019 19:20:27: 7000000 INFO @ Sat, 24 Aug 2019 19:20:28: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:20:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.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, 24 Aug 2019 19:20:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:20:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:20:36: 8000000 INFO @ Sat, 24 Aug 2019 19:20:36: 4000000 INFO @ Sat, 24 Aug 2019 19:20:42: 1000000 INFO @ Sat, 24 Aug 2019 19:20:45: 9000000 INFO @ Sat, 24 Aug 2019 19:20:45: 5000000 INFO @ Sat, 24 Aug 2019 19:20:52: 2000000 INFO @ Sat, 24 Aug 2019 19:20:54: 10000000 INFO @ Sat, 24 Aug 2019 19:20:54: 6000000 INFO @ Sat, 24 Aug 2019 19:21:02: 3000000 INFO @ Sat, 24 Aug 2019 19:21:03: 11000000 INFO @ Sat, 24 Aug 2019 19:21:03: 7000000 INFO @ Sat, 24 Aug 2019 19:21:12: 12000000 INFO @ Sat, 24 Aug 2019 19:21:12: 4000000 INFO @ Sat, 24 Aug 2019 19:21:12: 8000000 INFO @ Sat, 24 Aug 2019 19:21:21: 13000000 INFO @ Sat, 24 Aug 2019 19:21:21: 9000000 INFO @ Sat, 24 Aug 2019 19:21:22: 5000000 INFO @ Sat, 24 Aug 2019 19:21:29: 14000000 INFO @ Sat, 24 Aug 2019 19:21:30: 10000000 INFO @ Sat, 24 Aug 2019 19:21:32: 6000000 INFO @ Sat, 24 Aug 2019 19:21:35: #1 tag size is determined as 29 bps INFO @ Sat, 24 Aug 2019 19:21:35: #1 tag size = 29 INFO @ Sat, 24 Aug 2019 19:21:35: #1 total tags in treatment: 7274466 INFO @ Sat, 24 Aug 2019 19:21:35: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:21:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:21:35: #1 tags after filtering in treatment: 5027545 INFO @ Sat, 24 Aug 2019 19:21:35: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 24 Aug 2019 19:21:35: #1 finished! INFO @ Sat, 24 Aug 2019 19:21:35: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:21:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:21:36: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:21:36: 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 @ Sat, 24 Aug 2019 19:21:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.05_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/ERX2732453/ERX2732453.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:21:39: 11000000 INFO @ Sat, 24 Aug 2019 19:21:42: 7000000 INFO @ Sat, 24 Aug 2019 19:21:46: 12000000 INFO @ Sat, 24 Aug 2019 19:21:52: 8000000 INFO @ Sat, 24 Aug 2019 19:21:54: 13000000 INFO @ Sat, 24 Aug 2019 19:22:02: 9000000 INFO @ Sat, 24 Aug 2019 19:22:02: 14000000 INFO @ Sat, 24 Aug 2019 19:22:07: #1 tag size is determined as 29 bps INFO @ Sat, 24 Aug 2019 19:22:07: #1 tag size = 29 INFO @ Sat, 24 Aug 2019 19:22:07: #1 total tags in treatment: 7274466 INFO @ Sat, 24 Aug 2019 19:22:07: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:22:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:22:07: #1 tags after filtering in treatment: 5027545 INFO @ Sat, 24 Aug 2019 19:22:07: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 24 Aug 2019 19:22:07: #1 finished! INFO @ Sat, 24 Aug 2019 19:22:07: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:22:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:22:08: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:22:08: 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 @ Sat, 24 Aug 2019 19:22:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.10_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/ERX2732453/ERX2732453.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:22:12: 10000000 INFO @ Sat, 24 Aug 2019 19:22:21: 11000000 INFO @ Sat, 24 Aug 2019 19:22:30: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 19:22:40: 13000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 19:22:49: 14000000 INFO @ Sat, 24 Aug 2019 19:22:55: #1 tag size is determined as 29 bps INFO @ Sat, 24 Aug 2019 19:22:55: #1 tag size = 29 INFO @ Sat, 24 Aug 2019 19:22:55: #1 total tags in treatment: 7274466 INFO @ Sat, 24 Aug 2019 19:22:55: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:22:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:22:55: #1 tags after filtering in treatment: 5027545 INFO @ Sat, 24 Aug 2019 19:22:55: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 24 Aug 2019 19:22:55: #1 finished! INFO @ Sat, 24 Aug 2019 19:22:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:22:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:22:55: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:22:55: 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 @ Sat, 24 Aug 2019 19:22:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.20_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/ERX2732453/ERX2732453.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732453/ERX2732453.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling