Job ID = 2640769 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,172,820 reads read : 22,345,640 reads written : 22,345,640 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: 00:06:49 11172820 reads; of these: 11172820 (100.00%) were paired; of these: 2177415 (19.49%) aligned concordantly 0 times 6358163 (56.91%) aligned concordantly exactly 1 time 2637242 (23.60%) aligned concordantly >1 times ---- 2177415 pairs aligned concordantly 0 times; of these: 13337 (0.61%) aligned discordantly 1 time ---- 2164078 pairs aligned 0 times concordantly or discordantly; of these: 4328156 mates make up the pairs; of these: 4253797 (98.28%) aligned 0 times 30850 (0.71%) aligned exactly 1 time 43509 (1.01%) aligned >1 times 80.96% overall alignment rate Time searching: 00:06:49 Overall time: 00:06:49 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] 2260574 / 9003882 = 0.2511 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:19:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.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 19:19:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:19:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:19:46: 1000000 INFO @ Sat, 24 Aug 2019 19:19:55: 2000000 INFO @ Sat, 24 Aug 2019 19:20:04: 3000000 INFO @ Sat, 24 Aug 2019 19:20:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.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 19:20:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:20:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:20:13: 4000000 INFO @ Sat, 24 Aug 2019 19:20:17: 1000000 INFO @ Sat, 24 Aug 2019 19:20:22: 5000000 INFO @ Sat, 24 Aug 2019 19:20:27: 2000000 INFO @ Sat, 24 Aug 2019 19:20:31: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:20:37: 3000000 INFO @ Sat, 24 Aug 2019 19:20:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.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 19:20:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:20:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:20:41: 7000000 INFO @ Sat, 24 Aug 2019 19:20:46: 1000000 INFO @ Sat, 24 Aug 2019 19:20:47: 4000000 INFO @ Sat, 24 Aug 2019 19:20:51: 8000000 INFO @ Sat, 24 Aug 2019 19:20:54: 2000000 INFO @ Sat, 24 Aug 2019 19:20:55: 5000000 INFO @ Sat, 24 Aug 2019 19:20:59: 9000000 INFO @ Sat, 24 Aug 2019 19:21:02: 3000000 INFO @ Sat, 24 Aug 2019 19:21:03: 6000000 INFO @ Sat, 24 Aug 2019 19:21:07: 10000000 INFO @ Sat, 24 Aug 2019 19:21:10: 4000000 INFO @ Sat, 24 Aug 2019 19:21:12: 7000000 INFO @ Sat, 24 Aug 2019 19:21:15: 11000000 INFO @ Sat, 24 Aug 2019 19:21:19: 5000000 INFO @ Sat, 24 Aug 2019 19:21:20: 8000000 INFO @ Sat, 24 Aug 2019 19:21:23: 12000000 INFO @ Sat, 24 Aug 2019 19:21:28: 6000000 INFO @ Sat, 24 Aug 2019 19:21:28: 9000000 INFO @ Sat, 24 Aug 2019 19:21:31: 13000000 INFO @ Sat, 24 Aug 2019 19:21:35: #1 tag size is determined as 30 bps INFO @ Sat, 24 Aug 2019 19:21:35: #1 tag size = 30 INFO @ Sat, 24 Aug 2019 19:21:35: #1 total tags in treatment: 6735449 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: 4595438 INFO @ Sat, 24 Aug 2019 19:21:35: #1 Redundant rate of treatment: 0.32 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 19:21:35: #2 number of paired peaks: 28 WARNING @ Sat, 24 Aug 2019 19:21:35: 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 @ Sat, 24 Aug 2019 19:21:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.05_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/ERX2732454/ERX2732454.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:21:36: 7000000 INFO @ Sat, 24 Aug 2019 19:21:36: 10000000 INFO @ Sat, 24 Aug 2019 19:21:45: 8000000 INFO @ Sat, 24 Aug 2019 19:21:45: 11000000 INFO @ Sat, 24 Aug 2019 19:21:54: 9000000 INFO @ Sat, 24 Aug 2019 19:21:54: 12000000 INFO @ Sat, 24 Aug 2019 19:22:02: 13000000 INFO @ Sat, 24 Aug 2019 19:22:03: 10000000 INFO @ Sat, 24 Aug 2019 19:22:06: #1 tag size is determined as 30 bps INFO @ Sat, 24 Aug 2019 19:22:06: #1 tag size = 30 INFO @ Sat, 24 Aug 2019 19:22:06: #1 total tags in treatment: 6735449 INFO @ Sat, 24 Aug 2019 19:22:06: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:22:06: #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: 4595438 INFO @ Sat, 24 Aug 2019 19:22:07: #1 Redundant rate of treatment: 0.32 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 19:22:07: #2 number of paired peaks: 28 WARNING @ Sat, 24 Aug 2019 19:22:07: 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 @ Sat, 24 Aug 2019 19:22:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.10_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/ERX2732454/ERX2732454.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:22:12: 11000000 INFO @ Sat, 24 Aug 2019 19:22:20: 12000000 INFO @ Sat, 24 Aug 2019 19:22:27: 13000000 INFO @ Sat, 24 Aug 2019 19:22:31: #1 tag size is determined as 30 bps INFO @ Sat, 24 Aug 2019 19:22:31: #1 tag size = 30 INFO @ Sat, 24 Aug 2019 19:22:31: #1 total tags in treatment: 6735449 INFO @ Sat, 24 Aug 2019 19:22:31: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:22:31: #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 19:22:31: #1 tags after filtering in treatment: 4595438 INFO @ Sat, 24 Aug 2019 19:22:31: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 24 Aug 2019 19:22:31: #1 finished! INFO @ Sat, 24 Aug 2019 19:22:31: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:22:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:22:32: #2 number of paired peaks: 28 WARNING @ Sat, 24 Aug 2019 19:22:32: 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 @ Sat, 24 Aug 2019 19:22:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.20_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/ERX2732454/ERX2732454.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732454/ERX2732454.20_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。