Job ID = 2640759 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,281,502 reads read : 18,563,004 reads written : 18,563,004 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: 00:05:41 9281502 reads; of these: 9281502 (100.00%) were paired; of these: 2388510 (25.73%) aligned concordantly 0 times 5187735 (55.89%) aligned concordantly exactly 1 time 1705257 (18.37%) aligned concordantly >1 times ---- 2388510 pairs aligned concordantly 0 times; of these: 16473 (0.69%) aligned discordantly 1 time ---- 2372037 pairs aligned 0 times concordantly or discordantly; of these: 4744074 mates make up the pairs; of these: 4681354 (98.68%) aligned 0 times 27253 (0.57%) aligned exactly 1 time 35467 (0.75%) aligned >1 times 74.78% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 1470640 / 6906465 = 0.2129 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:15:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.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 19:15:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:15:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:15:18: 1000000 INFO @ Sat, 24 Aug 2019 19:15:28: 2000000 INFO @ Sat, 24 Aug 2019 19:15:38: 3000000 INFO @ Sat, 24 Aug 2019 19:15:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.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 19:15:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:15:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:15:48: 4000000 INFO @ Sat, 24 Aug 2019 19:15:48: 1000000 INFO @ Sat, 24 Aug 2019 19:15:58: 5000000 INFO @ Sat, 24 Aug 2019 19:15:58: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:16:08: 6000000 INFO @ Sat, 24 Aug 2019 19:16:08: 3000000 INFO @ Sat, 24 Aug 2019 19:16:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.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 19:16:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:16:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:16:18: 4000000 INFO @ Sat, 24 Aug 2019 19:16:18: 1000000 INFO @ Sat, 24 Aug 2019 19:16:18: 7000000 INFO @ Sat, 24 Aug 2019 19:16:26: 2000000 INFO @ Sat, 24 Aug 2019 19:16:28: 5000000 INFO @ Sat, 24 Aug 2019 19:16:28: 8000000 INFO @ Sat, 24 Aug 2019 19:16:35: 3000000 INFO @ Sat, 24 Aug 2019 19:16:38: 9000000 INFO @ Sat, 24 Aug 2019 19:16:38: 6000000 INFO @ Sat, 24 Aug 2019 19:16:43: 4000000 INFO @ Sat, 24 Aug 2019 19:16:47: 10000000 INFO @ Sat, 24 Aug 2019 19:16:48: 7000000 INFO @ Sat, 24 Aug 2019 19:16:51: 5000000 INFO @ Sat, 24 Aug 2019 19:16:56: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 19:16:56: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 19:16:56: #1 total tags in treatment: 5423338 INFO @ Sat, 24 Aug 2019 19:16:56: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:16:56: #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 19:16:56: #1 tags after filtering in treatment: 3934021 INFO @ Sat, 24 Aug 2019 19:16:56: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 19:16:56: #1 finished! INFO @ Sat, 24 Aug 2019 19:16:56: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:16:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:16:56: #2 number of paired peaks: 30 WARNING @ Sat, 24 Aug 2019 19:16:56: Too few paired peaks (30) 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 19:16:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.05_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/ERX2732450/ERX2732450.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:16:58: 8000000 INFO @ Sat, 24 Aug 2019 19:17:00: 6000000 INFO @ Sat, 24 Aug 2019 19:17:08: 9000000 INFO @ Sat, 24 Aug 2019 19:17:08: 7000000 INFO @ Sat, 24 Aug 2019 19:17:16: 8000000 INFO @ Sat, 24 Aug 2019 19:17:17: 10000000 INFO @ Sat, 24 Aug 2019 19:17:24: 9000000 INFO @ Sat, 24 Aug 2019 19:17:26: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 19:17:26: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 19:17:26: #1 total tags in treatment: 5423338 INFO @ Sat, 24 Aug 2019 19:17:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:17:26: #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 19:17:26: #1 tags after filtering in treatment: 3934021 INFO @ Sat, 24 Aug 2019 19:17:26: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 19:17:26: #1 finished! INFO @ Sat, 24 Aug 2019 19:17:26: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:17:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:17:26: #2 number of paired peaks: 30 WARNING @ Sat, 24 Aug 2019 19:17:26: Too few paired peaks (30) 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 19:17:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.10_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/ERX2732450/ERX2732450.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:17:35: 10000000 INFO @ Sat, 24 Aug 2019 19:17:44: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 19:17:44: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 19:17:44: #1 total tags in treatment: 5423338 INFO @ Sat, 24 Aug 2019 19:17:44: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:17:44: #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 19:17:44: #1 tags after filtering in treatment: 3934021 INFO @ Sat, 24 Aug 2019 19:17:44: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 19:17:44: #1 finished! INFO @ Sat, 24 Aug 2019 19:17:44: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:17:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:17:44: #2 number of paired peaks: 30 WARNING @ Sat, 24 Aug 2019 19:17:44: Too few paired peaks (30) 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 19:17:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.20_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/ERX2732450/ERX2732450.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732450/ERX2732450.20_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。