Job ID = 2641113 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,679,227 reads read : 23,358,454 reads written : 23,358,454 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: 00:16:44 11679227 reads; of these: 11679227 (100.00%) were paired; of these: 7669542 (65.67%) aligned concordantly 0 times 3722459 (31.87%) aligned concordantly exactly 1 time 287226 (2.46%) aligned concordantly >1 times ---- 7669542 pairs aligned concordantly 0 times; of these: 5429825 (70.80%) aligned discordantly 1 time ---- 2239717 pairs aligned 0 times concordantly or discordantly; of these: 4479434 mates make up the pairs; of these: 2735151 (61.06%) aligned 0 times 728984 (16.27%) aligned exactly 1 time 1015299 (22.67%) aligned >1 times 88.29% overall alignment rate Time searching: 00:16:44 Overall time: 00:16:44 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 12 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] 2118269 / 9435506 = 0.2245 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:09:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.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 22:09:57: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:09:57: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:10:07: 1000000 INFO @ Sat, 24 Aug 2019 22:10:17: 2000000 INFO @ Sat, 24 Aug 2019 22:10:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.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 22:10:27: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:10:27: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:10:28: 3000000 INFO @ Sat, 24 Aug 2019 22:10:37: 1000000 INFO @ Sat, 24 Aug 2019 22:10:39: 4000000 INFO @ Sat, 24 Aug 2019 22:10:48: 2000000 INFO @ Sat, 24 Aug 2019 22:10:51: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:10:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.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 22:10:57: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:10:57: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:11:00: 3000000 INFO @ Sat, 24 Aug 2019 22:11:03: 6000000 INFO @ Sat, 24 Aug 2019 22:11:10: 1000000 INFO @ Sat, 24 Aug 2019 22:11:12: 4000000 INFO @ Sat, 24 Aug 2019 22:11:16: 7000000 INFO @ Sat, 24 Aug 2019 22:11:22: 2000000 INFO @ Sat, 24 Aug 2019 22:11:24: 5000000 INFO @ Sat, 24 Aug 2019 22:11:27: 8000000 INFO @ Sat, 24 Aug 2019 22:11:31: 3000000 INFO @ Sat, 24 Aug 2019 22:11:34: 6000000 INFO @ Sat, 24 Aug 2019 22:11:37: 9000000 INFO @ Sat, 24 Aug 2019 22:11:40: 4000000 INFO @ Sat, 24 Aug 2019 22:11:46: 7000000 INFO @ Sat, 24 Aug 2019 22:11:48: 10000000 INFO @ Sat, 24 Aug 2019 22:11:48: 5000000 INFO @ Sat, 24 Aug 2019 22:11:56: 8000000 INFO @ Sat, 24 Aug 2019 22:11:57: 6000000 INFO @ Sat, 24 Aug 2019 22:11:59: 11000000 INFO @ Sat, 24 Aug 2019 22:12:05: 9000000 INFO @ Sat, 24 Aug 2019 22:12:06: 7000000 INFO @ Sat, 24 Aug 2019 22:12:10: 12000000 INFO @ Sat, 24 Aug 2019 22:12:14: 10000000 INFO @ Sat, 24 Aug 2019 22:12:15: 8000000 INFO @ Sat, 24 Aug 2019 22:12:22: 13000000 INFO @ Sat, 24 Aug 2019 22:12:24: 11000000 INFO @ Sat, 24 Aug 2019 22:12:25: 9000000 INFO @ Sat, 24 Aug 2019 22:12:33: 12000000 INFO @ Sat, 24 Aug 2019 22:12:34: 10000000 INFO @ Sat, 24 Aug 2019 22:12:35: 14000000 INFO @ Sat, 24 Aug 2019 22:12:42: 13000000 INFO @ Sat, 24 Aug 2019 22:12:43: 11000000 INFO @ Sat, 24 Aug 2019 22:12:47: 15000000 INFO @ Sat, 24 Aug 2019 22:12:52: 14000000 INFO @ Sat, 24 Aug 2019 22:12:53: 12000000 INFO @ Sat, 24 Aug 2019 22:12:59: 16000000 INFO @ Sat, 24 Aug 2019 22:13:01: 15000000 INFO @ Sat, 24 Aug 2019 22:13:02: 13000000 INFO @ Sat, 24 Aug 2019 22:13:04: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:13:04: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:13:04: #1 total tags in treatment: 3104673 INFO @ Sat, 24 Aug 2019 22:13:04: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:13:04: #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 22:13:04: #1 tags after filtering in treatment: 2791056 INFO @ Sat, 24 Aug 2019 22:13:04: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 24 Aug 2019 22:13:04: #1 finished! INFO @ Sat, 24 Aug 2019 22:13:04: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:13:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:13:04: #2 number of paired peaks: 33 WARNING @ Sat, 24 Aug 2019 22:13:04: Too few paired peaks (33) 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 22:13:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.05_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/SRX5546554/SRX5546554.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:13:10: 16000000 INFO @ Sat, 24 Aug 2019 22:13:11: 14000000 INFO @ Sat, 24 Aug 2019 22:13:13: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:13:13: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:13:13: #1 total tags in treatment: 3104673 INFO @ Sat, 24 Aug 2019 22:13:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:13:13: #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 22:13:14: #1 tags after filtering in treatment: 2791056 INFO @ Sat, 24 Aug 2019 22:13:14: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 24 Aug 2019 22:13:14: #1 finished! INFO @ Sat, 24 Aug 2019 22:13:14: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:13:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:13:14: #2 number of paired peaks: 33 WARNING @ Sat, 24 Aug 2019 22:13:14: Too few paired peaks (33) 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 22:13:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.10_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/SRX5546554/SRX5546554.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:13:20: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:13:29: 16000000 INFO @ Sat, 24 Aug 2019 22:13:32: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:13:32: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:13:32: #1 total tags in treatment: 3104673 INFO @ Sat, 24 Aug 2019 22:13:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:13:32: #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 22:13:32: #1 tags after filtering in treatment: 2791056 INFO @ Sat, 24 Aug 2019 22:13:32: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 24 Aug 2019 22:13:32: #1 finished! INFO @ Sat, 24 Aug 2019 22:13:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:13:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:13:32: #2 number of paired peaks: 33 WARNING @ Sat, 24 Aug 2019 22:13:32: Too few paired peaks (33) 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 22:13:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.20_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/SRX5546554/SRX5546554.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546554/SRX5546554.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。