Job ID = 2640898 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,701,652 reads read : 21,403,304 reads written : 21,403,304 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: 00:09:24 10701652 reads; of these: 10701652 (100.00%) were paired; of these: 3355756 (31.36%) aligned concordantly 0 times 4370912 (40.84%) aligned concordantly exactly 1 time 2974984 (27.80%) aligned concordantly >1 times ---- 3355756 pairs aligned concordantly 0 times; of these: 2935 (0.09%) aligned discordantly 1 time ---- 3352821 pairs aligned 0 times concordantly or discordantly; of these: 6705642 mates make up the pairs; of these: 6054058 (90.28%) aligned 0 times 151769 (2.26%) aligned exactly 1 time 499815 (7.45%) aligned >1 times 71.71% overall alignment rate Time searching: 00:09:24 Overall time: 00:09:24 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] 1445496 / 7343279 = 0.1968 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.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 20:10:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:10:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:10:57: 1000000 INFO @ Sat, 24 Aug 2019 20:11:04: 2000000 INFO @ Sat, 24 Aug 2019 20:11:11: 3000000 INFO @ Sat, 24 Aug 2019 20:11:19: 4000000 INFO @ Sat, 24 Aug 2019 20:11:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.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 20:11:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:11:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:11:26: 5000000 INFO @ Sat, 24 Aug 2019 20:11:27: 1000000 INFO @ Sat, 24 Aug 2019 20:11:33: 6000000 INFO @ Sat, 24 Aug 2019 20:11:35: 2000000 INFO @ Sat, 24 Aug 2019 20:11:40: 7000000 INFO @ Sat, 24 Aug 2019 20:11:42: 3000000 INFO @ Sat, 24 Aug 2019 20:11:48: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:11:49: 4000000 INFO @ Sat, 24 Aug 2019 20:11:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.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 20:11:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:11:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:11:55: 9000000 INFO @ Sat, 24 Aug 2019 20:11:57: 5000000 INFO @ Sat, 24 Aug 2019 20:11:59: 1000000 INFO @ Sat, 24 Aug 2019 20:12:02: 10000000 INFO @ Sat, 24 Aug 2019 20:12:04: 6000000 INFO @ Sat, 24 Aug 2019 20:12:07: 2000000 INFO @ Sat, 24 Aug 2019 20:12:10: 11000000 INFO @ Sat, 24 Aug 2019 20:12:12: 7000000 INFO @ Sat, 24 Aug 2019 20:12:16: 3000000 INFO @ Sat, 24 Aug 2019 20:12:17: 12000000 INFO @ Sat, 24 Aug 2019 20:12:19: 8000000 INFO @ Sat, 24 Aug 2019 20:12:20: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 20:12:20: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 20:12:20: #1 total tags in treatment: 5900664 INFO @ Sat, 24 Aug 2019 20:12:20: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:12:20: #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 20:12:20: #1 tags after filtering in treatment: 3641361 INFO @ Sat, 24 Aug 2019 20:12:20: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 24 Aug 2019 20:12:20: #1 finished! INFO @ Sat, 24 Aug 2019 20:12:20: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:12:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:12:21: #2 number of paired peaks: 68 WARNING @ Sat, 24 Aug 2019 20:12:21: Too few paired peaks (68) 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 20:12:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.05_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/SRX404612/SRX404612.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:12:25: 4000000 INFO @ Sat, 24 Aug 2019 20:12:26: 9000000 INFO @ Sat, 24 Aug 2019 20:12:34: 5000000 INFO @ Sat, 24 Aug 2019 20:12:34: 10000000 INFO @ Sat, 24 Aug 2019 20:12:41: 11000000 INFO @ Sat, 24 Aug 2019 20:12:42: 6000000 INFO @ Sat, 24 Aug 2019 20:12:49: 12000000 INFO @ Sat, 24 Aug 2019 20:12:51: 7000000 INFO @ Sat, 24 Aug 2019 20:12:52: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 20:12:52: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 20:12:52: #1 total tags in treatment: 5900664 INFO @ Sat, 24 Aug 2019 20:12:52: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:12:52: #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 20:12:52: #1 tags after filtering in treatment: 3641361 INFO @ Sat, 24 Aug 2019 20:12:52: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 24 Aug 2019 20:12:52: #1 finished! INFO @ Sat, 24 Aug 2019 20:12:52: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:12:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:12:53: #2 number of paired peaks: 68 WARNING @ Sat, 24 Aug 2019 20:12:53: Too few paired peaks (68) 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 20:12:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.10_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/SRX404612/SRX404612.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:12:59: 8000000 INFO @ Sat, 24 Aug 2019 20:13:08: 9000000 INFO @ Sat, 24 Aug 2019 20:13:16: 10000000 INFO @ Sat, 24 Aug 2019 20:13:24: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 20:13:33: 12000000 INFO @ Sat, 24 Aug 2019 20:13:36: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 20:13:36: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 20:13:36: #1 total tags in treatment: 5900664 INFO @ Sat, 24 Aug 2019 20:13:36: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:13:36: #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 20:13:37: #1 tags after filtering in treatment: 3641361 INFO @ Sat, 24 Aug 2019 20:13:37: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 24 Aug 2019 20:13:37: #1 finished! INFO @ Sat, 24 Aug 2019 20:13:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:13:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:13:37: #2 number of paired peaks: 68 WARNING @ Sat, 24 Aug 2019 20:13:37: Too few paired peaks (68) 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 20:13:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.20_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/SRX404612/SRX404612.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404612/SRX404612.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。