Job ID = 2640896 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 15,716,723 reads read : 31,433,446 reads written : 31,433,446 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: 00:12:45 15716723 reads; of these: 15716723 (100.00%) were paired; of these: 1382239 (8.79%) aligned concordantly 0 times 11750164 (74.76%) aligned concordantly exactly 1 time 2584320 (16.44%) aligned concordantly >1 times ---- 1382239 pairs aligned concordantly 0 times; of these: 17983 (1.30%) aligned discordantly 1 time ---- 1364256 pairs aligned 0 times concordantly or discordantly; of these: 2728512 mates make up the pairs; of these: 2222116 (81.44%) aligned 0 times 344832 (12.64%) aligned exactly 1 time 161564 (5.92%) aligned >1 times 92.93% overall alignment rate Time searching: 00:12:45 Overall time: 00:12:45 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] 396927 / 14343849 = 0.0277 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:23:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.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 20:23:49: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:23:49: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:23:55: 1000000 INFO @ Sat, 24 Aug 2019 20:24:02: 2000000 INFO @ Sat, 24 Aug 2019 20:24:08: 3000000 INFO @ Sat, 24 Aug 2019 20:24:14: 4000000 INFO @ Sat, 24 Aug 2019 20:24:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.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 20:24:19: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:24:19: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:24:21: 5000000 INFO @ Sat, 24 Aug 2019 20:24:26: 1000000 INFO @ Sat, 24 Aug 2019 20:24:27: 6000000 INFO @ Sat, 24 Aug 2019 20:24:33: 2000000 INFO @ Sat, 24 Aug 2019 20:24:33: 7000000 INFO @ Sat, 24 Aug 2019 20:24:40: 8000000 INFO @ Sat, 24 Aug 2019 20:24:40: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:24:46: 9000000 INFO @ Sat, 24 Aug 2019 20:24:47: 4000000 INFO @ Sat, 24 Aug 2019 20:24:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.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 20:24:49: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:24:49: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:24:53: 10000000 INFO @ Sat, 24 Aug 2019 20:24:55: 5000000 INFO @ Sat, 24 Aug 2019 20:24:57: 1000000 INFO @ Sat, 24 Aug 2019 20:24:59: 11000000 INFO @ Sat, 24 Aug 2019 20:25:02: 6000000 INFO @ Sat, 24 Aug 2019 20:25:05: 2000000 INFO @ Sat, 24 Aug 2019 20:25:06: 12000000 INFO @ Sat, 24 Aug 2019 20:25:09: 7000000 INFO @ Sat, 24 Aug 2019 20:25:12: 13000000 INFO @ Sat, 24 Aug 2019 20:25:13: 3000000 INFO @ Sat, 24 Aug 2019 20:25:16: 8000000 INFO @ Sat, 24 Aug 2019 20:25:19: 14000000 INFO @ Sat, 24 Aug 2019 20:25:21: 4000000 INFO @ Sat, 24 Aug 2019 20:25:24: 9000000 INFO @ Sat, 24 Aug 2019 20:25:25: 15000000 INFO @ Sat, 24 Aug 2019 20:25:29: 5000000 INFO @ Sat, 24 Aug 2019 20:25:31: 10000000 INFO @ Sat, 24 Aug 2019 20:25:32: 16000000 INFO @ Sat, 24 Aug 2019 20:25:37: 6000000 INFO @ Sat, 24 Aug 2019 20:25:38: 11000000 INFO @ Sat, 24 Aug 2019 20:25:38: 17000000 INFO @ Sat, 24 Aug 2019 20:25:45: 18000000 INFO @ Sat, 24 Aug 2019 20:25:45: 7000000 INFO @ Sat, 24 Aug 2019 20:25:45: 12000000 INFO @ Sat, 24 Aug 2019 20:25:51: 19000000 INFO @ Sat, 24 Aug 2019 20:25:53: 13000000 INFO @ Sat, 24 Aug 2019 20:25:53: 8000000 INFO @ Sat, 24 Aug 2019 20:25:58: 20000000 INFO @ Sat, 24 Aug 2019 20:26:00: 14000000 INFO @ Sat, 24 Aug 2019 20:26:01: 9000000 INFO @ Sat, 24 Aug 2019 20:26:04: 21000000 INFO @ Sat, 24 Aug 2019 20:26:07: 15000000 INFO @ Sat, 24 Aug 2019 20:26:09: 10000000 INFO @ Sat, 24 Aug 2019 20:26:11: 22000000 INFO @ Sat, 24 Aug 2019 20:26:14: 16000000 INFO @ Sat, 24 Aug 2019 20:26:17: 11000000 INFO @ Sat, 24 Aug 2019 20:26:17: 23000000 INFO @ Sat, 24 Aug 2019 20:26:22: 17000000 INFO @ Sat, 24 Aug 2019 20:26:24: 24000000 INFO @ Sat, 24 Aug 2019 20:26:25: 12000000 INFO @ Sat, 24 Aug 2019 20:26:29: 18000000 INFO @ Sat, 24 Aug 2019 20:26:30: 25000000 INFO @ Sat, 24 Aug 2019 20:26:34: 13000000 INFO @ Sat, 24 Aug 2019 20:26:38: 19000000 INFO @ Sat, 24 Aug 2019 20:26:39: 26000000 INFO @ Sat, 24 Aug 2019 20:26:44: 14000000 INFO @ Sat, 24 Aug 2019 20:26:47: 27000000 INFO @ Sat, 24 Aug 2019 20:26:48: 20000000 INFO @ Sat, 24 Aug 2019 20:26:53: 15000000 INFO @ Sat, 24 Aug 2019 20:26:55: 28000000 INFO @ Sat, 24 Aug 2019 20:26:56: 21000000 INFO @ Sat, 24 Aug 2019 20:26:58: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 20:26:58: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 20:26:58: #1 total tags in treatment: 13937895 INFO @ Sat, 24 Aug 2019 20:26:58: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:26:58: #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 20:26:59: #1 tags after filtering in treatment: 8216563 INFO @ Sat, 24 Aug 2019 20:26:59: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 24 Aug 2019 20:26:59: #1 finished! INFO @ Sat, 24 Aug 2019 20:26:59: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:26:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:26:59: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:26:59: 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 20:26:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.05_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/SRX404598/SRX404598.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:27:00: 16000000 INFO @ Sat, 24 Aug 2019 20:27:03: 22000000 INFO @ Sat, 24 Aug 2019 20:27:07: 17000000 INFO @ Sat, 24 Aug 2019 20:27:11: 23000000 INFO @ Sat, 24 Aug 2019 20:27:14: 18000000 INFO @ Sat, 24 Aug 2019 20:27:18: 24000000 INFO @ Sat, 24 Aug 2019 20:27:22: 19000000 INFO @ Sat, 24 Aug 2019 20:27:25: 25000000 INFO @ Sat, 24 Aug 2019 20:27:30: 20000000 INFO @ Sat, 24 Aug 2019 20:27:32: 26000000 INFO @ Sat, 24 Aug 2019 20:27:38: 21000000 INFO @ Sat, 24 Aug 2019 20:27:40: 27000000 INFO @ Sat, 24 Aug 2019 20:27:46: 22000000 INFO @ Sat, 24 Aug 2019 20:27:47: 28000000 INFO @ Sat, 24 Aug 2019 20:27:50: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 20:27:50: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 20:27:50: #1 total tags in treatment: 13937895 INFO @ Sat, 24 Aug 2019 20:27:50: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:27:50: #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 20:27:50: #1 tags after filtering in treatment: 8216563 INFO @ Sat, 24 Aug 2019 20:27:50: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 24 Aug 2019 20:27:50: #1 finished! INFO @ Sat, 24 Aug 2019 20:27:50: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:27:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:27:51: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:27:51: 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 20:27:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.10_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/SRX404598/SRX404598.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:27:54: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 20:28:02: 24000000 INFO @ Sat, 24 Aug 2019 20:28:10: 25000000 INFO @ Sat, 24 Aug 2019 20:28:18: 26000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 20:28:26: 27000000 INFO @ Sat, 24 Aug 2019 20:28:34: 28000000 INFO @ Sat, 24 Aug 2019 20:28:37: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 20:28:37: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 20:28:37: #1 total tags in treatment: 13937895 INFO @ Sat, 24 Aug 2019 20:28:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:28:37: #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 20:28:38: #1 tags after filtering in treatment: 8216563 INFO @ Sat, 24 Aug 2019 20:28:38: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 24 Aug 2019 20:28:38: #1 finished! INFO @ Sat, 24 Aug 2019 20:28:38: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:28:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:28:38: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:28:38: 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 20:28:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.20_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/SRX404598/SRX404598.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404598/SRX404598.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling