Job ID = 2640999 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,931,733 reads read : 23,863,466 reads written : 23,863,466 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: 00:17:15 11931733 reads; of these: 11931733 (100.00%) were paired; of these: 334574 (2.80%) aligned concordantly 0 times 10176172 (85.29%) aligned concordantly exactly 1 time 1420987 (11.91%) aligned concordantly >1 times ---- 334574 pairs aligned concordantly 0 times; of these: 112840 (33.73%) aligned discordantly 1 time ---- 221734 pairs aligned 0 times concordantly or discordantly; of these: 443468 mates make up the pairs; of these: 379402 (85.55%) aligned 0 times 26707 (6.02%) aligned exactly 1 time 37359 (8.42%) aligned >1 times 98.41% overall alignment rate Time searching: 00:17:15 Overall time: 00:17:15 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] 148959 / 11706679 = 0.0127 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:03:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.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 21:03:17: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:03:17: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:03:28: 1000000 INFO @ Sat, 24 Aug 2019 21:03:38: 2000000 INFO @ Sat, 24 Aug 2019 21:03:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.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 21:03:47: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:03:47: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:03:49: 3000000 INFO @ Sat, 24 Aug 2019 21:03:58: 1000000 INFO @ Sat, 24 Aug 2019 21:03:59: 4000000 INFO @ Sat, 24 Aug 2019 21:04:08: 2000000 INFO @ Sat, 24 Aug 2019 21:04:10: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:04:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.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 21:04:17: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:04:17: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:04:19: 3000000 INFO @ Sat, 24 Aug 2019 21:04:21: 6000000 INFO @ Sat, 24 Aug 2019 21:04:27: 1000000 INFO @ Sat, 24 Aug 2019 21:04:30: 4000000 INFO @ Sat, 24 Aug 2019 21:04:32: 7000000 INFO @ Sat, 24 Aug 2019 21:04:36: 2000000 INFO @ Sat, 24 Aug 2019 21:04:41: 5000000 INFO @ Sat, 24 Aug 2019 21:04:43: 8000000 INFO @ Sat, 24 Aug 2019 21:04:46: 3000000 INFO @ Sat, 24 Aug 2019 21:04:52: 6000000 INFO @ Sat, 24 Aug 2019 21:04:54: 9000000 INFO @ Sat, 24 Aug 2019 21:04:56: 4000000 INFO @ Sat, 24 Aug 2019 21:05:03: 7000000 INFO @ Sat, 24 Aug 2019 21:05:05: 10000000 INFO @ Sat, 24 Aug 2019 21:05:05: 5000000 INFO @ Sat, 24 Aug 2019 21:05:14: 8000000 INFO @ Sat, 24 Aug 2019 21:05:15: 6000000 INFO @ Sat, 24 Aug 2019 21:05:17: 11000000 INFO @ Sat, 24 Aug 2019 21:05:24: 9000000 INFO @ Sat, 24 Aug 2019 21:05:25: 7000000 INFO @ Sat, 24 Aug 2019 21:05:28: 12000000 INFO @ Sat, 24 Aug 2019 21:05:34: 8000000 INFO @ Sat, 24 Aug 2019 21:05:34: 10000000 INFO @ Sat, 24 Aug 2019 21:05:39: 13000000 INFO @ Sat, 24 Aug 2019 21:05:44: 9000000 INFO @ Sat, 24 Aug 2019 21:05:45: 11000000 INFO @ Sat, 24 Aug 2019 21:05:50: 14000000 INFO @ Sat, 24 Aug 2019 21:05:53: 10000000 INFO @ Sat, 24 Aug 2019 21:05:55: 12000000 INFO @ Sat, 24 Aug 2019 21:06:00: 15000000 INFO @ Sat, 24 Aug 2019 21:06:03: 11000000 INFO @ Sat, 24 Aug 2019 21:06:06: 13000000 INFO @ Sat, 24 Aug 2019 21:06:11: 16000000 INFO @ Sat, 24 Aug 2019 21:06:12: 12000000 INFO @ Sat, 24 Aug 2019 21:06:17: 14000000 INFO @ Sat, 24 Aug 2019 21:06:22: 13000000 INFO @ Sat, 24 Aug 2019 21:06:22: 17000000 INFO @ Sat, 24 Aug 2019 21:06:28: 15000000 INFO @ Sat, 24 Aug 2019 21:06:31: 14000000 INFO @ Sat, 24 Aug 2019 21:06:33: 18000000 INFO @ Sat, 24 Aug 2019 21:06:39: 16000000 INFO @ Sat, 24 Aug 2019 21:06:41: 15000000 INFO @ Sat, 24 Aug 2019 21:06:44: 19000000 INFO @ Sat, 24 Aug 2019 21:06:49: 17000000 INFO @ Sat, 24 Aug 2019 21:06:50: 16000000 INFO @ Sat, 24 Aug 2019 21:06:54: 20000000 INFO @ Sat, 24 Aug 2019 21:07:00: 17000000 INFO @ Sat, 24 Aug 2019 21:07:00: 18000000 INFO @ Sat, 24 Aug 2019 21:07:05: 21000000 INFO @ Sat, 24 Aug 2019 21:07:10: 18000000 INFO @ Sat, 24 Aug 2019 21:07:11: 19000000 INFO @ Sat, 24 Aug 2019 21:07:16: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:07:19: 19000000 INFO @ Sat, 24 Aug 2019 21:07:22: 20000000 INFO @ Sat, 24 Aug 2019 21:07:27: 23000000 INFO @ Sat, 24 Aug 2019 21:07:29: 20000000 INFO @ Sat, 24 Aug 2019 21:07:29: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:07:29: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:07:29: #1 total tags in treatment: 11448783 INFO @ Sat, 24 Aug 2019 21:07:29: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:07:29: #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 21:07:29: #1 tags after filtering in treatment: 8512332 INFO @ Sat, 24 Aug 2019 21:07:29: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 24 Aug 2019 21:07:29: #1 finished! INFO @ Sat, 24 Aug 2019 21:07:29: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:07:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:07:30: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:07:30: 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 21:07:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.05_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/SRX4936105/SRX4936105.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:07:32: 21000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:07:38: 21000000 INFO @ Sat, 24 Aug 2019 21:07:42: 22000000 INFO @ Sat, 24 Aug 2019 21:07:47: 22000000 INFO @ Sat, 24 Aug 2019 21:07:53: 23000000 INFO @ Sat, 24 Aug 2019 21:07:55: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:07:55: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:07:55: #1 total tags in treatment: 11448783 INFO @ Sat, 24 Aug 2019 21:07:55: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:07:55: #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 21:07:56: #1 tags after filtering in treatment: 8512332 INFO @ Sat, 24 Aug 2019 21:07:56: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 24 Aug 2019 21:07:56: #1 finished! INFO @ Sat, 24 Aug 2019 21:07:56: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:07:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:07:56: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:07:56: 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 21:07:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.10_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/SRX4936105/SRX4936105.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:07:57: 23000000 INFO @ Sat, 24 Aug 2019 21:07:58: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:07:58: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:07:58: #1 total tags in treatment: 11448783 INFO @ Sat, 24 Aug 2019 21:07:58: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:07:58: #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 21:07:59: #1 tags after filtering in treatment: 8512332 INFO @ Sat, 24 Aug 2019 21:07:59: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 24 Aug 2019 21:07:59: #1 finished! INFO @ Sat, 24 Aug 2019 21:07:59: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:07:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:07:59: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:07:59: 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 21:07:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.20_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/SRX4936105/SRX4936105.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936105/SRX4936105.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling