Job ID = 2640992 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,994,882 reads read : 25,989,764 reads written : 25,989,764 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: 00:00:01 Multiseed full-index search: 00:18:01 12994882 reads; of these: 12994882 (100.00%) were paired; of these: 453384 (3.49%) aligned concordantly 0 times 10891344 (83.81%) aligned concordantly exactly 1 time 1650154 (12.70%) aligned concordantly >1 times ---- 453384 pairs aligned concordantly 0 times; of these: 82135 (18.12%) aligned discordantly 1 time ---- 371249 pairs aligned 0 times concordantly or discordantly; of these: 742498 mates make up the pairs; of these: 688913 (92.78%) aligned 0 times 23220 (3.13%) aligned exactly 1 time 30365 (4.09%) aligned >1 times 97.35% overall alignment rate Time searching: 00:18:02 Overall time: 00:18:02 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] 184164 / 12620633 = 0.0146 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:06:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.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 21:06:01: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:06:01: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:06:10: 1000000 INFO @ Sat, 24 Aug 2019 21:06:18: 2000000 INFO @ Sat, 24 Aug 2019 21:06:27: 3000000 INFO @ Sat, 24 Aug 2019 21:06:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.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 21:06:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:06:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:06:36: 4000000 INFO @ Sat, 24 Aug 2019 21:06:39: 1000000 INFO @ Sat, 24 Aug 2019 21:06:44: 5000000 INFO @ Sat, 24 Aug 2019 21:06:46: 2000000 INFO @ Sat, 24 Aug 2019 21:06:53: 6000000 INFO @ Sat, 24 Aug 2019 21:06:54: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:07:01: 4000000 INFO @ Sat, 24 Aug 2019 21:07:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.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 21:07:01: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:07:01: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:07:01: 7000000 INFO @ Sat, 24 Aug 2019 21:07:08: 5000000 INFO @ Sat, 24 Aug 2019 21:07:10: 8000000 INFO @ Sat, 24 Aug 2019 21:07:11: 1000000 INFO @ Sat, 24 Aug 2019 21:07:16: 6000000 INFO @ Sat, 24 Aug 2019 21:07:18: 9000000 INFO @ Sat, 24 Aug 2019 21:07:22: 2000000 INFO @ Sat, 24 Aug 2019 21:07:23: 7000000 INFO @ Sat, 24 Aug 2019 21:07:27: 10000000 INFO @ Sat, 24 Aug 2019 21:07:31: 8000000 INFO @ Sat, 24 Aug 2019 21:07:32: 3000000 INFO @ Sat, 24 Aug 2019 21:07:35: 11000000 INFO @ Sat, 24 Aug 2019 21:07:38: 9000000 INFO @ Sat, 24 Aug 2019 21:07:42: 4000000 INFO @ Sat, 24 Aug 2019 21:07:44: 12000000 INFO @ Sat, 24 Aug 2019 21:07:46: 10000000 INFO @ Sat, 24 Aug 2019 21:07:51: 5000000 INFO @ Sat, 24 Aug 2019 21:07:52: 13000000 INFO @ Sat, 24 Aug 2019 21:07:53: 11000000 INFO @ Sat, 24 Aug 2019 21:08:00: 14000000 INFO @ Sat, 24 Aug 2019 21:08:01: 12000000 INFO @ Sat, 24 Aug 2019 21:08:01: 6000000 INFO @ Sat, 24 Aug 2019 21:08:08: 13000000 INFO @ Sat, 24 Aug 2019 21:08:09: 15000000 INFO @ Sat, 24 Aug 2019 21:08:11: 7000000 INFO @ Sat, 24 Aug 2019 21:08:15: 14000000 INFO @ Sat, 24 Aug 2019 21:08:17: 16000000 INFO @ Sat, 24 Aug 2019 21:08:21: 8000000 INFO @ Sat, 24 Aug 2019 21:08:23: 15000000 INFO @ Sat, 24 Aug 2019 21:08:26: 17000000 INFO @ Sat, 24 Aug 2019 21:08:30: 16000000 INFO @ Sat, 24 Aug 2019 21:08:31: 9000000 INFO @ Sat, 24 Aug 2019 21:08:34: 18000000 INFO @ Sat, 24 Aug 2019 21:08:37: 17000000 INFO @ Sat, 24 Aug 2019 21:08:41: 10000000 INFO @ Sat, 24 Aug 2019 21:08:43: 19000000 INFO @ Sat, 24 Aug 2019 21:08:45: 18000000 INFO @ Sat, 24 Aug 2019 21:08:51: 11000000 INFO @ Sat, 24 Aug 2019 21:08:51: 20000000 INFO @ Sat, 24 Aug 2019 21:08:52: 19000000 INFO @ Sat, 24 Aug 2019 21:08:59: 21000000 INFO @ Sat, 24 Aug 2019 21:08:59: 20000000 INFO @ Sat, 24 Aug 2019 21:09:00: 12000000 INFO @ Sat, 24 Aug 2019 21:09:07: 21000000 INFO @ Sat, 24 Aug 2019 21:09:07: 22000000 INFO @ Sat, 24 Aug 2019 21:09:10: 13000000 INFO @ Sat, 24 Aug 2019 21:09:14: 22000000 INFO @ Sat, 24 Aug 2019 21:09:16: 23000000 INFO @ Sat, 24 Aug 2019 21:09:20: 14000000 INFO @ Sat, 24 Aug 2019 21:09:21: 23000000 INFO @ Sat, 24 Aug 2019 21:09:24: 24000000 INFO @ Sat, 24 Aug 2019 21:09:29: 24000000 INFO @ Sat, 24 Aug 2019 21:09:30: 15000000 INFO @ Sat, 24 Aug 2019 21:09:32: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:09:32: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:09:32: #1 total tags in treatment: 12357766 INFO @ Sat, 24 Aug 2019 21:09:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:09:32: #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 21:09:32: #1 tags after filtering in treatment: 9011390 INFO @ Sat, 24 Aug 2019 21:09:32: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 21:09:32: #1 finished! INFO @ Sat, 24 Aug 2019 21:09:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:09:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:09:33: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:09:33: 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 21:09:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.05_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/SRX4936098/SRX4936098.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:09:36: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:09:36: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:09:36: #1 total tags in treatment: 12357766 INFO @ Sat, 24 Aug 2019 21:09:36: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:09:36: #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 21:09:36: #1 tags after filtering in treatment: 9011390 INFO @ Sat, 24 Aug 2019 21:09:36: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 21:09:36: #1 finished! INFO @ Sat, 24 Aug 2019 21:09:36: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:09:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:09:37: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:09:37: 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 21:09:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.10_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/SRX4936098/SRX4936098.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:09:39: 16000000 INFO @ Sat, 24 Aug 2019 21:09:49: 17000000 INFO @ Sat, 24 Aug 2019 21:09:58: 18000000 INFO @ Sat, 24 Aug 2019 21:10:08: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:10:17: 20000000 INFO @ Sat, 24 Aug 2019 21:10:27: 21000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:10:36: 22000000 INFO @ Sat, 24 Aug 2019 21:10:46: 23000000 INFO @ Sat, 24 Aug 2019 21:10:55: 24000000 INFO @ Sat, 24 Aug 2019 21:11:04: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:11:04: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:11:04: #1 total tags in treatment: 12357766 INFO @ Sat, 24 Aug 2019 21:11:04: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:11:04: #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 21:11:04: #1 tags after filtering in treatment: 9011390 INFO @ Sat, 24 Aug 2019 21:11:04: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 21:11:04: #1 finished! INFO @ Sat, 24 Aug 2019 21:11:04: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:11:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:11:05: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:11:05: 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 21:11:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.20_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/SRX4936098/SRX4936098.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936098/SRX4936098.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling