Job ID = 2641110 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,154,420 reads read : 22,308,840 reads written : 22,308,840 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: 00:15:42 11154420 reads; of these: 11154420 (100.00%) were paired; of these: 6244595 (55.98%) aligned concordantly 0 times 4515138 (40.48%) aligned concordantly exactly 1 time 394687 (3.54%) aligned concordantly >1 times ---- 6244595 pairs aligned concordantly 0 times; of these: 4566823 (73.13%) aligned discordantly 1 time ---- 1677772 pairs aligned 0 times concordantly or discordantly; of these: 3355544 mates make up the pairs; of these: 1872091 (55.79%) aligned 0 times 557947 (16.63%) aligned exactly 1 time 925506 (27.58%) aligned >1 times 91.61% overall alignment rate Time searching: 00:15:42 Overall time: 00:15:42 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] 1179468 / 9472367 = 0.1245 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:07:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.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 22:07:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:07:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:07:59: 1000000 INFO @ Sat, 24 Aug 2019 22:08:08: 2000000 INFO @ Sat, 24 Aug 2019 22:08:16: 3000000 INFO @ Sat, 24 Aug 2019 22:08:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.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 22:08:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:08:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:08:25: 4000000 INFO @ Sat, 24 Aug 2019 22:08:30: 1000000 INFO @ Sat, 24 Aug 2019 22:08:34: 5000000 INFO @ Sat, 24 Aug 2019 22:08:39: 2000000 INFO @ Sat, 24 Aug 2019 22:08:43: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:08:48: 3000000 INFO @ Sat, 24 Aug 2019 22:08:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.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 22:08:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:08:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:08:52: 7000000 INFO @ Sat, 24 Aug 2019 22:08:57: 4000000 INFO @ Sat, 24 Aug 2019 22:09:00: 1000000 INFO @ Sat, 24 Aug 2019 22:09:02: 8000000 INFO @ Sat, 24 Aug 2019 22:09:06: 5000000 INFO @ Sat, 24 Aug 2019 22:09:10: 2000000 INFO @ Sat, 24 Aug 2019 22:09:12: 9000000 INFO @ Sat, 24 Aug 2019 22:09:16: 6000000 INFO @ Sat, 24 Aug 2019 22:09:21: 3000000 INFO @ Sat, 24 Aug 2019 22:09:21: 10000000 INFO @ Sat, 24 Aug 2019 22:09:26: 7000000 INFO @ Sat, 24 Aug 2019 22:09:30: 11000000 INFO @ Sat, 24 Aug 2019 22:09:31: 4000000 INFO @ Sat, 24 Aug 2019 22:09:36: 8000000 INFO @ Sat, 24 Aug 2019 22:09:39: 12000000 INFO @ Sat, 24 Aug 2019 22:09:41: 5000000 INFO @ Sat, 24 Aug 2019 22:09:46: 9000000 INFO @ Sat, 24 Aug 2019 22:09:48: 13000000 INFO @ Sat, 24 Aug 2019 22:09:52: 6000000 INFO @ Sat, 24 Aug 2019 22:09:56: 10000000 INFO @ Sat, 24 Aug 2019 22:09:57: 14000000 INFO @ Sat, 24 Aug 2019 22:10:02: 7000000 INFO @ Sat, 24 Aug 2019 22:10:06: 11000000 INFO @ Sat, 24 Aug 2019 22:10:07: 15000000 INFO @ Sat, 24 Aug 2019 22:10:12: 8000000 INFO @ Sat, 24 Aug 2019 22:10:16: 12000000 INFO @ Sat, 24 Aug 2019 22:10:16: 16000000 INFO @ Sat, 24 Aug 2019 22:10:21: 9000000 INFO @ Sat, 24 Aug 2019 22:10:26: 13000000 INFO @ Sat, 24 Aug 2019 22:10:27: 17000000 INFO @ Sat, 24 Aug 2019 22:10:30: 10000000 INFO @ Sat, 24 Aug 2019 22:10:36: 14000000 INFO @ Sat, 24 Aug 2019 22:10:37: 18000000 INFO @ Sat, 24 Aug 2019 22:10:37: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:10:37: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:10:37: #1 total tags in treatment: 4269765 INFO @ Sat, 24 Aug 2019 22:10:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:10:37: #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 22:10:37: #1 tags after filtering in treatment: 3782980 INFO @ Sat, 24 Aug 2019 22:10:37: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 24 Aug 2019 22:10:37: #1 finished! INFO @ Sat, 24 Aug 2019 22:10:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:10:38: #2 number of paired peaks: 25 WARNING @ Sat, 24 Aug 2019 22:10:38: Too few paired peaks (25) 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 22:10:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.05_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/SRX5546551/SRX5546551.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:10:39: 11000000 INFO @ Sat, 24 Aug 2019 22:10:45: 15000000 INFO @ Sat, 24 Aug 2019 22:10:48: 12000000 INFO @ Sat, 24 Aug 2019 22:10:54: 16000000 INFO @ Sat, 24 Aug 2019 22:10:57: 13000000 INFO @ Sat, 24 Aug 2019 22:11:03: 17000000 INFO @ Sat, 24 Aug 2019 22:11:06: 14000000 INFO @ Sat, 24 Aug 2019 22:11:14: 18000000 INFO @ Sat, 24 Aug 2019 22:11:14: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:11:14: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:11:14: #1 total tags in treatment: 4269765 INFO @ Sat, 24 Aug 2019 22:11:14: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:11:14: #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 22:11:15: #1 tags after filtering in treatment: 3782980 INFO @ Sat, 24 Aug 2019 22:11:15: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 24 Aug 2019 22:11:15: #1 finished! INFO @ Sat, 24 Aug 2019 22:11:15: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:11:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:11:15: 15000000 INFO @ Sat, 24 Aug 2019 22:11:15: #2 number of paired peaks: 25 WARNING @ Sat, 24 Aug 2019 22:11:15: Too few paired peaks (25) 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 22:11:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.10_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/SRX5546551/SRX5546551.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:11:23: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:11:32: 17000000 INFO @ Sat, 24 Aug 2019 22:11:40: 18000000 INFO @ Sat, 24 Aug 2019 22:11:41: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:11:41: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:11:41: #1 total tags in treatment: 4269765 INFO @ Sat, 24 Aug 2019 22:11:41: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:11:41: #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 22:11:41: #1 tags after filtering in treatment: 3782980 INFO @ Sat, 24 Aug 2019 22:11:41: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 24 Aug 2019 22:11:41: #1 finished! INFO @ Sat, 24 Aug 2019 22:11:41: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:11:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:11:41: #2 number of paired peaks: 25 WARNING @ Sat, 24 Aug 2019 22:11:41: Too few paired peaks (25) 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 22:11:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.20_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/SRX5546551/SRX5546551.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546551/SRX5546551.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。