Job ID = 2641011 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 14,428,359 reads read : 28,856,718 reads written : 28,856,718 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: 00:18:44 14428359 reads; of these: 14428359 (100.00%) were paired; of these: 1791089 (12.41%) aligned concordantly 0 times 10796192 (74.83%) aligned concordantly exactly 1 time 1841078 (12.76%) aligned concordantly >1 times ---- 1791089 pairs aligned concordantly 0 times; of these: 1088172 (60.75%) aligned discordantly 1 time ---- 702917 pairs aligned 0 times concordantly or discordantly; of these: 1405834 mates make up the pairs; of these: 820483 (58.36%) aligned 0 times 185057 (13.16%) aligned exactly 1 time 400294 (28.47%) aligned >1 times 97.16% overall alignment rate Time searching: 00:18:44 Overall time: 00:18:44 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] 1291146 / 13723414 = 0.0941 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:16:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.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 21:16:36: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:16:36: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:16:46: 1000000 INFO @ Sat, 24 Aug 2019 21:16:55: 2000000 INFO @ Sat, 24 Aug 2019 21:17:04: 3000000 INFO @ Sat, 24 Aug 2019 21:17:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.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 21:17:06: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:17:06: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:17:14: 4000000 INFO @ Sat, 24 Aug 2019 21:17:14: 1000000 INFO @ Sat, 24 Aug 2019 21:17:23: 2000000 INFO @ Sat, 24 Aug 2019 21:17:23: 5000000 INFO @ Sat, 24 Aug 2019 21:17:31: 3000000 INFO @ Sat, 24 Aug 2019 21:17:32: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:17:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.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 21:17:36: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:17:36: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:17:39: 4000000 INFO @ Sat, 24 Aug 2019 21:17:42: 7000000 INFO @ Sat, 24 Aug 2019 21:17:46: 1000000 INFO @ Sat, 24 Aug 2019 21:17:48: 5000000 INFO @ Sat, 24 Aug 2019 21:17:51: 8000000 INFO @ Sat, 24 Aug 2019 21:17:55: 2000000 INFO @ Sat, 24 Aug 2019 21:17:56: 6000000 INFO @ Sat, 24 Aug 2019 21:18:00: 9000000 INFO @ Sat, 24 Aug 2019 21:18:04: 7000000 INFO @ Sat, 24 Aug 2019 21:18:05: 3000000 INFO @ Sat, 24 Aug 2019 21:18:10: 10000000 INFO @ Sat, 24 Aug 2019 21:18:12: 8000000 INFO @ Sat, 24 Aug 2019 21:18:14: 4000000 INFO @ Sat, 24 Aug 2019 21:18:20: 11000000 INFO @ Sat, 24 Aug 2019 21:18:21: 9000000 INFO @ Sat, 24 Aug 2019 21:18:23: 5000000 INFO @ Sat, 24 Aug 2019 21:18:29: 10000000 INFO @ Sat, 24 Aug 2019 21:18:29: 12000000 INFO @ Sat, 24 Aug 2019 21:18:33: 6000000 INFO @ Sat, 24 Aug 2019 21:18:37: 11000000 INFO @ Sat, 24 Aug 2019 21:18:38: 13000000 INFO @ Sat, 24 Aug 2019 21:18:42: 7000000 INFO @ Sat, 24 Aug 2019 21:18:46: 12000000 INFO @ Sat, 24 Aug 2019 21:18:48: 14000000 INFO @ Sat, 24 Aug 2019 21:18:51: 8000000 INFO @ Sat, 24 Aug 2019 21:18:54: 13000000 INFO @ Sat, 24 Aug 2019 21:18:57: 15000000 INFO @ Sat, 24 Aug 2019 21:19:01: 9000000 INFO @ Sat, 24 Aug 2019 21:19:02: 14000000 INFO @ Sat, 24 Aug 2019 21:19:07: 16000000 INFO @ Sat, 24 Aug 2019 21:19:10: 10000000 INFO @ Sat, 24 Aug 2019 21:19:10: 15000000 INFO @ Sat, 24 Aug 2019 21:19:16: 17000000 INFO @ Sat, 24 Aug 2019 21:19:19: 16000000 INFO @ Sat, 24 Aug 2019 21:19:20: 11000000 INFO @ Sat, 24 Aug 2019 21:19:26: 18000000 INFO @ Sat, 24 Aug 2019 21:19:27: 17000000 INFO @ Sat, 24 Aug 2019 21:19:29: 12000000 INFO @ Sat, 24 Aug 2019 21:19:35: 18000000 INFO @ Sat, 24 Aug 2019 21:19:35: 19000000 INFO @ Sat, 24 Aug 2019 21:19:39: 13000000 INFO @ Sat, 24 Aug 2019 21:19:43: 19000000 INFO @ Sat, 24 Aug 2019 21:19:45: 20000000 INFO @ Sat, 24 Aug 2019 21:19:48: 14000000 INFO @ Sat, 24 Aug 2019 21:19:52: 20000000 INFO @ Sat, 24 Aug 2019 21:19:54: 21000000 INFO @ Sat, 24 Aug 2019 21:19:57: 15000000 INFO @ Sat, 24 Aug 2019 21:20:00: 21000000 INFO @ Sat, 24 Aug 2019 21:20:03: 22000000 INFO @ Sat, 24 Aug 2019 21:20:07: 16000000 INFO @ Sat, 24 Aug 2019 21:20:08: 22000000 INFO @ Sat, 24 Aug 2019 21:20:13: 23000000 INFO @ Sat, 24 Aug 2019 21:20:16: 17000000 INFO @ Sat, 24 Aug 2019 21:20:16: 23000000 INFO @ Sat, 24 Aug 2019 21:20:22: 24000000 INFO @ Sat, 24 Aug 2019 21:20:25: 24000000 INFO @ Sat, 24 Aug 2019 21:20:26: 18000000 INFO @ Sat, 24 Aug 2019 21:20:32: 25000000 INFO @ Sat, 24 Aug 2019 21:20:33: 25000000 INFO @ Sat, 24 Aug 2019 21:20:35: 19000000 INFO @ Sat, 24 Aug 2019 21:20:36: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:20:36: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:20:36: #1 total tags in treatment: 11400604 INFO @ Sat, 24 Aug 2019 21:20:36: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:20:36: #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 21:20:36: #1 tags after filtering in treatment: 8114561 INFO @ Sat, 24 Aug 2019 21:20:36: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:20:36: #1 finished! INFO @ Sat, 24 Aug 2019 21:20:36: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:20:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:20:37: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:20:37: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:20:37: #1 total tags in treatment: 11400604 INFO @ Sat, 24 Aug 2019 21:20:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:20:37: #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 21:20:37: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:20:37: 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 21:20:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.05_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/SRX4936117/SRX4936117.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:20:37: #1 tags after filtering in treatment: 8114561 INFO @ Sat, 24 Aug 2019 21:20:37: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:20:37: #1 finished! INFO @ Sat, 24 Aug 2019 21:20:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:20:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:20:38: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:20:38: 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 21:20:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.10_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/SRX4936117/SRX4936117.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:20:44: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:20:54: 21000000 INFO @ Sat, 24 Aug 2019 21:21:03: 22000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:21:12: 23000000 INFO @ Sat, 24 Aug 2019 21:21:21: 24000000 INFO @ Sat, 24 Aug 2019 21:21:30: 25000000 INFO @ Sat, 24 Aug 2019 21:21:34: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:21:34: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:21:34: #1 total tags in treatment: 11400604 INFO @ Sat, 24 Aug 2019 21:21:34: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:21:34: #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 21:21:35: #1 tags after filtering in treatment: 8114561 INFO @ Sat, 24 Aug 2019 21:21:35: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:21:35: #1 finished! INFO @ Sat, 24 Aug 2019 21:21:35: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:21:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:21:35: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:21:35: 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 21:21:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.20_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/SRX4936117/SRX4936117.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936117/SRX4936117.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling