Job ID = 2641248 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,776,633 reads read : 9,553,266 reads written : 9,553,266 spots read : 4,700,006 reads read : 9,400,012 reads written : 9,400,012 spots read : 4,737,945 reads read : 9,475,890 reads written : 9,475,890 spots read : 4,688,448 reads read : 9,376,896 reads written : 9,376,896 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: 00:08:37 18903032 reads; of these: 18903032 (100.00%) were paired; of these: 6339262 (33.54%) aligned concordantly 0 times 11048441 (58.45%) aligned concordantly exactly 1 time 1515329 (8.02%) aligned concordantly >1 times ---- 6339262 pairs aligned concordantly 0 times; of these: 29946 (0.47%) aligned discordantly 1 time ---- 6309316 pairs aligned 0 times concordantly or discordantly; of these: 12618632 mates make up the pairs; of these: 10216151 (80.96%) aligned 0 times 2054311 (16.28%) aligned exactly 1 time 348170 (2.76%) aligned >1 times 72.98% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 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 8 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] 524920 / 12591705 = 0.0417 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:40:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.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 22:40:17: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:40:17: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:40:23: 1000000 INFO @ Sat, 24 Aug 2019 22:40:29: 2000000 INFO @ Sat, 24 Aug 2019 22:40:35: 3000000 INFO @ Sat, 24 Aug 2019 22:40:41: 4000000 INFO @ Sat, 24 Aug 2019 22:40:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.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 22:40:46: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:40:46: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:40:48: 5000000 INFO @ Sat, 24 Aug 2019 22:40:53: 1000000 INFO @ Sat, 24 Aug 2019 22:40:54: 6000000 INFO @ Sat, 24 Aug 2019 22:41:00: 7000000 INFO @ Sat, 24 Aug 2019 22:41:00: 2000000 INFO @ Sat, 24 Aug 2019 22:41:06: 8000000 INFO @ Sat, 24 Aug 2019 22:41:07: 3000000 INFO @ Sat, 24 Aug 2019 22:41:12: 9000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:41:14: 4000000 INFO @ Sat, 24 Aug 2019 22:41:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.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 22:41:16: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:41:16: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:41:19: 10000000 INFO @ Sat, 24 Aug 2019 22:41:22: 5000000 INFO @ Sat, 24 Aug 2019 22:41:25: 11000000 INFO @ Sat, 24 Aug 2019 22:41:25: 1000000 INFO @ Sat, 24 Aug 2019 22:41:29: 6000000 INFO @ Sat, 24 Aug 2019 22:41:31: 12000000 INFO @ Sat, 24 Aug 2019 22:41:34: 2000000 INFO @ Sat, 24 Aug 2019 22:41:36: 7000000 INFO @ Sat, 24 Aug 2019 22:41:38: 13000000 INFO @ Sat, 24 Aug 2019 22:41:42: 3000000 INFO @ Sat, 24 Aug 2019 22:41:43: 8000000 INFO @ Sat, 24 Aug 2019 22:41:44: 14000000 INFO @ Sat, 24 Aug 2019 22:41:50: 9000000 INFO @ Sat, 24 Aug 2019 22:41:50: 15000000 INFO @ Sat, 24 Aug 2019 22:41:51: 4000000 INFO @ Sat, 24 Aug 2019 22:41:56: 16000000 INFO @ Sat, 24 Aug 2019 22:41:57: 10000000 INFO @ Sat, 24 Aug 2019 22:41:59: 5000000 INFO @ Sat, 24 Aug 2019 22:42:03: 17000000 INFO @ Sat, 24 Aug 2019 22:42:04: 11000000 INFO @ Sat, 24 Aug 2019 22:42:08: 6000000 INFO @ Sat, 24 Aug 2019 22:42:09: 18000000 INFO @ Sat, 24 Aug 2019 22:42:11: 12000000 INFO @ Sat, 24 Aug 2019 22:42:15: 19000000 INFO @ Sat, 24 Aug 2019 22:42:17: 7000000 INFO @ Sat, 24 Aug 2019 22:42:18: 13000000 INFO @ Sat, 24 Aug 2019 22:42:22: 20000000 INFO @ Sat, 24 Aug 2019 22:42:25: 14000000 INFO @ Sat, 24 Aug 2019 22:42:25: 8000000 INFO @ Sat, 24 Aug 2019 22:42:28: 21000000 INFO @ Sat, 24 Aug 2019 22:42:32: 15000000 INFO @ Sat, 24 Aug 2019 22:42:34: 9000000 INFO @ Sat, 24 Aug 2019 22:42:34: 22000000 INFO @ Sat, 24 Aug 2019 22:42:39: 16000000 INFO @ Sat, 24 Aug 2019 22:42:40: 23000000 INFO @ Sat, 24 Aug 2019 22:42:42: 10000000 INFO @ Sat, 24 Aug 2019 22:42:46: 17000000 INFO @ Sat, 24 Aug 2019 22:42:47: 24000000 INFO @ Sat, 24 Aug 2019 22:42:50: 11000000 INFO @ Sat, 24 Aug 2019 22:42:53: 25000000 INFO @ Sat, 24 Aug 2019 22:42:53: 18000000 INFO @ Sat, 24 Aug 2019 22:42:59: 12000000 INFO @ Sat, 24 Aug 2019 22:42:59: 26000000 INFO @ Sat, 24 Aug 2019 22:43:00: 19000000 INFO @ Sat, 24 Aug 2019 22:43:03: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:43:03: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:43:03: #1 total tags in treatment: 12039421 INFO @ Sat, 24 Aug 2019 22:43:03: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:43:03: #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 22:43:03: #1 tags after filtering in treatment: 8553664 INFO @ Sat, 24 Aug 2019 22:43:03: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 22:43:03: #1 finished! INFO @ Sat, 24 Aug 2019 22:43:03: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:43:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:43:03: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:43:03: 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 22:43:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.05_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/SRX6403224/SRX6403224.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:43:07: 20000000 INFO @ Sat, 24 Aug 2019 22:43:07: 13000000 INFO @ Sat, 24 Aug 2019 22:43:14: 21000000 INFO @ Sat, 24 Aug 2019 22:43:16: 14000000 INFO @ Sat, 24 Aug 2019 22:43:21: 22000000 INFO @ Sat, 24 Aug 2019 22:43:24: 15000000 INFO @ Sat, 24 Aug 2019 22:43:28: 23000000 INFO @ Sat, 24 Aug 2019 22:43:32: 16000000 INFO @ Sat, 24 Aug 2019 22:43:35: 24000000 INFO @ Sat, 24 Aug 2019 22:43:41: 17000000 INFO @ Sat, 24 Aug 2019 22:43:42: 25000000 INFO @ Sat, 24 Aug 2019 22:43:49: 26000000 INFO @ Sat, 24 Aug 2019 22:43:49: 18000000 INFO @ Sat, 24 Aug 2019 22:43:53: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:43:53: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:43:53: #1 total tags in treatment: 12039421 INFO @ Sat, 24 Aug 2019 22:43:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:43:53: #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 22:43:53: #1 tags after filtering in treatment: 8553664 INFO @ Sat, 24 Aug 2019 22:43:53: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 22:43:53: #1 finished! INFO @ Sat, 24 Aug 2019 22:43:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:43:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:43:54: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:43:54: 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 22:43:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.10_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/SRX6403224/SRX6403224.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:43:57: 19000000 INFO @ Sat, 24 Aug 2019 22:44:05: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:44:13: 21000000 INFO @ Sat, 24 Aug 2019 22:44:21: 22000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:44:29: 23000000 INFO @ Sat, 24 Aug 2019 22:44:37: 24000000 INFO @ Sat, 24 Aug 2019 22:44:45: 25000000 INFO @ Sat, 24 Aug 2019 22:44:53: 26000000 INFO @ Sat, 24 Aug 2019 22:44:58: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:44:58: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:44:58: #1 total tags in treatment: 12039421 INFO @ Sat, 24 Aug 2019 22:44:58: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:44:58: #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 22:44:58: #1 tags after filtering in treatment: 8553664 INFO @ Sat, 24 Aug 2019 22:44:58: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 22:44:58: #1 finished! INFO @ Sat, 24 Aug 2019 22:44:58: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:44:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:44:59: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:44:59: 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 22:44:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.20_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/SRX6403224/SRX6403224.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403224/SRX6403224.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling