Job ID = 2010919 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 29,748,899 reads read : 59,497,798 reads written : 59,497,798 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1105631.sra.cache’: 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: 00:37:47 29748899 reads; of these: 29748899 (100.00%) were paired; of these: 4033485 (13.56%) aligned concordantly 0 times 21278411 (71.53%) aligned concordantly exactly 1 time 4437003 (14.91%) aligned concordantly >1 times ---- 4033485 pairs aligned concordantly 0 times; of these: 933785 (23.15%) aligned discordantly 1 time ---- 3099700 pairs aligned 0 times concordantly or discordantly; of these: 6199400 mates make up the pairs; of these: 4735458 (76.39%) aligned 0 times 882418 (14.23%) aligned exactly 1 time 581524 (9.38%) aligned >1 times 92.04% overall alignment rate Time searching: 00:37:47 Overall time: 00:37:47 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 24 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] 18509909 / 26532874 = 0.6976 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 06 Jul 2019 02:18:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.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, 06 Jul 2019 02:18:44: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:18:44: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:18:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.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, 06 Jul 2019 02:18:45: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:18:45: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:18:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.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, 06 Jul 2019 02:18:46: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:18:46: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:18:55: 1000000 INFO @ Sat, 06 Jul 2019 02:18:58: 1000000 INFO @ Sat, 06 Jul 2019 02:18:59: 1000000 INFO @ Sat, 06 Jul 2019 02:19:04: 2000000 INFO @ Sat, 06 Jul 2019 02:19:11: 2000000 INFO @ Sat, 06 Jul 2019 02:19:12: 2000000 INFO @ Sat, 06 Jul 2019 02:19:14: 3000000 INFO @ Sat, 06 Jul 2019 02:19:24: 3000000 INFO @ Sat, 06 Jul 2019 02:19:25: 3000000 INFO @ Sat, 06 Jul 2019 02:19:25: 4000000 INFO @ Sat, 06 Jul 2019 02:19:36: 5000000 INFO @ Sat, 06 Jul 2019 02:19:37: 4000000 INFO @ Sat, 06 Jul 2019 02:19:39: 4000000 INFO @ Sat, 06 Jul 2019 02:19:46: 6000000 INFO @ Sat, 06 Jul 2019 02:19:50: 5000000 INFO @ Sat, 06 Jul 2019 02:19:52: 5000000 INFO @ Sat, 06 Jul 2019 02:19:57: 7000000 INFO @ Sat, 06 Jul 2019 02:20:03: 6000000 INFO @ Sat, 06 Jul 2019 02:20:06: 6000000 INFO @ Sat, 06 Jul 2019 02:20:07: 8000000 INFO @ Sat, 06 Jul 2019 02:20:16: 7000000 INFO @ Sat, 06 Jul 2019 02:20:17: 9000000 INFO @ Sat, 06 Jul 2019 02:20:20: 7000000 INFO @ Sat, 06 Jul 2019 02:20:27: 10000000 INFO @ Sat, 06 Jul 2019 02:20:29: 8000000 INFO @ Sat, 06 Jul 2019 02:20:34: 8000000 INFO @ Sat, 06 Jul 2019 02:20:37: 11000000 INFO @ Sat, 06 Jul 2019 02:20:41: 9000000 INFO @ Sat, 06 Jul 2019 02:20:47: 9000000 INFO @ Sat, 06 Jul 2019 02:20:48: 12000000 INFO @ Sat, 06 Jul 2019 02:20:53: 10000000 INFO @ Sat, 06 Jul 2019 02:20:57: 13000000 INFO @ Sat, 06 Jul 2019 02:20:59: 10000000 INFO @ Sat, 06 Jul 2019 02:21:05: 11000000 INFO @ Sat, 06 Jul 2019 02:21:07: 14000000 INFO @ Sat, 06 Jul 2019 02:21:12: 11000000 INFO @ Sat, 06 Jul 2019 02:21:17: 12000000 INFO @ Sat, 06 Jul 2019 02:21:17: 15000000 INFO @ Sat, 06 Jul 2019 02:21:25: 12000000 INFO @ Sat, 06 Jul 2019 02:21:27: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:21:29: 13000000 INFO @ Sat, 06 Jul 2019 02:21:36: 17000000 INFO @ Sat, 06 Jul 2019 02:21:37: 13000000 INFO @ Sat, 06 Jul 2019 02:21:41: 14000000 INFO @ Sat, 06 Jul 2019 02:21:43: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 02:21:43: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 02:21:43: #1 total tags in treatment: 7796220 INFO @ Sat, 06 Jul 2019 02:21:43: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:21:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:21:43: #1 tags after filtering in treatment: 5272538 INFO @ Sat, 06 Jul 2019 02:21:43: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 06 Jul 2019 02:21:43: #1 finished! INFO @ Sat, 06 Jul 2019 02:21:43: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:21:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:21:44: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:21:44: 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, 06 Jul 2019 02:21:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.10_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/SRX424390/SRX424390.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 02:21:50: 14000000 INFO @ Sat, 06 Jul 2019 02:21:54: 15000000 INFO @ Sat, 06 Jul 2019 02:22:04: 15000000 INFO @ Sat, 06 Jul 2019 02:22:06: 16000000 INFO @ Sat, 06 Jul 2019 02:22:17: 16000000 INFO @ Sat, 06 Jul 2019 02:22:18: 17000000 INFO @ Sat, 06 Jul 2019 02:22:26: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 02:22:26: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 02:22:26: #1 total tags in treatment: 7796220 INFO @ Sat, 06 Jul 2019 02:22:26: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:22:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:22:26: #1 tags after filtering in treatment: 5272538 INFO @ Sat, 06 Jul 2019 02:22:26: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 06 Jul 2019 02:22:26: #1 finished! INFO @ Sat, 06 Jul 2019 02:22:26: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:22:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:22:26: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:22:26: 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, 06 Jul 2019 02:22:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.20_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/SRX424390/SRX424390.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:22:30: 17000000 INFO @ Sat, 06 Jul 2019 02:22:39: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 02:22:39: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 02:22:39: #1 total tags in treatment: 7796220 INFO @ Sat, 06 Jul 2019 02:22:39: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:22:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:22:39: #1 tags after filtering in treatment: 5272538 INFO @ Sat, 06 Jul 2019 02:22:39: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 06 Jul 2019 02:22:39: #1 finished! INFO @ Sat, 06 Jul 2019 02:22:39: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:22:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:22:40: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:22:40: 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, 06 Jul 2019 02:22:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.05_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/SRX424390/SRX424390.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424390/SRX424390.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling