Job ID = 2011938 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 15,891,734 reads read : 31,783,468 reads written : 31,783,468 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: 00:12:52 15891734 reads; of these: 15891734 (100.00%) were paired; of these: 11091151 (69.79%) aligned concordantly 0 times 4070823 (25.62%) aligned concordantly exactly 1 time 729760 (4.59%) aligned concordantly >1 times ---- 11091151 pairs aligned concordantly 0 times; of these: 2555398 (23.04%) aligned discordantly 1 time ---- 8535753 pairs aligned 0 times concordantly or discordantly; of these: 17071506 mates make up the pairs; of these: 15569679 (91.20%) aligned 0 times 529829 (3.10%) aligned exactly 1 time 971998 (5.69%) aligned >1 times 51.01% overall alignment rate Time searching: 00:12:52 Overall time: 00:12:52 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] 1268002 / 7193882 = 0.1763 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 03:57:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.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 03:57:44: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:57:44: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:57:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.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 03:57:45: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:57:45: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:57:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.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 03:57:46: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:57:46: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:57:54: 1000000 INFO @ Sat, 06 Jul 2019 03:57:56: 1000000 INFO @ Sat, 06 Jul 2019 03:57:57: 1000000 INFO @ Sat, 06 Jul 2019 03:58:04: 2000000 INFO @ Sat, 06 Jul 2019 03:58:06: 2000000 INFO @ Sat, 06 Jul 2019 03:58:08: 2000000 INFO @ Sat, 06 Jul 2019 03:58:14: 3000000 INFO @ Sat, 06 Jul 2019 03:58:17: 3000000 INFO @ Sat, 06 Jul 2019 03:58:21: 3000000 INFO @ Sat, 06 Jul 2019 03:58:23: 4000000 INFO @ Sat, 06 Jul 2019 03:58:29: 4000000 INFO @ Sat, 06 Jul 2019 03:58:33: 5000000 INFO @ Sat, 06 Jul 2019 03:58:33: 4000000 INFO @ Sat, 06 Jul 2019 03:58:40: 5000000 INFO @ Sat, 06 Jul 2019 03:58:44: 6000000 INFO @ Sat, 06 Jul 2019 03:58:46: 5000000 INFO @ Sat, 06 Jul 2019 03:58:49: 6000000 INFO @ Sat, 06 Jul 2019 03:58:55: 7000000 INFO @ Sat, 06 Jul 2019 03:58:56: 6000000 INFO @ Sat, 06 Jul 2019 03:58:58: 7000000 INFO @ Sat, 06 Jul 2019 03:59:05: 8000000 INFO @ Sat, 06 Jul 2019 03:59:06: 7000000 INFO @ Sat, 06 Jul 2019 03:59:07: 8000000 INFO @ Sat, 06 Jul 2019 03:59:13: 9000000 INFO @ Sat, 06 Jul 2019 03:59:15: 9000000 INFO @ Sat, 06 Jul 2019 03:59:16: 8000000 INFO @ Sat, 06 Jul 2019 03:59:22: 10000000 INFO @ Sat, 06 Jul 2019 03:59:24: 10000000 INFO @ Sat, 06 Jul 2019 03:59:26: 9000000 INFO @ Sat, 06 Jul 2019 03:59:32: 11000000 INFO @ Sat, 06 Jul 2019 03:59:33: 11000000 INFO @ Sat, 06 Jul 2019 03:59:35: 10000000 INFO @ Sat, 06 Jul 2019 03:59:42: 12000000 INFO @ Sat, 06 Jul 2019 03:59:42: 12000000 INFO @ Sat, 06 Jul 2019 03:59:44: 11000000 INFO @ Sat, 06 Jul 2019 03:59:51: 13000000 INFO @ Sat, 06 Jul 2019 03:59:52: 13000000 INFO @ Sat, 06 Jul 2019 03:59:52: 12000000 INFO @ Sat, 06 Jul 2019 03:59:57: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:59:57: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:59:57: #1 total tags in treatment: 4028621 INFO @ Sat, 06 Jul 2019 03:59:57: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:59:57: #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 03:59:57: #1 tags after filtering in treatment: 2782891 INFO @ Sat, 06 Jul 2019 03:59:57: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 06 Jul 2019 03:59:57: #1 finished! INFO @ Sat, 06 Jul 2019 03:59:57: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:59:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:59:57: #2 number of paired peaks: 27 WARNING @ Sat, 06 Jul 2019 03:59:57: Too few paired peaks (27) 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 03:59:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.10_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/SRX5624297/SRX5624297.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:59:59: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:59:59: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:59:59: #1 total tags in treatment: 4028621 INFO @ Sat, 06 Jul 2019 03:59:59: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:59:59: #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 03:59:59: #1 tags after filtering in treatment: 2782891 INFO @ Sat, 06 Jul 2019 03:59:59: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 06 Jul 2019 03:59:59: #1 finished! INFO @ Sat, 06 Jul 2019 03:59:59: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:59:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 04:00:00: #2 number of paired peaks: 27 WARNING @ Sat, 06 Jul 2019 04:00:00: Too few paired peaks (27) 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 04:00:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.05_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/SRX5624297/SRX5624297.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 04:00:01: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 04:00:06: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 04:00:06: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 04:00:06: #1 total tags in treatment: 4028621 INFO @ Sat, 06 Jul 2019 04:00:06: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 04:00:06: #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 04:00:06: #1 tags after filtering in treatment: 2782891 INFO @ Sat, 06 Jul 2019 04:00:06: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 06 Jul 2019 04:00:06: #1 finished! INFO @ Sat, 06 Jul 2019 04:00:06: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 04:00:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 04:00:06: #2 number of paired peaks: 27 WARNING @ Sat, 06 Jul 2019 04:00:06: Too few paired peaks (27) 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 04:00:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.20_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/SRX5624297/SRX5624297.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624297/SRX5624297.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。