Job ID = 2009909 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,600,684 reads read : 17,201,368 reads written : 17,201,368 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: 00:07:02 8600684 reads; of these: 8600684 (100.00%) were paired; of these: 638841 (7.43%) aligned concordantly 0 times 6364500 (74.00%) aligned concordantly exactly 1 time 1597343 (18.57%) aligned concordantly >1 times ---- 638841 pairs aligned concordantly 0 times; of these: 69513 (10.88%) aligned discordantly 1 time ---- 569328 pairs aligned 0 times concordantly or discordantly; of these: 1138656 mates make up the pairs; of these: 834086 (73.25%) aligned 0 times 212104 (18.63%) aligned exactly 1 time 92466 (8.12%) aligned >1 times 95.15% overall alignment rate Time searching: 00:07:02 Overall time: 00:07:02 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] 348507 / 8024990 = 0.0434 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 @ Fri, 05 Jul 2019 20:59:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.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 @ Fri, 05 Jul 2019 20:59:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:59:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:59:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.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 @ Fri, 05 Jul 2019 20:59:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:59:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:59:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.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 @ Fri, 05 Jul 2019 20:59:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:59:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:59:38: 1000000 INFO @ Fri, 05 Jul 2019 20:59:39: 1000000 INFO @ Fri, 05 Jul 2019 20:59:41: 1000000 INFO @ Fri, 05 Jul 2019 20:59:44: 2000000 INFO @ Fri, 05 Jul 2019 20:59:46: 2000000 INFO @ Fri, 05 Jul 2019 20:59:50: 2000000 INFO @ Fri, 05 Jul 2019 20:59:51: 3000000 INFO @ Fri, 05 Jul 2019 20:59:53: 3000000 INFO @ Fri, 05 Jul 2019 20:59:57: 4000000 INFO @ Fri, 05 Jul 2019 20:59:58: 3000000 INFO @ Fri, 05 Jul 2019 21:00:00: 4000000 INFO @ Fri, 05 Jul 2019 21:00:04: 5000000 INFO @ Fri, 05 Jul 2019 21:00:07: 4000000 INFO @ Fri, 05 Jul 2019 21:00:07: 5000000 INFO @ Fri, 05 Jul 2019 21:00:10: 6000000 INFO @ Fri, 05 Jul 2019 21:00:14: 6000000 INFO @ Fri, 05 Jul 2019 21:00:15: 5000000 INFO @ Fri, 05 Jul 2019 21:00:16: 7000000 INFO @ Fri, 05 Jul 2019 21:00:22: 7000000 INFO @ Fri, 05 Jul 2019 21:00:23: 8000000 INFO @ Fri, 05 Jul 2019 21:00:24: 6000000 INFO @ Fri, 05 Jul 2019 21:00:29: 8000000 INFO @ Fri, 05 Jul 2019 21:00:29: 9000000 INFO @ Fri, 05 Jul 2019 21:00:33: 7000000 INFO @ Fri, 05 Jul 2019 21:00:36: 10000000 INFO @ Fri, 05 Jul 2019 21:00:36: 9000000 INFO @ Fri, 05 Jul 2019 21:00:41: 8000000 INFO @ Fri, 05 Jul 2019 21:00:42: 11000000 INFO @ Fri, 05 Jul 2019 21:00:43: 10000000 INFO @ Fri, 05 Jul 2019 21:00:49: 12000000 INFO @ Fri, 05 Jul 2019 21:00:50: 9000000 INFO @ Fri, 05 Jul 2019 21:00:52: 11000000 INFO @ Fri, 05 Jul 2019 21:00:56: 13000000 INFO @ Fri, 05 Jul 2019 21:00:59: 10000000 INFO @ Fri, 05 Jul 2019 21:01:00: 12000000 INFO @ Fri, 05 Jul 2019 21:01:03: 14000000 INFO @ Fri, 05 Jul 2019 21:01:07: 13000000 INFO @ Fri, 05 Jul 2019 21:01:08: 11000000 INFO @ Fri, 05 Jul 2019 21:01:10: 15000000 INFO @ Fri, 05 Jul 2019 21:01:14: 14000000 INFO @ Fri, 05 Jul 2019 21:01:15: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:01:15: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:01:15: #1 total tags in treatment: 7614140 INFO @ Fri, 05 Jul 2019 21:01:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:01:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:01:15: #1 tags after filtering in treatment: 5180222 INFO @ Fri, 05 Jul 2019 21:01:15: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 21:01:15: #1 finished! INFO @ Fri, 05 Jul 2019 21:01:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:01:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:01:15: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:01:15: 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 @ Fri, 05 Jul 2019 21:01:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.05_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/SRX2339846/SRX2339846.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:01:16: 12000000 INFO @ Fri, 05 Jul 2019 21:01:21: 15000000 INFO @ Fri, 05 Jul 2019 21:01:25: 13000000 INFO @ Fri, 05 Jul 2019 21:01:26: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:01:26: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:01:26: #1 total tags in treatment: 7614140 INFO @ Fri, 05 Jul 2019 21:01:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:01:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:01:26: #1 tags after filtering in treatment: 5180222 INFO @ Fri, 05 Jul 2019 21:01:26: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 21:01:26: #1 finished! INFO @ Fri, 05 Jul 2019 21:01:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:01:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:01:27: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:01:27: 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 @ Fri, 05 Jul 2019 21:01:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.10_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/SRX2339846/SRX2339846.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:01:33: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 21:01:41: 15000000 INFO @ Fri, 05 Jul 2019 21:01:47: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:01:47: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:01:47: #1 total tags in treatment: 7614140 INFO @ Fri, 05 Jul 2019 21:01:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:01:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:01:47: #1 tags after filtering in treatment: 5180222 INFO @ Fri, 05 Jul 2019 21:01:47: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 21:01:47: #1 finished! INFO @ Fri, 05 Jul 2019 21:01:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:01:48: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:01:48: 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 @ Fri, 05 Jul 2019 21:01:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.20_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/SRX2339846/SRX2339846.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339846/SRX2339846.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。