Job ID = 2010012 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 23,468,431 reads read : 46,936,862 reads written : 46,936,862 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: 00:11:16 23468431 reads; of these: 23468431 (100.00%) were paired; of these: 4969254 (21.17%) aligned concordantly 0 times 13559207 (57.78%) aligned concordantly exactly 1 time 4939970 (21.05%) aligned concordantly >1 times ---- 4969254 pairs aligned concordantly 0 times; of these: 201063 (4.05%) aligned discordantly 1 time ---- 4768191 pairs aligned 0 times concordantly or discordantly; of these: 9536382 mates make up the pairs; of these: 8803706 (92.32%) aligned 0 times 453919 (4.76%) aligned exactly 1 time 278757 (2.92%) aligned >1 times 81.24% overall alignment rate Time searching: 00:11:16 Overall time: 00:11:16 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] 5423647 / 18691608 = 0.2902 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 21:23:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.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 21:23:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:23:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:23:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.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 21:23:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:23:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:23:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.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 21:23:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:23:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:23:45: 1000000 INFO @ Fri, 05 Jul 2019 21:23:47: 1000000 INFO @ Fri, 05 Jul 2019 21:23:48: 1000000 INFO @ Fri, 05 Jul 2019 21:23:52: 2000000 INFO @ Fri, 05 Jul 2019 21:23:55: 2000000 INFO @ Fri, 05 Jul 2019 21:23:56: 2000000 INFO @ Fri, 05 Jul 2019 21:24:00: 3000000 INFO @ Fri, 05 Jul 2019 21:24:02: 3000000 INFO @ Fri, 05 Jul 2019 21:24:04: 3000000 INFO @ Fri, 05 Jul 2019 21:24:07: 4000000 INFO @ Fri, 05 Jul 2019 21:24:10: 4000000 INFO @ Fri, 05 Jul 2019 21:24:12: 4000000 INFO @ Fri, 05 Jul 2019 21:24:14: 5000000 INFO @ Fri, 05 Jul 2019 21:24:18: 5000000 INFO @ Fri, 05 Jul 2019 21:24:20: 5000000 INFO @ Fri, 05 Jul 2019 21:24:22: 6000000 INFO @ Fri, 05 Jul 2019 21:24:26: 6000000 INFO @ Fri, 05 Jul 2019 21:24:28: 6000000 INFO @ Fri, 05 Jul 2019 21:24:29: 7000000 INFO @ Fri, 05 Jul 2019 21:24:34: 7000000 INFO @ Fri, 05 Jul 2019 21:24:36: 8000000 INFO @ Fri, 05 Jul 2019 21:24:36: 7000000 INFO @ Fri, 05 Jul 2019 21:24:42: 8000000 INFO @ Fri, 05 Jul 2019 21:24:43: 9000000 INFO @ Fri, 05 Jul 2019 21:24:45: 8000000 INFO @ Fri, 05 Jul 2019 21:24:50: 10000000 INFO @ Fri, 05 Jul 2019 21:24:51: 9000000 INFO @ Fri, 05 Jul 2019 21:24:53: 9000000 INFO @ Fri, 05 Jul 2019 21:24:58: 11000000 INFO @ Fri, 05 Jul 2019 21:24:59: 10000000 INFO @ Fri, 05 Jul 2019 21:25:01: 10000000 INFO @ Fri, 05 Jul 2019 21:25:05: 12000000 INFO @ Fri, 05 Jul 2019 21:25:07: 11000000 INFO @ Fri, 05 Jul 2019 21:25:09: 11000000 INFO @ Fri, 05 Jul 2019 21:25:12: 13000000 INFO @ Fri, 05 Jul 2019 21:25:15: 12000000 INFO @ Fri, 05 Jul 2019 21:25:18: 12000000 INFO @ Fri, 05 Jul 2019 21:25:19: 14000000 INFO @ Fri, 05 Jul 2019 21:25:23: 13000000 INFO @ Fri, 05 Jul 2019 21:25:26: 13000000 INFO @ Fri, 05 Jul 2019 21:25:26: 15000000 INFO @ Fri, 05 Jul 2019 21:25:31: 14000000 INFO @ Fri, 05 Jul 2019 21:25:34: 16000000 INFO @ Fri, 05 Jul 2019 21:25:34: 14000000 INFO @ Fri, 05 Jul 2019 21:25:39: 15000000 INFO @ Fri, 05 Jul 2019 21:25:41: 17000000 INFO @ Fri, 05 Jul 2019 21:25:42: 15000000 INFO @ Fri, 05 Jul 2019 21:25:47: 16000000 INFO @ Fri, 05 Jul 2019 21:25:47: 18000000 INFO @ Fri, 05 Jul 2019 21:25:50: 16000000 INFO @ Fri, 05 Jul 2019 21:25:54: 19000000 INFO @ Fri, 05 Jul 2019 21:25:55: 17000000 INFO @ Fri, 05 Jul 2019 21:25:58: 17000000 INFO @ Fri, 05 Jul 2019 21:26:01: 20000000 INFO @ Fri, 05 Jul 2019 21:26:02: 18000000 INFO @ Fri, 05 Jul 2019 21:26:06: 18000000 INFO @ Fri, 05 Jul 2019 21:26:08: 21000000 INFO @ Fri, 05 Jul 2019 21:26:10: 19000000 INFO @ Fri, 05 Jul 2019 21:26:13: 19000000 INFO @ Fri, 05 Jul 2019 21:26:15: 22000000 INFO @ Fri, 05 Jul 2019 21:26:17: 20000000 INFO @ Fri, 05 Jul 2019 21:26:21: 20000000 INFO @ Fri, 05 Jul 2019 21:26:22: 23000000 INFO @ Fri, 05 Jul 2019 21:26:25: 21000000 INFO @ Fri, 05 Jul 2019 21:26:28: 21000000 INFO @ Fri, 05 Jul 2019 21:26:29: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 21:26:33: 22000000 INFO @ Fri, 05 Jul 2019 21:26:35: 25000000 INFO @ Fri, 05 Jul 2019 21:26:36: 22000000 INFO @ Fri, 05 Jul 2019 21:26:40: 23000000 INFO @ Fri, 05 Jul 2019 21:26:42: 26000000 INFO @ Fri, 05 Jul 2019 21:26:44: 23000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 21:26:48: 24000000 INFO @ Fri, 05 Jul 2019 21:26:49: 27000000 INFO @ Fri, 05 Jul 2019 21:26:51: #1 tag size is determined as 24 bps INFO @ Fri, 05 Jul 2019 21:26:51: #1 tag size = 24 INFO @ Fri, 05 Jul 2019 21:26:51: #1 total tags in treatment: 13077405 INFO @ Fri, 05 Jul 2019 21:26:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:26:51: #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 21:26:51: 24000000 INFO @ Fri, 05 Jul 2019 21:26:51: #1 tags after filtering in treatment: 5220204 INFO @ Fri, 05 Jul 2019 21:26:51: #1 Redundant rate of treatment: 0.60 INFO @ Fri, 05 Jul 2019 21:26:51: #1 finished! INFO @ Fri, 05 Jul 2019 21:26:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:26:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:26:52: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:26:52: 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 21:26:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.05_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/SRX235689/SRX235689.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:26:55: 25000000 INFO @ Fri, 05 Jul 2019 21:26:59: 25000000 INFO @ Fri, 05 Jul 2019 21:27:03: 26000000 INFO @ Fri, 05 Jul 2019 21:27:06: 26000000 INFO @ Fri, 05 Jul 2019 21:27:10: 27000000 INFO @ Fri, 05 Jul 2019 21:27:12: #1 tag size is determined as 24 bps INFO @ Fri, 05 Jul 2019 21:27:12: #1 tag size = 24 INFO @ Fri, 05 Jul 2019 21:27:12: #1 total tags in treatment: 13077405 INFO @ Fri, 05 Jul 2019 21:27:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:27:12: #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 21:27:13: #1 tags after filtering in treatment: 5220204 INFO @ Fri, 05 Jul 2019 21:27:13: #1 Redundant rate of treatment: 0.60 INFO @ Fri, 05 Jul 2019 21:27:13: #1 finished! INFO @ Fri, 05 Jul 2019 21:27:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:27:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:27:13: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:27:13: 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 21:27:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.10_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/SRX235689/SRX235689.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:27:14: 27000000 INFO @ Fri, 05 Jul 2019 21:27:16: #1 tag size is determined as 24 bps INFO @ Fri, 05 Jul 2019 21:27:16: #1 tag size = 24 INFO @ Fri, 05 Jul 2019 21:27:16: #1 total tags in treatment: 13077405 INFO @ Fri, 05 Jul 2019 21:27:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:27:16: #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 21:27:16: #1 tags after filtering in treatment: 5220204 INFO @ Fri, 05 Jul 2019 21:27:16: #1 Redundant rate of treatment: 0.60 INFO @ Fri, 05 Jul 2019 21:27:16: #1 finished! INFO @ Fri, 05 Jul 2019 21:27:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:27:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:27:17: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:27:17: 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 21:27:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.20_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/SRX235689/SRX235689.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX235689/SRX235689.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling