Job ID = 2641006 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,435,536 reads read : 22,871,072 reads written : 22,871,072 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: 00:15:49 11435536 reads; of these: 11435536 (100.00%) were paired; of these: 2644881 (23.13%) aligned concordantly 0 times 7717366 (67.49%) aligned concordantly exactly 1 time 1073289 (9.39%) aligned concordantly >1 times ---- 2644881 pairs aligned concordantly 0 times; of these: 1746306 (66.03%) aligned discordantly 1 time ---- 898575 pairs aligned 0 times concordantly or discordantly; of these: 1797150 mates make up the pairs; of these: 873292 (48.59%) aligned 0 times 375235 (20.88%) aligned exactly 1 time 548623 (30.53%) aligned >1 times 96.18% overall alignment rate Time searching: 00:15:49 Overall time: 00:15:49 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] 976209 / 10535947 = 0.0927 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:06:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.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 21:06:59: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:06:59: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:07:08: 1000000 INFO @ Sat, 24 Aug 2019 21:07:17: 2000000 INFO @ Sat, 24 Aug 2019 21:07:26: 3000000 INFO @ Sat, 24 Aug 2019 21:07:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.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 21:07:29: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:07:29: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:07:35: 4000000 INFO @ Sat, 24 Aug 2019 21:07:40: 1000000 INFO @ Sat, 24 Aug 2019 21:07:44: 5000000 INFO @ Sat, 24 Aug 2019 21:07:50: 2000000 INFO @ Sat, 24 Aug 2019 21:07:53: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:07:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.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 21:07:59: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:07:59: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:08:01: 3000000 INFO @ Sat, 24 Aug 2019 21:08:03: 7000000 INFO @ Sat, 24 Aug 2019 21:08:10: 1000000 INFO @ Sat, 24 Aug 2019 21:08:12: 4000000 INFO @ Sat, 24 Aug 2019 21:08:12: 8000000 INFO @ Sat, 24 Aug 2019 21:08:20: 2000000 INFO @ Sat, 24 Aug 2019 21:08:21: 9000000 INFO @ Sat, 24 Aug 2019 21:08:22: 5000000 INFO @ Sat, 24 Aug 2019 21:08:30: 10000000 INFO @ Sat, 24 Aug 2019 21:08:31: 3000000 INFO @ Sat, 24 Aug 2019 21:08:33: 6000000 INFO @ Sat, 24 Aug 2019 21:08:40: 11000000 INFO @ Sat, 24 Aug 2019 21:08:42: 4000000 INFO @ Sat, 24 Aug 2019 21:08:44: 7000000 INFO @ Sat, 24 Aug 2019 21:08:49: 12000000 INFO @ Sat, 24 Aug 2019 21:08:52: 5000000 INFO @ Sat, 24 Aug 2019 21:08:55: 8000000 INFO @ Sat, 24 Aug 2019 21:08:58: 13000000 INFO @ Sat, 24 Aug 2019 21:09:03: 6000000 INFO @ Sat, 24 Aug 2019 21:09:05: 9000000 INFO @ Sat, 24 Aug 2019 21:09:07: 14000000 INFO @ Sat, 24 Aug 2019 21:09:14: 7000000 INFO @ Sat, 24 Aug 2019 21:09:16: 10000000 INFO @ Sat, 24 Aug 2019 21:09:17: 15000000 INFO @ Sat, 24 Aug 2019 21:09:25: 8000000 INFO @ Sat, 24 Aug 2019 21:09:26: 16000000 INFO @ Sat, 24 Aug 2019 21:09:27: 11000000 INFO @ Sat, 24 Aug 2019 21:09:35: 17000000 INFO @ Sat, 24 Aug 2019 21:09:35: 9000000 INFO @ Sat, 24 Aug 2019 21:09:37: 12000000 INFO @ Sat, 24 Aug 2019 21:09:44: 18000000 INFO @ Sat, 24 Aug 2019 21:09:46: 10000000 INFO @ Sat, 24 Aug 2019 21:09:48: 13000000 INFO @ Sat, 24 Aug 2019 21:09:54: 19000000 INFO @ Sat, 24 Aug 2019 21:09:57: 11000000 INFO @ Sat, 24 Aug 2019 21:09:59: 14000000 INFO @ Sat, 24 Aug 2019 21:10:03: 20000000 INFO @ Sat, 24 Aug 2019 21:10:03: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:10:03: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:10:03: #1 total tags in treatment: 7949488 INFO @ Sat, 24 Aug 2019 21:10:03: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:10:03: #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 21:10:04: #1 tags after filtering in treatment: 6135806 INFO @ Sat, 24 Aug 2019 21:10:04: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 24 Aug 2019 21:10:04: #1 finished! INFO @ Sat, 24 Aug 2019 21:10:04: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:10:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:10:04: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:10:04: 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 21:10:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.05_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/SRX4936112/SRX4936112.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:10:07: 12000000 INFO @ Sat, 24 Aug 2019 21:10:10: 15000000 INFO @ Sat, 24 Aug 2019 21:10:18: 13000000 INFO @ Sat, 24 Aug 2019 21:10:20: 16000000 INFO @ Sat, 24 Aug 2019 21:10:29: 14000000 INFO @ Sat, 24 Aug 2019 21:10:31: 17000000 INFO @ Sat, 24 Aug 2019 21:10:39: 15000000 INFO @ Sat, 24 Aug 2019 21:10:41: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:10:50: 16000000 INFO @ Sat, 24 Aug 2019 21:10:52: 19000000 INFO @ Sat, 24 Aug 2019 21:11:00: 17000000 INFO @ Sat, 24 Aug 2019 21:11:03: 20000000 INFO @ Sat, 24 Aug 2019 21:11:04: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:11:04: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:11:04: #1 total tags in treatment: 7949488 INFO @ Sat, 24 Aug 2019 21:11:04: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:11:04: #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 21:11:04: #1 tags after filtering in treatment: 6135806 INFO @ Sat, 24 Aug 2019 21:11:04: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 24 Aug 2019 21:11:04: #1 finished! INFO @ Sat, 24 Aug 2019 21:11:04: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:11:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:11:04: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:11:04: 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 21:11:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.10_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/SRX4936112/SRX4936112.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:11:11: 18000000 INFO @ Sat, 24 Aug 2019 21:11:21: 19000000 INFO @ Sat, 24 Aug 2019 21:11:32: 20000000 INFO @ Sat, 24 Aug 2019 21:11:32: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:11:32: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:11:32: #1 total tags in treatment: 7949488 INFO @ Sat, 24 Aug 2019 21:11:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:11:32: #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 21:11:32: #1 tags after filtering in treatment: 6135806 INFO @ Sat, 24 Aug 2019 21:11:32: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 24 Aug 2019 21:11:32: #1 finished! INFO @ Sat, 24 Aug 2019 21:11:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:11:33: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:11:33: 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 21:11:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.20_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/SRX4936112/SRX4936112.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936112/SRX4936112.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling