Job ID = 2641010 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,986,344 reads read : 27,972,688 reads written : 27,972,688 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: 00:19:07 13986344 reads; of these: 13986344 (100.00%) were paired; of these: 1620531 (11.59%) aligned concordantly 0 times 10591243 (75.73%) aligned concordantly exactly 1 time 1774570 (12.69%) aligned concordantly >1 times ---- 1620531 pairs aligned concordantly 0 times; of these: 1024086 (63.19%) aligned discordantly 1 time ---- 596445 pairs aligned 0 times concordantly or discordantly; of these: 1192890 mates make up the pairs; of these: 640556 (53.70%) aligned 0 times 187883 (15.75%) aligned exactly 1 time 364451 (30.55%) aligned >1 times 97.71% overall alignment rate Time searching: 00:19:07 Overall time: 00:19:07 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] 533012 / 13387427 = 0.0398 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:16:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.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 21:16:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:16:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:16:24: 1000000 INFO @ Sat, 24 Aug 2019 21:16:37: 2000000 INFO @ Sat, 24 Aug 2019 21:16:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.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 21:16:41: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:16:41: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:16:50: 3000000 INFO @ Sat, 24 Aug 2019 21:16:52: 1000000 INFO @ Sat, 24 Aug 2019 21:17:02: 2000000 INFO @ Sat, 24 Aug 2019 21:17:02: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:17:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.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 21:17:11: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:17:11: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:17:13: 3000000 INFO @ Sat, 24 Aug 2019 21:17:15: 5000000 INFO @ Sat, 24 Aug 2019 21:17:22: 1000000 INFO @ Sat, 24 Aug 2019 21:17:23: 4000000 INFO @ Sat, 24 Aug 2019 21:17:28: 6000000 INFO @ Sat, 24 Aug 2019 21:17:33: 2000000 INFO @ Sat, 24 Aug 2019 21:17:34: 5000000 INFO @ Sat, 24 Aug 2019 21:17:41: 7000000 INFO @ Sat, 24 Aug 2019 21:17:44: 3000000 INFO @ Sat, 24 Aug 2019 21:17:45: 6000000 INFO @ Sat, 24 Aug 2019 21:17:54: 8000000 INFO @ Sat, 24 Aug 2019 21:17:55: 4000000 INFO @ Sat, 24 Aug 2019 21:17:55: 7000000 INFO @ Sat, 24 Aug 2019 21:18:05: 5000000 INFO @ Sat, 24 Aug 2019 21:18:06: 8000000 INFO @ Sat, 24 Aug 2019 21:18:07: 9000000 INFO @ Sat, 24 Aug 2019 21:18:16: 6000000 INFO @ Sat, 24 Aug 2019 21:18:16: 9000000 INFO @ Sat, 24 Aug 2019 21:18:20: 10000000 INFO @ Sat, 24 Aug 2019 21:18:26: 7000000 INFO @ Sat, 24 Aug 2019 21:18:27: 10000000 INFO @ Sat, 24 Aug 2019 21:18:32: 11000000 INFO @ Sat, 24 Aug 2019 21:18:37: 8000000 INFO @ Sat, 24 Aug 2019 21:18:37: 11000000 INFO @ Sat, 24 Aug 2019 21:18:45: 12000000 INFO @ Sat, 24 Aug 2019 21:18:48: 9000000 INFO @ Sat, 24 Aug 2019 21:18:48: 12000000 INFO @ Sat, 24 Aug 2019 21:18:58: 10000000 INFO @ Sat, 24 Aug 2019 21:18:58: 13000000 INFO @ Sat, 24 Aug 2019 21:18:58: 13000000 INFO @ Sat, 24 Aug 2019 21:19:09: 11000000 INFO @ Sat, 24 Aug 2019 21:19:09: 14000000 INFO @ Sat, 24 Aug 2019 21:19:11: 14000000 INFO @ Sat, 24 Aug 2019 21:19:20: 12000000 INFO @ Sat, 24 Aug 2019 21:19:20: 15000000 INFO @ Sat, 24 Aug 2019 21:19:24: 15000000 INFO @ Sat, 24 Aug 2019 21:19:30: 13000000 INFO @ Sat, 24 Aug 2019 21:19:30: 16000000 INFO @ Sat, 24 Aug 2019 21:19:37: 16000000 INFO @ Sat, 24 Aug 2019 21:19:41: 14000000 INFO @ Sat, 24 Aug 2019 21:19:41: 17000000 INFO @ Sat, 24 Aug 2019 21:19:50: 17000000 INFO @ Sat, 24 Aug 2019 21:19:52: 15000000 INFO @ Sat, 24 Aug 2019 21:19:52: 18000000 INFO @ Sat, 24 Aug 2019 21:20:02: 16000000 INFO @ Sat, 24 Aug 2019 21:20:02: 19000000 INFO @ Sat, 24 Aug 2019 21:20:03: 18000000 INFO @ Sat, 24 Aug 2019 21:20:13: 17000000 INFO @ Sat, 24 Aug 2019 21:20:13: 20000000 INFO @ Sat, 24 Aug 2019 21:20:16: 19000000 INFO @ Sat, 24 Aug 2019 21:20:23: 18000000 INFO @ Sat, 24 Aug 2019 21:20:23: 21000000 INFO @ Sat, 24 Aug 2019 21:20:29: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:20:34: 19000000 INFO @ Sat, 24 Aug 2019 21:20:34: 22000000 INFO @ Sat, 24 Aug 2019 21:20:42: 21000000 INFO @ Sat, 24 Aug 2019 21:20:44: 20000000 INFO @ Sat, 24 Aug 2019 21:20:45: 23000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:20:55: 22000000 INFO @ Sat, 24 Aug 2019 21:20:55: 21000000 INFO @ Sat, 24 Aug 2019 21:20:55: 24000000 INFO @ Sat, 24 Aug 2019 21:21:05: 22000000 INFO @ Sat, 24 Aug 2019 21:21:06: 25000000 INFO @ Sat, 24 Aug 2019 21:21:08: 23000000 INFO @ Sat, 24 Aug 2019 21:21:16: 23000000 INFO @ Sat, 24 Aug 2019 21:21:17: 26000000 INFO @ Sat, 24 Aug 2019 21:21:19: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:21:19: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:21:19: #1 total tags in treatment: 11851514 INFO @ Sat, 24 Aug 2019 21:21:19: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:21:19: #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 21:21:20: #1 tags after filtering in treatment: 8444633 INFO @ Sat, 24 Aug 2019 21:21:20: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:21:20: #1 finished! INFO @ Sat, 24 Aug 2019 21:21:20: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:21:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:21:20: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:21:20: 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 21:21:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.10_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/SRX4936116/SRX4936116.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:21:21: 24000000 INFO @ Sat, 24 Aug 2019 21:21:26: 24000000 INFO @ Sat, 24 Aug 2019 21:21:33: 25000000 INFO @ Sat, 24 Aug 2019 21:21:37: 25000000 INFO @ Sat, 24 Aug 2019 21:21:46: 26000000 INFO @ Sat, 24 Aug 2019 21:21:47: 26000000 INFO @ Sat, 24 Aug 2019 21:21:49: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:21:49: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:21:49: #1 total tags in treatment: 11851514 INFO @ Sat, 24 Aug 2019 21:21:49: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:21:49: #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 21:21:50: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:21:50: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:21:50: #1 total tags in treatment: 11851514 INFO @ Sat, 24 Aug 2019 21:21:50: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:21:50: #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 21:21:50: #1 tags after filtering in treatment: 8444633 INFO @ Sat, 24 Aug 2019 21:21:50: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:21:50: #1 finished! INFO @ Sat, 24 Aug 2019 21:21:50: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:21:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:21:50: #1 tags after filtering in treatment: 8444633 INFO @ Sat, 24 Aug 2019 21:21:50: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:21:50: #1 finished! INFO @ Sat, 24 Aug 2019 21:21:50: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:21:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:21:50: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:21:50: 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 21:21:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.05_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/SRX4936116/SRX4936116.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:21:51: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:21:51: 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 21:21:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.20_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/SRX4936116/SRX4936116.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936116/SRX4936116.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling