Job ID = 2011677 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 19,663,033 reads read : 39,326,066 reads written : 39,326,066 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: 00:31:21 19663033 reads; of these: 19663033 (100.00%) were paired; of these: 3725275 (18.95%) aligned concordantly 0 times 13062329 (66.43%) aligned concordantly exactly 1 time 2875429 (14.62%) aligned concordantly >1 times ---- 3725275 pairs aligned concordantly 0 times; of these: 1917440 (51.47%) aligned discordantly 1 time ---- 1807835 pairs aligned 0 times concordantly or discordantly; of these: 3615670 mates make up the pairs; of these: 2431493 (67.25%) aligned 0 times 289270 (8.00%) aligned exactly 1 time 894907 (24.75%) aligned >1 times 93.82% overall alignment rate Time searching: 00:31:21 Overall time: 00:31:21 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 24 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] 755154 / 17734635 = 0.0426 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 03:23:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.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 03:23:28: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:23:28: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:23:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.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 03:23:28: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:23:28: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:23:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.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 03:23:29: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:23:29: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:23:37: 1000000 INFO @ Sat, 06 Jul 2019 03:23:39: 1000000 INFO @ Sat, 06 Jul 2019 03:23:40: 1000000 INFO @ Sat, 06 Jul 2019 03:23:45: 2000000 INFO @ Sat, 06 Jul 2019 03:23:49: 2000000 INFO @ Sat, 06 Jul 2019 03:23:52: 2000000 INFO @ Sat, 06 Jul 2019 03:23:54: 3000000 INFO @ Sat, 06 Jul 2019 03:23:59: 3000000 INFO @ Sat, 06 Jul 2019 03:24:02: 4000000 INFO @ Sat, 06 Jul 2019 03:24:04: 3000000 INFO @ Sat, 06 Jul 2019 03:24:09: 4000000 INFO @ Sat, 06 Jul 2019 03:24:11: 5000000 INFO @ Sat, 06 Jul 2019 03:24:15: 4000000 INFO @ Sat, 06 Jul 2019 03:24:19: 5000000 INFO @ Sat, 06 Jul 2019 03:24:19: 6000000 INFO @ Sat, 06 Jul 2019 03:24:27: 5000000 INFO @ Sat, 06 Jul 2019 03:24:28: 7000000 INFO @ Sat, 06 Jul 2019 03:24:28: 6000000 INFO @ Sat, 06 Jul 2019 03:24:36: 8000000 INFO @ Sat, 06 Jul 2019 03:24:38: 7000000 INFO @ Sat, 06 Jul 2019 03:24:39: 6000000 INFO @ Sat, 06 Jul 2019 03:24:45: 9000000 INFO @ Sat, 06 Jul 2019 03:24:48: 8000000 INFO @ Sat, 06 Jul 2019 03:24:51: 7000000 INFO @ Sat, 06 Jul 2019 03:24:53: 10000000 INFO @ Sat, 06 Jul 2019 03:24:57: 9000000 INFO @ Sat, 06 Jul 2019 03:25:02: 11000000 INFO @ Sat, 06 Jul 2019 03:25:02: 8000000 INFO @ Sat, 06 Jul 2019 03:25:07: 10000000 INFO @ Sat, 06 Jul 2019 03:25:10: 12000000 INFO @ Sat, 06 Jul 2019 03:25:14: 9000000 INFO @ Sat, 06 Jul 2019 03:25:17: 11000000 INFO @ Sat, 06 Jul 2019 03:25:19: 13000000 INFO @ Sat, 06 Jul 2019 03:25:25: 10000000 INFO @ Sat, 06 Jul 2019 03:25:27: 12000000 INFO @ Sat, 06 Jul 2019 03:25:27: 14000000 INFO @ Sat, 06 Jul 2019 03:25:36: 15000000 INFO @ Sat, 06 Jul 2019 03:25:36: 13000000 INFO @ Sat, 06 Jul 2019 03:25:37: 11000000 INFO @ Sat, 06 Jul 2019 03:25:44: 16000000 INFO @ Sat, 06 Jul 2019 03:25:46: 14000000 INFO @ Sat, 06 Jul 2019 03:25:49: 12000000 INFO @ Sat, 06 Jul 2019 03:25:53: 17000000 INFO @ Sat, 06 Jul 2019 03:25:56: 15000000 INFO @ Sat, 06 Jul 2019 03:26:00: 13000000 INFO @ Sat, 06 Jul 2019 03:26:01: 18000000 INFO @ Sat, 06 Jul 2019 03:26:06: 16000000 INFO @ Sat, 06 Jul 2019 03:26:09: 19000000 INFO @ Sat, 06 Jul 2019 03:26:12: 14000000 INFO @ Sat, 06 Jul 2019 03:26:15: 17000000 INFO @ Sat, 06 Jul 2019 03:26:18: 20000000 INFO @ Sat, 06 Jul 2019 03:26:24: 15000000 INFO @ Sat, 06 Jul 2019 03:26:25: 18000000 INFO @ Sat, 06 Jul 2019 03:26:26: 21000000 INFO @ Sat, 06 Jul 2019 03:26:35: 19000000 INFO @ Sat, 06 Jul 2019 03:26:35: 22000000 INFO @ Sat, 06 Jul 2019 03:26:35: 16000000 INFO @ Sat, 06 Jul 2019 03:26:43: 23000000 INFO @ Sat, 06 Jul 2019 03:26:44: 20000000 INFO @ Sat, 06 Jul 2019 03:26:47: 17000000 INFO @ Sat, 06 Jul 2019 03:26:52: 24000000 INFO @ Sat, 06 Jul 2019 03:26:54: 21000000 INFO @ Sat, 06 Jul 2019 03:26:59: 18000000 INFO @ Sat, 06 Jul 2019 03:27:00: 25000000 INFO @ Sat, 06 Jul 2019 03:27:04: 22000000 INFO @ Sat, 06 Jul 2019 03:27:09: 26000000 INFO @ Sat, 06 Jul 2019 03:27:10: 19000000 INFO @ Sat, 06 Jul 2019 03:27:13: 23000000 INFO @ Sat, 06 Jul 2019 03:27:17: 27000000 INFO @ Sat, 06 Jul 2019 03:27:22: 20000000 INFO @ Sat, 06 Jul 2019 03:27:23: 24000000 INFO @ Sat, 06 Jul 2019 03:27:25: 28000000 INFO @ Sat, 06 Jul 2019 03:27:33: 25000000 INFO @ Sat, 06 Jul 2019 03:27:33: 21000000 INFO @ Sat, 06 Jul 2019 03:27:34: 29000000 INFO @ Sat, 06 Jul 2019 03:27:42: 30000000 INFO @ Sat, 06 Jul 2019 03:27:42: 26000000 INFO @ Sat, 06 Jul 2019 03:27:45: 22000000 INFO @ Sat, 06 Jul 2019 03:27:51: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:27:52: 27000000 INFO @ Sat, 06 Jul 2019 03:27:57: 23000000 INFO @ Sat, 06 Jul 2019 03:27:59: 32000000 INFO @ Sat, 06 Jul 2019 03:28:02: 28000000 INFO @ Sat, 06 Jul 2019 03:28:08: 33000000 INFO @ Sat, 06 Jul 2019 03:28:09: 24000000 INFO @ Sat, 06 Jul 2019 03:28:11: 29000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:28:16: 34000000 INFO @ Sat, 06 Jul 2019 03:28:20: 25000000 INFO @ Sat, 06 Jul 2019 03:28:21: 30000000 INFO @ Sat, 06 Jul 2019 03:28:25: 35000000 INFO @ Sat, 06 Jul 2019 03:28:28: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:28:28: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:28:28: #1 total tags in treatment: 15229636 INFO @ Sat, 06 Jul 2019 03:28:28: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:28:28: #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 03:28:28: #1 tags after filtering in treatment: 10059021 INFO @ Sat, 06 Jul 2019 03:28:28: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 06 Jul 2019 03:28:28: #1 finished! INFO @ Sat, 06 Jul 2019 03:28:28: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:28:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:28:29: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:28:29: 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, 06 Jul 2019 03:28:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.10_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/SRX4560559/SRX4560559.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:28:31: 31000000 INFO @ Sat, 06 Jul 2019 03:28:32: 26000000 INFO @ Sat, 06 Jul 2019 03:28:40: 32000000 INFO @ Sat, 06 Jul 2019 03:28:44: 27000000 INFO @ Sat, 06 Jul 2019 03:28:50: 33000000 INFO @ Sat, 06 Jul 2019 03:28:56: 28000000 INFO @ Sat, 06 Jul 2019 03:29:00: 34000000 INFO @ Sat, 06 Jul 2019 03:29:08: 29000000 INFO @ Sat, 06 Jul 2019 03:29:09: 35000000 INFO @ Sat, 06 Jul 2019 03:29:13: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:29:13: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:29:13: #1 total tags in treatment: 15229636 INFO @ Sat, 06 Jul 2019 03:29:13: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:29:13: #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 03:29:13: #1 tags after filtering in treatment: 10059021 INFO @ Sat, 06 Jul 2019 03:29:13: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 06 Jul 2019 03:29:13: #1 finished! INFO @ Sat, 06 Jul 2019 03:29:13: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:29:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:29:14: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:29:14: 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, 06 Jul 2019 03:29:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.20_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/SRX4560559/SRX4560559.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:29:20: 30000000 INFO @ Sat, 06 Jul 2019 03:29:33: 31000000 INFO @ Sat, 06 Jul 2019 03:29:45: 32000000 INFO @ Sat, 06 Jul 2019 03:29:57: 33000000 INFO @ Sat, 06 Jul 2019 03:30:09: 34000000 INFO @ Sat, 06 Jul 2019 03:30:21: 35000000 INFO @ Sat, 06 Jul 2019 03:30:26: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:30:26: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:30:26: #1 total tags in treatment: 15229636 INFO @ Sat, 06 Jul 2019 03:30:26: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:30:26: #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 03:30:27: #1 tags after filtering in treatment: 10059021 INFO @ Sat, 06 Jul 2019 03:30:27: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 06 Jul 2019 03:30:27: #1 finished! INFO @ Sat, 06 Jul 2019 03:30:27: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:30:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:30:27: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:30:27: 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 @ Sat, 06 Jul 2019 03:30:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.05_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/SRX4560559/SRX4560559.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560559/SRX4560559.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling