Job ID = 2641124 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,397,719 reads read : 20,795,438 reads written : 20,795,438 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: 00:15:28 10397719 reads; of these: 10397719 (100.00%) were paired; of these: 3139569 (30.19%) aligned concordantly 0 times 6130184 (58.96%) aligned concordantly exactly 1 time 1127966 (10.85%) aligned concordantly >1 times ---- 3139569 pairs aligned concordantly 0 times; of these: 2331836 (74.27%) aligned discordantly 1 time ---- 807733 pairs aligned 0 times concordantly or discordantly; of these: 1615466 mates make up the pairs; of these: 740657 (45.85%) aligned 0 times 127382 (7.89%) aligned exactly 1 time 747427 (46.27%) aligned >1 times 96.44% overall alignment rate Time searching: 00:15:28 Overall time: 00:15:28 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] 304496 / 9588744 = 0.0318 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:07:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.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 22:07:49: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:07:49: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:08:01: 1000000 INFO @ Sat, 24 Aug 2019 22:08:12: 2000000 INFO @ Sat, 24 Aug 2019 22:08:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.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 22:08:18: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:08:18: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:08:24: 3000000 INFO @ Sat, 24 Aug 2019 22:08:27: 1000000 INFO @ Sat, 24 Aug 2019 22:08:35: 2000000 INFO @ Sat, 24 Aug 2019 22:08:37: 4000000 INFO @ Sat, 24 Aug 2019 22:08:43: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:08:48: 5000000 INFO @ Sat, 24 Aug 2019 22:08:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.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 22:08:49: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:08:49: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:08:51: 4000000 INFO @ Sat, 24 Aug 2019 22:08:58: 1000000 INFO @ Sat, 24 Aug 2019 22:09:00: 6000000 INFO @ Sat, 24 Aug 2019 22:09:00: 5000000 INFO @ Sat, 24 Aug 2019 22:09:08: 2000000 INFO @ Sat, 24 Aug 2019 22:09:09: 6000000 INFO @ Sat, 24 Aug 2019 22:09:12: 7000000 INFO @ Sat, 24 Aug 2019 22:09:17: 7000000 INFO @ Sat, 24 Aug 2019 22:09:18: 3000000 INFO @ Sat, 24 Aug 2019 22:09:23: 8000000 INFO @ Sat, 24 Aug 2019 22:09:26: 8000000 INFO @ Sat, 24 Aug 2019 22:09:28: 4000000 INFO @ Sat, 24 Aug 2019 22:09:34: 9000000 INFO @ Sat, 24 Aug 2019 22:09:36: 9000000 INFO @ Sat, 24 Aug 2019 22:09:37: 5000000 INFO @ Sat, 24 Aug 2019 22:09:43: 10000000 INFO @ Sat, 24 Aug 2019 22:09:47: 6000000 INFO @ Sat, 24 Aug 2019 22:09:48: 10000000 INFO @ Sat, 24 Aug 2019 22:09:51: 11000000 INFO @ Sat, 24 Aug 2019 22:09:56: 7000000 INFO @ Sat, 24 Aug 2019 22:09:59: 12000000 INFO @ Sat, 24 Aug 2019 22:10:00: 11000000 INFO @ Sat, 24 Aug 2019 22:10:06: 8000000 INFO @ Sat, 24 Aug 2019 22:10:08: 13000000 INFO @ Sat, 24 Aug 2019 22:10:13: 12000000 INFO @ Sat, 24 Aug 2019 22:10:15: 9000000 INFO @ Sat, 24 Aug 2019 22:10:16: 14000000 INFO @ Sat, 24 Aug 2019 22:10:24: 15000000 INFO @ Sat, 24 Aug 2019 22:10:25: 13000000 INFO @ Sat, 24 Aug 2019 22:10:25: 10000000 INFO @ Sat, 24 Aug 2019 22:10:32: 16000000 INFO @ Sat, 24 Aug 2019 22:10:34: 11000000 INFO @ Sat, 24 Aug 2019 22:10:36: 14000000 INFO @ Sat, 24 Aug 2019 22:10:40: 17000000 INFO @ Sat, 24 Aug 2019 22:10:43: 12000000 INFO @ Sat, 24 Aug 2019 22:10:47: 15000000 INFO @ Sat, 24 Aug 2019 22:10:48: 18000000 INFO @ Sat, 24 Aug 2019 22:10:53: 13000000 INFO @ Sat, 24 Aug 2019 22:10:57: 19000000 INFO @ Sat, 24 Aug 2019 22:10:58: 16000000 INFO @ Sat, 24 Aug 2019 22:11:00: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:11:00: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:11:00: #1 total tags in treatment: 7000481 INFO @ Sat, 24 Aug 2019 22:11:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:11:00: #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 22:11:01: #1 tags after filtering in treatment: 5443358 INFO @ Sat, 24 Aug 2019 22:11:01: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 24 Aug 2019 22:11:01: #1 finished! INFO @ Sat, 24 Aug 2019 22:11:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:11:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:11:01: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:11:01: 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 22:11:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.10_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/SRX5546562/SRX5546562.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:11:02: 14000000 INFO @ Sat, 24 Aug 2019 22:11:09: 17000000 INFO @ Sat, 24 Aug 2019 22:11:12: 15000000 INFO @ Sat, 24 Aug 2019 22:11:21: 18000000 INFO @ Sat, 24 Aug 2019 22:11:21: 16000000 INFO @ Sat, 24 Aug 2019 22:11:30: 17000000 INFO @ Sat, 24 Aug 2019 22:11:32: 19000000 INFO @ Sat, 24 Aug 2019 22:11:37: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:11:37: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:11:37: #1 total tags in treatment: 7000481 INFO @ Sat, 24 Aug 2019 22:11:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:11:37: #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 22:11:37: #1 tags after filtering in treatment: 5443358 INFO @ Sat, 24 Aug 2019 22:11:37: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 24 Aug 2019 22:11:37: #1 finished! INFO @ Sat, 24 Aug 2019 22:11:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:11:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:11:37: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:11:37: 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 22:11:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.05_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/SRX5546562/SRX5546562.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:11:40: 18000000 INFO @ Sat, 24 Aug 2019 22:11:48: 19000000 INFO @ Sat, 24 Aug 2019 22:11:52: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:11:52: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:11:52: #1 total tags in treatment: 7000481 INFO @ Sat, 24 Aug 2019 22:11:52: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:11:52: #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 22:11:53: #1 tags after filtering in treatment: 5443358 INFO @ Sat, 24 Aug 2019 22:11:53: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 24 Aug 2019 22:11:53: #1 finished! INFO @ Sat, 24 Aug 2019 22:11:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:11:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:11:53: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:11:53: 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 22:11:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.20_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/SRX5546562/SRX5546562.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546562/SRX5546562.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。