Job ID = 2641107 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,280,226 reads read : 20,560,452 reads written : 20,560,452 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: 00:15:39 10280226 reads; of these: 10280226 (100.00%) were paired; of these: 5785456 (56.28%) aligned concordantly 0 times 4049248 (39.39%) aligned concordantly exactly 1 time 445522 (4.33%) aligned concordantly >1 times ---- 5785456 pairs aligned concordantly 0 times; of these: 3914922 (67.67%) aligned discordantly 1 time ---- 1870534 pairs aligned 0 times concordantly or discordantly; of these: 3741068 mates make up the pairs; of these: 2462870 (65.83%) aligned 0 times 351758 (9.40%) aligned exactly 1 time 926440 (24.76%) aligned >1 times 88.02% overall alignment rate Time searching: 00:15:39 Overall time: 00:15:39 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 8 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] 99574 / 8401923 = 0.0119 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:03:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.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 22:03:59: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:03:59: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:04:07: 1000000 INFO @ Sat, 24 Aug 2019 22:04:15: 2000000 INFO @ Sat, 24 Aug 2019 22:04:23: 3000000 INFO @ Sat, 24 Aug 2019 22:04:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.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 22:04:29: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:04:29: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:04:34: 4000000 INFO @ Sat, 24 Aug 2019 22:04:38: 1000000 INFO @ Sat, 24 Aug 2019 22:04:44: 5000000 INFO @ Sat, 24 Aug 2019 22:04:47: 2000000 INFO @ Sat, 24 Aug 2019 22:04:55: 6000000 INFO @ Sat, 24 Aug 2019 22:04:56: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:04:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.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 22:04:59: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:04:59: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:05:05: 4000000 INFO @ Sat, 24 Aug 2019 22:05:06: 7000000 INFO @ Sat, 24 Aug 2019 22:05:08: 1000000 INFO @ Sat, 24 Aug 2019 22:05:14: 5000000 INFO @ Sat, 24 Aug 2019 22:05:17: 2000000 INFO @ Sat, 24 Aug 2019 22:05:17: 8000000 INFO @ Sat, 24 Aug 2019 22:05:23: 6000000 INFO @ Sat, 24 Aug 2019 22:05:26: 3000000 INFO @ Sat, 24 Aug 2019 22:05:28: 9000000 INFO @ Sat, 24 Aug 2019 22:05:32: 7000000 INFO @ Sat, 24 Aug 2019 22:05:35: 4000000 INFO @ Sat, 24 Aug 2019 22:05:39: 10000000 INFO @ Sat, 24 Aug 2019 22:05:41: 8000000 INFO @ Sat, 24 Aug 2019 22:05:44: 5000000 INFO @ Sat, 24 Aug 2019 22:05:49: 11000000 INFO @ Sat, 24 Aug 2019 22:05:50: 9000000 INFO @ Sat, 24 Aug 2019 22:05:53: 6000000 INFO @ Sat, 24 Aug 2019 22:05:59: 10000000 INFO @ Sat, 24 Aug 2019 22:06:00: 12000000 INFO @ Sat, 24 Aug 2019 22:06:02: 7000000 INFO @ Sat, 24 Aug 2019 22:06:08: 11000000 INFO @ Sat, 24 Aug 2019 22:06:11: 8000000 INFO @ Sat, 24 Aug 2019 22:06:11: 13000000 INFO @ Sat, 24 Aug 2019 22:06:17: 12000000 INFO @ Sat, 24 Aug 2019 22:06:20: 9000000 INFO @ Sat, 24 Aug 2019 22:06:22: 14000000 INFO @ Sat, 24 Aug 2019 22:06:26: 13000000 INFO @ Sat, 24 Aug 2019 22:06:29: 10000000 INFO @ Sat, 24 Aug 2019 22:06:33: 15000000 INFO @ Sat, 24 Aug 2019 22:06:34: 14000000 INFO @ Sat, 24 Aug 2019 22:06:38: 11000000 INFO @ Sat, 24 Aug 2019 22:06:43: 15000000 INFO @ Sat, 24 Aug 2019 22:06:44: 16000000 INFO @ Sat, 24 Aug 2019 22:06:47: 12000000 INFO @ Sat, 24 Aug 2019 22:06:52: 16000000 INFO @ Sat, 24 Aug 2019 22:06:54: 17000000 INFO @ Sat, 24 Aug 2019 22:06:56: 13000000 INFO @ Sat, 24 Aug 2019 22:07:01: 17000000 INFO @ Sat, 24 Aug 2019 22:07:04: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:07:04: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:07:04: #1 total tags in treatment: 4441675 INFO @ Sat, 24 Aug 2019 22:07:04: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:07:04: #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 22:07:04: #1 tags after filtering in treatment: 3947150 INFO @ Sat, 24 Aug 2019 22:07:04: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 24 Aug 2019 22:07:04: #1 finished! INFO @ Sat, 24 Aug 2019 22:07:04: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:07:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:07:04: #2 number of paired peaks: 26 WARNING @ Sat, 24 Aug 2019 22:07:04: Too few paired peaks (26) 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 22:07:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.05_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/SRX5546548/SRX5546548.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:07:05: 14000000 INFO @ Sat, 24 Aug 2019 22:07:09: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:07:09: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:07:09: #1 total tags in treatment: 4441675 INFO @ Sat, 24 Aug 2019 22:07:09: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:07:09: #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 22:07:09: #1 tags after filtering in treatment: 3947150 INFO @ Sat, 24 Aug 2019 22:07:09: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 24 Aug 2019 22:07:09: #1 finished! INFO @ Sat, 24 Aug 2019 22:07:09: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:07:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:07:10: #2 number of paired peaks: 26 WARNING @ Sat, 24 Aug 2019 22:07:10: Too few paired peaks (26) 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 22:07:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.10_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/SRX5546548/SRX5546548.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:07:13: 15000000 INFO @ Sat, 24 Aug 2019 22:07:22: 16000000 INFO @ Sat, 24 Aug 2019 22:07:30: 17000000 INFO @ Sat, 24 Aug 2019 22:07:38: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:07:38: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:07:38: #1 total tags in treatment: 4441675 INFO @ Sat, 24 Aug 2019 22:07:38: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:07:38: #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 22:07:38: #1 tags after filtering in treatment: 3947150 INFO @ Sat, 24 Aug 2019 22:07:38: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 24 Aug 2019 22:07:38: #1 finished! INFO @ Sat, 24 Aug 2019 22:07:38: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:07:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:07:38: #2 number of paired peaks: 26 WARNING @ Sat, 24 Aug 2019 22:07:38: Too few paired peaks (26) 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 22:07:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.20_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/SRX5546548/SRX5546548.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546548/SRX5546548.20_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。