Job ID = 2011948 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,923,531 reads read : 27,847,062 reads written : 27,847,062 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: 00:07:55 13923531 reads; of these: 13923531 (100.00%) were paired; of these: 12427667 (89.26%) aligned concordantly 0 times 1265227 (9.09%) aligned concordantly exactly 1 time 230637 (1.66%) aligned concordantly >1 times ---- 12427667 pairs aligned concordantly 0 times; of these: 1555930 (12.52%) aligned discordantly 1 time ---- 10871737 pairs aligned 0 times concordantly or discordantly; of these: 21743474 mates make up the pairs; of these: 20807972 (95.70%) aligned 0 times 356415 (1.64%) aligned exactly 1 time 579087 (2.66%) aligned >1 times 25.28% overall alignment rate Time searching: 00:07:55 Overall time: 00:07:55 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_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] 336049 / 2963844 = 0.1134 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 03:51:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.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 03:51:00: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:51:00: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:51:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.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 03:51:00: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:51:00: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:51:09: 1000000 INFO @ Sat, 06 Jul 2019 03:51:09: 1000000 INFO @ Sat, 06 Jul 2019 03:51:17: 2000000 INFO @ Sat, 06 Jul 2019 03:51:18: 2000000 INFO @ Sat, 06 Jul 2019 03:51:25: 3000000 INFO @ Sat, 06 Jul 2019 03:51:26: 3000000 INFO @ Sat, 06 Jul 2019 03:51:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.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 03:51:31: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:51:31: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:51:33: 4000000 INFO @ Sat, 06 Jul 2019 03:51:35: 4000000 INFO @ Sat, 06 Jul 2019 03:51:38: 1000000 INFO @ Sat, 06 Jul 2019 03:51:41: 5000000 INFO @ Sat, 06 Jul 2019 03:51:44: 5000000 INFO @ Sat, 06 Jul 2019 03:51:45: 2000000 INFO @ Sat, 06 Jul 2019 03:51:49: 6000000 INFO @ Sat, 06 Jul 2019 03:51:52: 3000000 INFO @ Sat, 06 Jul 2019 03:51:52: 6000000 INFO @ Sat, 06 Jul 2019 03:51:52: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:51:52: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:51:52: #1 total tags in treatment: 1346501 INFO @ Sat, 06 Jul 2019 03:51:52: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:51:52: #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 03:51:52: #1 tags after filtering in treatment: 1149885 INFO @ Sat, 06 Jul 2019 03:51:52: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 06 Jul 2019 03:51:52: #1 finished! INFO @ Sat, 06 Jul 2019 03:51:52: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:51:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:51:52: #2 number of paired peaks: 31 WARNING @ Sat, 06 Jul 2019 03:51:52: Too few paired peaks (31) 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 03:51:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.05_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/SRX5624307/SRX5624307.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:51:55: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:51:55: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:51:55: #1 total tags in treatment: 1346501 INFO @ Sat, 06 Jul 2019 03:51:55: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:51:55: #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 03:51:55: #1 tags after filtering in treatment: 1149885 INFO @ Sat, 06 Jul 2019 03:51:55: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 06 Jul 2019 03:51:55: #1 finished! INFO @ Sat, 06 Jul 2019 03:51:55: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:51:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:51:55: #2 number of paired peaks: 31 WARNING @ Sat, 06 Jul 2019 03:51:55: Too few paired peaks (31) 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 03:51:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.10_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/SRX5624307/SRX5624307.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:51:58: 4000000 INFO @ Sat, 06 Jul 2019 03:52:05: 5000000 INFO @ Sat, 06 Jul 2019 03:52:11: 6000000 INFO @ Sat, 06 Jul 2019 03:52:14: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:52:14: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:52:14: #1 total tags in treatment: 1346501 INFO @ Sat, 06 Jul 2019 03:52:14: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:52:14: #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 03:52:14: #1 tags after filtering in treatment: 1149885 INFO @ Sat, 06 Jul 2019 03:52:14: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 06 Jul 2019 03:52:14: #1 finished! INFO @ Sat, 06 Jul 2019 03:52:14: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:52:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:52:14: #2 number of paired peaks: 31 WARNING @ Sat, 06 Jul 2019 03:52:14: Too few paired peaks (31) 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 03:52:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.20_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/SRX5624307/SRX5624307.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624307/SRX5624307.20_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。