Job ID = 2640934 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,783,563 reads read : 19,783,563 reads written : 19,783,563 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: 00:06:26 19783563 reads; of these: 19783563 (100.00%) were unpaired; of these: 611001 (3.09%) aligned 0 times 17350688 (87.70%) aligned exactly 1 time 1821874 (9.21%) aligned >1 times 96.91% overall alignment rate Time searching: 00:06:26 Overall time: 00:06:26 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_rmdupse_core] 9536007 / 19172562 = 0.4974 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:27:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.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 20:27:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:27:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:27:57: 1000000 INFO @ Sat, 24 Aug 2019 20:28:08: 2000000 INFO @ Sat, 24 Aug 2019 20:28:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.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 20:28:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:28:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:28:19: 3000000 INFO @ Sat, 24 Aug 2019 20:28:26: 1000000 INFO @ Sat, 24 Aug 2019 20:28:31: 4000000 INFO @ Sat, 24 Aug 2019 20:28:37: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:28:43: 5000000 INFO @ Sat, 24 Aug 2019 20:28:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.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 20:28:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:28:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:28:49: 3000000 INFO @ Sat, 24 Aug 2019 20:28:55: 1000000 INFO @ Sat, 24 Aug 2019 20:28:57: 6000000 INFO @ Sat, 24 Aug 2019 20:29:00: 4000000 INFO @ Sat, 24 Aug 2019 20:29:06: 2000000 INFO @ Sat, 24 Aug 2019 20:29:10: 7000000 INFO @ Sat, 24 Aug 2019 20:29:12: 5000000 INFO @ Sat, 24 Aug 2019 20:29:16: 3000000 INFO @ Sat, 24 Aug 2019 20:29:24: 8000000 INFO @ Sat, 24 Aug 2019 20:29:26: 6000000 INFO @ Sat, 24 Aug 2019 20:29:27: 4000000 INFO @ Sat, 24 Aug 2019 20:29:38: 5000000 INFO @ Sat, 24 Aug 2019 20:29:38: 9000000 INFO @ Sat, 24 Aug 2019 20:29:40: 7000000 INFO @ Sat, 24 Aug 2019 20:29:48: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:29:48: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:29:48: #1 total tags in treatment: 9636555 INFO @ Sat, 24 Aug 2019 20:29:48: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:29:48: #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 20:29:48: #1 tags after filtering in treatment: 9636555 INFO @ Sat, 24 Aug 2019 20:29:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:29:48: #1 finished! INFO @ Sat, 24 Aug 2019 20:29:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:29:49: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:29:49: 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 20:29:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.05_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/SRX4703455/SRX4703455.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:29:50: 6000000 INFO @ Sat, 24 Aug 2019 20:29:53: 8000000 INFO @ Sat, 24 Aug 2019 20:30:02: 7000000 INFO @ Sat, 24 Aug 2019 20:30:07: 9000000 INFO @ Sat, 24 Aug 2019 20:30:15: 8000000 INFO @ Sat, 24 Aug 2019 20:30:15: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:30:15: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:30:15: #1 total tags in treatment: 9636555 INFO @ Sat, 24 Aug 2019 20:30:15: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:30:15: #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 20:30:16: #1 tags after filtering in treatment: 9636555 INFO @ Sat, 24 Aug 2019 20:30:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:30:16: #1 finished! INFO @ Sat, 24 Aug 2019 20:30:16: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:30:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:30:16: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:30:16: 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 20:30:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.10_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/SRX4703455/SRX4703455.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:30:25: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 20:30:32: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:30:32: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:30:32: #1 total tags in treatment: 9636555 INFO @ Sat, 24 Aug 2019 20:30:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:30:32: #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 20:30:32: #1 tags after filtering in treatment: 9636555 INFO @ Sat, 24 Aug 2019 20:30:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:30:32: #1 finished! INFO @ Sat, 24 Aug 2019 20:30:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:30:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:30:33: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:30:33: 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 20:30:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.20_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/SRX4703455/SRX4703455.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703455/SRX4703455.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。