Job ID = 2010803 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T15:40:59 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 457,541 reads read : 915,082 reads written : 457,541 reads 0-length : 457,541 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: 00:00:11 457541 reads; of these: 457541 (100.00%) were unpaired; of these: 51810 (11.32%) aligned 0 times 353031 (77.16%) aligned exactly 1 time 52700 (11.52%) aligned >1 times 88.68% overall alignment rate Time searching: 00:00:11 Overall time: 00:00:11 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_rmdupse_core] 18254 / 405731 = 0.0450 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 00:42:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.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 00:42:42: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:42:42: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:42:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.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 00:42:43: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:42:43: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:42:47: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 00:42:47: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 00:42:47: #1 total tags in treatment: 387477 INFO @ Sat, 06 Jul 2019 00:42:47: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:42:47: #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 00:42:47: #1 tags after filtering in treatment: 387477 INFO @ Sat, 06 Jul 2019 00:42:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:42:47: #1 finished! INFO @ Sat, 06 Jul 2019 00:42:47: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:42:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:42:47: #2 number of paired peaks: 75 WARNING @ Sat, 06 Jul 2019 00:42:47: Too few paired peaks (75) 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 00:42:47: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:42:47: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 00:42:47: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 00:42:47: #1 total tags in treatment: 387477 INFO @ Sat, 06 Jul 2019 00:42:47: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:42:47: #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 00:42:47: #1 tags after filtering in treatment: 387477 INFO @ Sat, 06 Jul 2019 00:42:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:42:47: #1 finished! INFO @ Sat, 06 Jul 2019 00:42:47: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:42:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:42:47: #2 number of paired peaks: 75 WARNING @ Sat, 06 Jul 2019 00:42:47: Too few paired peaks (75) 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 00:42:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.10_peaks.narrowPeakcut: : No such file or directory/home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.05_peaks.narrowPeak : No such file or directory pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.05_model.r’: No such file or directory rm: rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.05_*.xls’cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.10_model.r’: No such file or directory : No such file or directory rm: rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.05_peaks.narrowPeak’cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.10_*.xls’: No such file or directory: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:43:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.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 00:43:18: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:43:18: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:43:22: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 00:43:22: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 00:43:22: #1 total tags in treatment: 387477 INFO @ Sat, 06 Jul 2019 00:43:22: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:43:22: #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 00:43:22: #1 tags after filtering in treatment: 387477 INFO @ Sat, 06 Jul 2019 00:43:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:43:22: #1 finished! INFO @ Sat, 06 Jul 2019 00:43:22: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:43:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:43:22: #2 number of paired peaks: 75 WARNING @ Sat, 06 Jul 2019 00:43:22: Too few paired peaks (75) 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 00:43:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.20_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/SRX4140914/SRX4140914.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140914/SRX4140914.20_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。