Job ID = 2641079 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T12:12:27 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 : 9,296,500 reads read : 18,593,000 reads written : 9,296,500 reads 0-length : 9,296,500 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: 00:01:39 9296500 reads; of these: 9296500 (100.00%) were unpaired; of these: 179665 (1.93%) aligned 0 times 8241952 (88.66%) aligned exactly 1 time 874883 (9.41%) aligned >1 times 98.07% overall alignment rate Time searching: 00:01:39 Overall time: 00:01:39 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_rmdupse_core] 3850818 / 9116835 = 0.4224 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:18:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.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 21:18:19: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:18:19: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:18:27: 1000000 INFO @ Sat, 24 Aug 2019 21:18:34: 2000000 INFO @ Sat, 24 Aug 2019 21:18:42: 3000000 INFO @ Sat, 24 Aug 2019 21:18:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.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 21:18:48: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:18:48: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:18:50: 4000000 INFO @ Sat, 24 Aug 2019 21:18:55: 1000000 INFO @ Sat, 24 Aug 2019 21:18:58: 5000000 INFO @ Sat, 24 Aug 2019 21:19:00: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:19:00: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:19:00: #1 total tags in treatment: 5266017 INFO @ Sat, 24 Aug 2019 21:19:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:19:00: #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 21:19:00: #1 tags after filtering in treatment: 5266017 INFO @ Sat, 24 Aug 2019 21:19:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:19:00: #1 finished! INFO @ Sat, 24 Aug 2019 21:19:00: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:19:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:19:01: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:19:01: 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 21:19:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.05_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/SRX5257273/SRX5257273.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:19:01: 2000000 INFO @ Sat, 24 Aug 2019 21:19:08: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:19:16: 4000000 INFO @ Sat, 24 Aug 2019 21:19:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.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 21:19:19: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:19:19: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:19:23: 5000000 INFO @ Sat, 24 Aug 2019 21:19:24: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:19:24: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:19:24: #1 total tags in treatment: 5266017 INFO @ Sat, 24 Aug 2019 21:19:24: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:19:24: #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 21:19:25: #1 tags after filtering in treatment: 5266017 INFO @ Sat, 24 Aug 2019 21:19:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:19:25: #1 finished! INFO @ Sat, 24 Aug 2019 21:19:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:19:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:19:25: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:19:25: 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 21:19:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.10_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/SRX5257273/SRX5257273.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:19:25: 1000000 INFO @ Sat, 24 Aug 2019 21:19:31: 2000000 INFO @ Sat, 24 Aug 2019 21:19:38: 3000000 INFO @ Sat, 24 Aug 2019 21:19:47: 4000000 INFO @ Sat, 24 Aug 2019 21:19:55: 5000000 INFO @ Sat, 24 Aug 2019 21:19:58: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:19:58: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:19:58: #1 total tags in treatment: 5266017 INFO @ Sat, 24 Aug 2019 21:19:58: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:19:58: #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 21:19:58: #1 tags after filtering in treatment: 5266017 INFO @ Sat, 24 Aug 2019 21:19:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:19:58: #1 finished! INFO @ Sat, 24 Aug 2019 21:19:58: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:19:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:19:58: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:19:58: 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 21:19:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.20_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/SRX5257273/SRX5257273.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257273/SRX5257273.20_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。