Job ID = 2010259 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T12:58:48 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 : 9,333,478 reads read : 18,666,956 reads written : 9,333,478 reads 0-length : 9,333,478 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: 00:02:11 9333478 reads; of these: 9333478 (100.00%) were unpaired; of these: 853744 (9.15%) aligned 0 times 7352816 (78.78%) aligned exactly 1 time 1126918 (12.07%) aligned >1 times 90.85% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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] 2817279 / 8479734 = 0.3322 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 @ Fri, 05 Jul 2019 22:06:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.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 @ Fri, 05 Jul 2019 22:06:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:06:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:06:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.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 @ Fri, 05 Jul 2019 22:06:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:06:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.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 @ Fri, 05 Jul 2019 22:06:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:06:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:06:28: 1000000 INFO @ Fri, 05 Jul 2019 22:06:28: 1000000 INFO @ Fri, 05 Jul 2019 22:06:29: 1000000 INFO @ Fri, 05 Jul 2019 22:06:36: 2000000 INFO @ Fri, 05 Jul 2019 22:06:37: 2000000 INFO @ Fri, 05 Jul 2019 22:06:38: 2000000 INFO @ Fri, 05 Jul 2019 22:06:44: 3000000 INFO @ Fri, 05 Jul 2019 22:06:45: 3000000 INFO @ Fri, 05 Jul 2019 22:06:48: 3000000 INFO @ Fri, 05 Jul 2019 22:06:52: 4000000 INFO @ Fri, 05 Jul 2019 22:06:53: 4000000 INFO @ Fri, 05 Jul 2019 22:06:57: 4000000 INFO @ Fri, 05 Jul 2019 22:07:00: 5000000 INFO @ Fri, 05 Jul 2019 22:07:01: 5000000 INFO @ Fri, 05 Jul 2019 22:07:05: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:07:05: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:07:05: #1 total tags in treatment: 5662455 INFO @ Fri, 05 Jul 2019 22:07:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:07:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 22:07:05: #1 tags after filtering in treatment: 5662455 INFO @ Fri, 05 Jul 2019 22:07:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:07:05: #1 finished! INFO @ Fri, 05 Jul 2019 22:07:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:07:06: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:07:06: 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 @ Fri, 05 Jul 2019 22:07:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.10_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/SRX3294615/SRX3294615.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:07:06: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:07:06: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:07:06: #1 total tags in treatment: 5662455 INFO @ Fri, 05 Jul 2019 22:07:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:07:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 22:07:06: #1 tags after filtering in treatment: 5662455 INFO @ Fri, 05 Jul 2019 22:07:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:07:06: #1 finished! INFO @ Fri, 05 Jul 2019 22:07:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:07:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:07:07: 5000000 INFO @ Fri, 05 Jul 2019 22:07:07: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:07:07: 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 @ Fri, 05 Jul 2019 22:07:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.20_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/SRX3294615/SRX3294615.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:07:13: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:07:13: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:07:13: #1 total tags in treatment: 5662455 INFO @ Fri, 05 Jul 2019 22:07:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:07:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 22:07:13: #1 tags after filtering in treatment: 5662455 INFO @ Fri, 05 Jul 2019 22:07:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:07:13: #1 finished! INFO @ Fri, 05 Jul 2019 22:07:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:07:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:07:13: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:07:13: 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 @ Fri, 05 Jul 2019 22:07:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.05_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/SRX3294615/SRX3294615.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294615/SRX3294615.05_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。