Job ID = 4289098 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:27:46 fasterq-dump.2.9.6 sys: timeout exhausted while creating file within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-12-10T04:27:46 fasterq-dump.2.9.6 err: timeout exhausted while creating file within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra73/SRR/008076/SRR8269997' 2019-12-10T04:27:46 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR8269997' ) -> RC(rcNS,rcFile,rcCreating,rcTimeout,rcExhausted) 2019-12-10T04:27:46 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcFile,rcCreating,rcTimeout,rcExhausted) spots read : 13,806,995 reads read : 27,613,990 reads written : 13,806,995 reads 0-length : 13,806,995 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: 00:03:10 13806995 reads; of these: 13806995 (100.00%) were unpaired; of these: 1246401 (9.03%) aligned 0 times 5646525 (40.90%) aligned exactly 1 time 6914069 (50.08%) aligned >1 times 90.97% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 8682902 / 12560594 = 0.6913 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:43:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.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 @ Tue, 10 Dec 2019 13:43:31: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:43:31: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:43:42: 1000000 INFO @ Tue, 10 Dec 2019 13:43:53: 2000000 INFO @ Tue, 10 Dec 2019 13:44:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.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 @ Tue, 10 Dec 2019 13:44:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:44:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:44:04: 3000000 INFO @ Tue, 10 Dec 2019 13:44:13: 1000000 INFO @ Tue, 10 Dec 2019 13:44:13: #1 tag size is determined as 76 bps INFO @ Tue, 10 Dec 2019 13:44:13: #1 tag size = 76 INFO @ Tue, 10 Dec 2019 13:44:13: #1 total tags in treatment: 3877692 INFO @ Tue, 10 Dec 2019 13:44:13: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:44:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:44:13: #1 tags after filtering in treatment: 3877692 INFO @ Tue, 10 Dec 2019 13:44:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:44:13: #1 finished! INFO @ Tue, 10 Dec 2019 13:44:13: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:44:14: #2 number of paired peaks: 32 WARNING @ Tue, 10 Dec 2019 13:44:14: Too few paired peaks (32) 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 @ Tue, 10 Dec 2019 13:44:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.05_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/SRX5086841/SRX5086841.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:44:24: 2000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:44:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.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 @ Tue, 10 Dec 2019 13:44:31: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:44:31: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:44:36: 3000000 INFO @ Tue, 10 Dec 2019 13:44:45: 1000000 INFO @ Tue, 10 Dec 2019 13:44:48: #1 tag size is determined as 76 bps INFO @ Tue, 10 Dec 2019 13:44:48: #1 tag size = 76 INFO @ Tue, 10 Dec 2019 13:44:48: #1 total tags in treatment: 3877692 INFO @ Tue, 10 Dec 2019 13:44:48: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:44:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:44:48: #1 tags after filtering in treatment: 3877692 INFO @ Tue, 10 Dec 2019 13:44:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:44:48: #1 finished! INFO @ Tue, 10 Dec 2019 13:44:48: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:44:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:44:48: #2 number of paired peaks: 32 WARNING @ Tue, 10 Dec 2019 13:44:48: Too few paired peaks (32) 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 @ Tue, 10 Dec 2019 13:44:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.10_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/SRX5086841/SRX5086841.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:44:56: 2000000 INFO @ Tue, 10 Dec 2019 13:45:07: 3000000 INFO @ Tue, 10 Dec 2019 13:45:16: #1 tag size is determined as 76 bps INFO @ Tue, 10 Dec 2019 13:45:16: #1 tag size = 76 INFO @ Tue, 10 Dec 2019 13:45:16: #1 total tags in treatment: 3877692 INFO @ Tue, 10 Dec 2019 13:45:16: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:45:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:45:17: #1 tags after filtering in treatment: 3877692 INFO @ Tue, 10 Dec 2019 13:45:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:45:17: #1 finished! INFO @ Tue, 10 Dec 2019 13:45:17: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:45:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:45:17: #2 number of paired peaks: 32 WARNING @ Tue, 10 Dec 2019 13:45:17: Too few paired peaks (32) 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 @ Tue, 10 Dec 2019 13:45:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086841/SRX5086841.20_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。