Job ID = 2010834 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T15:53:33 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T15:53:33 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/007064/SRR7234532' 2019-07-05T15:53:33 fasterq-dump.2.9.6 err: invalid accession 'SRR7234532' 2019-07-05T15:53:48 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T15:53:48 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/007064/SRR7234532' 2019-07-05T15:53:48 fasterq-dump.2.9.6 err: invalid accession 'SRR7234532' 2019-07-05T15:54:04 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T15:54:04 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/007064/SRR7234532' 2019-07-05T15:54:04 fasterq-dump.2.9.6 err: invalid accession 'SRR7234532' spots read : 5,870,464 reads read : 11,740,928 reads written : 5,870,464 reads 0-length : 5,870,464 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: 00:02:04 5870464 reads; of these: 5870464 (100.00%) were unpaired; of these: 295343 (5.03%) aligned 0 times 4915529 (83.73%) aligned exactly 1 time 659592 (11.24%) aligned >1 times 94.97% overall alignment rate Time searching: 00:02:04 Overall time: 00:02:04 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] 1400696 / 5575121 = 0.2512 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 01:04:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.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 01:04:39: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:04:39: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:04:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.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 01:04:40: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:04:40: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:04:49: 1000000 INFO @ Sat, 06 Jul 2019 01:04:54: 1000000 INFO @ Sat, 06 Jul 2019 01:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.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 01:04:58: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:04:58: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:04:58: 2000000 INFO @ Sat, 06 Jul 2019 01:05:09: 2000000 INFO @ Sat, 06 Jul 2019 01:05:09: 3000000 INFO @ Sat, 06 Jul 2019 01:05:12: 1000000 INFO @ Sat, 06 Jul 2019 01:05:19: 4000000 INFO @ Sat, 06 Jul 2019 01:05:20: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:05:20: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:05:20: #1 total tags in treatment: 4174425 INFO @ Sat, 06 Jul 2019 01:05:20: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:05:20: #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 01:05:20: #1 tags after filtering in treatment: 4174425 INFO @ Sat, 06 Jul 2019 01:05:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:05:20: #1 finished! INFO @ Sat, 06 Jul 2019 01:05:20: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:05:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:05:21: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 01:05:21: Too few paired peaks (28) 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 01:05:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.05_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/SRX4140941/SRX4140941.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:05:22: 3000000 INFO @ Sat, 06 Jul 2019 01:05:26: 2000000 INFO @ Sat, 06 Jul 2019 01:05:36: 4000000 INFO @ Sat, 06 Jul 2019 01:05:38: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:05:38: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:05:38: #1 total tags in treatment: 4174425 INFO @ Sat, 06 Jul 2019 01:05:38: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:05:38: #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 01:05:38: #1 tags after filtering in treatment: 4174425 INFO @ Sat, 06 Jul 2019 01:05:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:05:38: #1 finished! INFO @ Sat, 06 Jul 2019 01:05:38: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:05:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:05:38: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 01:05:38: Too few paired peaks (28) 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 01:05:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.10_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/SRX4140941/SRX4140941.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:05:39: 3000000 INFO @ Sat, 06 Jul 2019 01:05:52: 4000000 INFO @ Sat, 06 Jul 2019 01:05:54: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:05:54: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:05:54: #1 total tags in treatment: 4174425 INFO @ Sat, 06 Jul 2019 01:05:54: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:05:54: #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 01:05:54: #1 tags after filtering in treatment: 4174425 INFO @ Sat, 06 Jul 2019 01:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:05:54: #1 finished! INFO @ Sat, 06 Jul 2019 01:05:54: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:05:54: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 01:05:54: Too few paired peaks (28) 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 01:05:54: Process for pairing-model is terminated! BedGraph に変換しました。 cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.20_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140941/SRX4140941.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。