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biologger / speciesprimer

The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.
GNU General Public License v3.0
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ValueError: Your XML file was empty #3

Closed aiqubo closed 4 years ago

aiqubo commented 4 years ago

Could you help me about tihs error? Thank you very much! “”“ 27 Apr 2020 05:44:26: Run blastn -task megablast -num_threads 8 -query rRNA.part-0 -max_target_seqs 5 -max_hsps 1 -out rRNA_0_results.xml -outfmt 5 -db ref_prok_rep_genomes 27 Apr 2020 05:44:27: > Blast duration: 0:00:00 27 Apr 2020 05:44:27: Run: qc_blast_parser(rRNA) 27 Apr 2020 05:44:27: Run: blastresults_files(Bifidobacterium_animalis) 27 Apr 2020 05:44:27: > A problem with the BLAST results file /primerdesign/Bifidobacterium_animalis/rRNA_QC/rRNA_0_results.xml was detected. Please check if the file was removed and start$ 27 Apr 2020 05:44:27: ['fatal error while working on', 'Bifidobacterium_animalis', 'check logfile', '/primerdesign/speciesprimer_2020_04_27.log'] fatal error while working on Bifidobacterium_animalis Traceback (most recent call last): File "/pipeline//speciesprimer.py", line 4165, in main run_pipeline_for_target(target, config) File "/pipeline//speciesprimer.py", line 4056, in run_pipeline_for_target qc = QualityControl(config).quality_control(qc_gene) File "/pipeline//speciesprimer.py", line 1245, in quality_control passed_list = self.qc_blast_parser(qc_gene) File "/pipeline//speciesprimer.py", line 1060, in qc_blast_parser parse_blastresults() File "/pipeline//speciesprimer.py", line 974, in parse_blastresults blast_record_list = blapa.parse_BLASTfile(filename) File "/pipeline//speciesprimer.py", line 2152, in parse_BLASTfile record_list = list(blast_records) File "/usr/local/lib/python3.5/dist-packages/Bio/Blast/NCBIXML.py", line 798, in parse raise ValueError("Your XML file was empty") ValueError: Your XML file was empty 27 Apr 2020 05:44:27: > Error report: 27 Apr 2020 05:44:27: > for target Bifidobacterium_animalis 27 Apr 2020 05:44:27: > Error 1: 27 Apr 2020 05:44:27: > A problem with the BLAST results file /primerdesign/Bifidobacterium_animalis/rRNA_QC/rRNA_0_results.xml was detected. Please check if the file was removed and start$ 27 Apr 2020 05:44:27: > for target Bifidobacterium_animalis 27 Apr 2020 05:44:27: > Error 2: 27 Apr 2020 05:44:27: > fatal error while working on Bifidobacterium_animalis check logfile /primerdesign/speciesprimer_2020_04_27.log ”“”

aiqubo commented 4 years ago

work now, After I updated the blastdb use command as follow ""update_blastdb.pl --passive --decompress ref_prok_rep_genomes""