pdb_seqres.txt parse error when execute hmmsearch

[ssn1771]

hi, i met a parse error when executing hmmsearch in pdb_seqres.txt. the log is:

(WorkflowManagementActor pid=7511) RuntimeError: hmmsearch failed: (WorkflowManagementActor pid=7511) stdout: (WorkflowManagementActor pid=7511) # hmmsearch :: search profile(s) against a sequence database (WorkflowManagementActor pid=7511) # HMMER 3.3.2 (Nov 2020); http://hmmer.org/ (WorkflowManagementActor pid=7511) # Copyright (C) 2020 Howard Hughes Medical Institute. (WorkflowManagementActor pid=7511) # Freely distributed under the BSD open source license. (WorkflowManagementActor pid=7511) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - (WorkflowManagementActor pid=7511) # query HMM file: /tmp/tmph1wus5n3/query.hmm (WorkflowManagementActor pid=7511) # target sequence database: /uniprot/pdb_seqres.txt (WorkflowManagementActor pid=7511) # MSA of all hits saved to file: ./alignments/5ZNG_1|Chain A|NBS-LRR type protein|Oryza sativa subsp. japonica (39947)/hmm_output.sto (WorkflowManagementActor pid=7511) # show alignments in output: no (WorkflowManagementActor pid=7511) # sequence reporting threshold: E-value <= 100 (WorkflowManagementActor pid=7511) # domain reporting threshold: E-value <= 100 (WorkflowManagementActor pid=7511) # sequence inclusion threshold: E-value <= 100 (WorkflowManagementActor pid=7511) # domain inclusion threshold: E-value <= 100 (WorkflowManagementActor pid=7511) # MSV filter P threshold: <= 0.1 (WorkflowManagementActor pid=7511) # Vit filter P threshold: <= 0.1 (WorkflowManagementActor pid=7511) # Fwd filter P threshold: <= 0.1 (WorkflowManagementActor pid=7511) # number of worker threads: 12 (WorkflowManagementActor pid=7511) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - (WorkflowManagementActor pid=7511) (WorkflowManagementActor pid=7511) Query: query [M=137] (WorkflowManagementActor pid=7511) (WorkflowManagementActor pid=7511) (WorkflowManagementActor pid=7511) stderr: (WorkflowManagementActor pid=7511) Parse failed (sequence file /uniprot/pdb_seqres.txt): (WorkflowManagementActor pid=7511) Line 1366526: illegal character 0

[Shenggan]

You can try to re-download pdb_seqres.txt, or refer this issue https://github.com/deepmind/alphafold/issues/560

[ssn1771]

thanks, removing the lines including "0" works