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phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Apache License 2.0
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mob_recon does not reconstruct plasmids sequences #158

Closed maricleon closed 1 month ago

maricleon commented 5 months ago

I am encountering an issue with the reconstruction of plasmid sequences using mob_recon. While all other files are successfully generated, the actual sequences remain absent. The recurring warning message I receive suggests a potential cause for this problem. Despite thoroughly checking my Blast installation and finding it apparently in order, the issue persists.

2024-01-20 10:06:39,240 root WARNING: No BLASTN results to parse from file test/tmp/orit_blast_results.txt [in /home/company/leomar1/program_files/miniconda3/envs/tools/lib/python3.11/site-packages/mob_suite/blast/init__.py:181]

kbessonov1984 commented 1 month ago

Hi, There might be no contigs identified of plasmid origin but rather chromosomal. Plasmid contigs are identified by looking to key markers such as oriT, mpf, replicon, MOB allele sequences and by alignment to the reference plasmid sequences (plasmid database). If no plasmid contigs are found, no plasmid FASTA files are generated. If you could provide an example input file, then we could further help you. For plasmid identification logic and contig filtering you can check the source code here