snayfach / MAGpurify

Improvement of metagenome-assembled genomes
GNU General Public License v3.0
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MAGpurify module errors #27

Open cmaggior opened 3 months ago

cmaggior commented 3 months ago

Hi there,

I'm getting errors with the majority of the MAGpurify modules, such as:

^[[1m• Calling genes with Prodigal^[[0m
  all genes: /home/cm2074/magpurify_singles/phylo-markers/genes.[ffn|faa]
^[[1m
• Identifying PhyEco phylogenetic marker genes with HMMER^[[0m

Error encountered executing:
hmmsearch --noali --domtblout /home/cm2074/magpurify_singles/phylo-markers/phyeco.hmmsearch --cpu 1 --cut_ga /home/share/apps/magpurify/MAGpurify-db-v1.0/phylo-markers/PhyEco.hmm /home/cm2074/magpurify_singles/phylo-markers/genes.faa

Error message:
b'\nError: File existence/permissions problem in trying to open HMM file /home/share/apps/magpurify/MAGpurify-db-v1.0/phylo-markers/PhyEco.hmm.\nHMM file /home/share/apps/magpurify/MAGpurify-db-v1.0/phylo-markers/PhyEco.hmm not found (nor an .h3m binary of it)\n\n'

And:

^[[1m• Searching database with BLASTN^[[0m

Error encountered executing:
blastn -query /home/cm2074/metabat_singles/GDB2_bin.1.fa -db /home/share/apps/magpurify/MAGpurify-db-v1.0/known-contam/hg38/hg38 -out /home/cm2074/magpurify_singles/known-contam/hg38.m8 -outfmt '6 std qlen slen' -max_target_seqs 1 -max_hsps 1 -qcov_hsp_perc 25 -perc_identity 98 -evalue 1e-$

Error message:
b'Warning: [blastn] Examining 5 or more matches is recommended\nBLAST Database error: Database memory map file error\n'

I'm a bit confused on why this is happening; any ideas?