magpurify errors

Question

[shevch2009]

Hello all! I am tring to clean obtained mags with the magpurify. For some mags it worked ok, but for some I keep getting error for phylo-markers module:

magpurify phylo-markers /path/bin.5.fa /path/magpurify_results --threads 16
Calling genes with Prodigal
 all genes: /path/magpurify_results/phylo-markers/genes.[ffn|faa]

Identifying PhyEco phylogenetic marker genes with HMMER
  mm results: /path/magpurify_results/phylo-markers/phyeco.hmmsearch
  marker genes: /path/magpurify_results/phylo-markers/markers

Performing pairwise BLAST alignment of marker genes against database
 blast results: /path/magpurify_results/phylo-markers/alns

Finding taxonomic outliers
Traceback (most recent call last):
  File "/path/miniconda3/bin/magpurify", line 10, in <module>
    sys.exit(cli())
             ^^^^^
  File "/path/miniconda3/lib/python3.12/site-packages/magpurify/cli.py", line 116, in cli
    args["func"](args)
  File "/path/miniconda3/lib/python3.12/site-packages/magpurify/modules/phylo.py", line 419, in main
    flagged = flag_contigs(args["db"], args["tmp_dir"], args)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/path/miniconda3/lib/python3.12/site-packages/magpurify/modules/phylo.py", line 372, in flag_contigs
    bin.genes[aln["qname"]].annotations.append(annotation)
    ~~~~~~~~~^^^^^^^^^^^^^^
KeyError: 'k127_4584534_11'

So, this - KeyError: 'k127_4584534_11' is always different for different bin, is just name of contig that tool don't recognize?

And when I try use gc-content, it also will give me error for the same bin, that gave error with the phylo-markers

magpurify gc-content /path/bin.5.fa /path/magpurify_results
Computing mean contig GC content
Traceback (most recent call last):
  File "/path/miniconda3/bin/magpurify", line 10, in <module>
    sys.exit(cli())
             ^^^^^
  File "/path/miniconda3/lib/python3.12/site-packages/magpurify/cli.py", line 116, in cli
    args["func"](args)
  File "/path/miniconda3/lib/python3.12/site-packages/magpurify/modules/gc.py", line 68, in main
    contig.gc = round(SeqUtils.GC(seq), 2)
                      ^^^^^^^^^^^
AttributeError: module 'Bio.SeqUtils' has no attribute 'GC'

If I run modules tetra-freq, clade-markers and known-contam, it will work fine

magpurify clade-markers /path/bin.5.fa /path/magpurify_results --threads 16
Reading database info

Calling genes with Prodigal
  all genes: /path/magpurify_results/clade-markers/genes.[ffn|faa]

Performing pairwise alignment of genes against MetaPhlan2 database of clade-specific genes
  alignments: /path/magpurify_results/clade-markers/genes.m8

Finding top hits to database
  2118 genes with a database hit

Classifying genes at each taxonomic rank
  kingdom: 104 classified genes
  phylum: 0 classified genes
  class: 0 classified genes
  order: 0 classified genes
  family: 0 classified genes
  genus: 0 classified genes
  species: 0 classified genes

Taxonomically classifying contigs
  total contigs: 995
  kingdom: 94 classified contigs
  phylum: 0 classified contigs
  class: 0 classified contigs
  order: 0 classified contigs
  family: 0 classified contigs
  genus: 0 classified contigs
  species: 0 classified contigs

Taxonomically classifying genome
  consensus taxon: None

Identifying taxonomically discordant contigs
  0 flagged contigs: /path/magpurify_results/clade-markers/flagged_contigs

Has anyone encountered something like this? Are there any solutions?

I would appreciate any suggestions.

Thanks, Alla

Answer 1

[Mensur Dlakic]

A general answer is to always Google the error message. Hopefully you do that in the future. This is the outcome of Googling AttributeError: module 'Bio.SeqUtils' has no attribute 'GC':

https://www.google.com/search?q=AttributeError%3A+module+%27Bio.SeqUtils%27+has+no+attribute+%27GC%27

To save you some reading, in newer BioPython versions there is no GC function. That means you either have to dig through magpurify source and replace GC with its current equivalent (not recommended), or you downgrade BioPython:

pip install biopython==1.79

[shevch2009]

Thanks

What about phylo-markers module error, I tried to look for it :) But haven't found anything. And why it's not working for some but not all bins...

[Mensur Dlakic]

To me that sounds like an error in sequence header formatting. Maybe some contig headers are repeated? Or their sequences are short or missing? Are there N or X characters in such contigs?

Another general advice: if a tool works for some contigs but not the others, see what is different about those contigs.

[shevch2009]

Thank you

[shevch2009]

Strange but there are no such headers or contig names in my fasta files

[Mensur Dlakic]

There is absolutely no chance that a contig labeled k127_4584534 doesn't exist in your fasta files. These names are not made up out of thin air - they are read from the file. If you can't find what's wrong with that contig but instead you simply delete it, it is a safe bet that particular error will go away.

[shevch2009]

I have checked with my eyes, and I didn't find it, I have only one contig that starts with k127_458 .... but the name is different - k127_4587812

Why it should be the name of contig? When the error not specified that it's about bin? The last line -

File "/path/miniconda3/lib/python3.12/site-packages/magpurify/modules/phylo.py", line 372, in flag_contigs bin.genes[aln["qname"]].annotations.append(annotation)

I saw some issues on github, I didn't even open them, because they were not answered ... some of them were 2021 ..

Looks like I need to find another tool then.

[Mensur Dlakic]

By the way, these errors are not unique. If you look through the magpurify GitHub issues, both types have been reported already.

• https://github.com/snayfach/MAGpurify/issues/28
• https://github.com/snayfach/MAGpurify/issues/19

Signing off.