Low coverage - output files missing

[brambloemen]

Hello!

I was trying out strainy for phasing E coli MAGs from a metagenomic assembly (ONT R10 data). Specifically, I generated an initial Flye assembly from all reads of a complex metagenomics sample. I then extracted all reads aligning to contigs classified as E. coli.

Next, I used the following commands to generate a new assembly and run strainy on it: flye --nano-hq {input.reads} --meta --no-alt-contigs --keep-haplotypes -i 0 --out-dir Ecoli/Flye strainy.py Ecoli/ecolreads.fastq.gz -g Ecoli/Flye/assembly_graph.gfa -o out_strainy -m nano -t 10

Strainy ran succesfully, but in the out_strainy directory, i see none of these output files:

• alignment_phased.bam
• strain_unitigs.gfa
• strain_contigs.gfa
• strain_variants.vcf A
• reference_unitig_info_table.csv
• phased_unitig_info_table.csv
• multiplicity_stats.txt

I do see these files/directories though: adj_M bam clusters flye_inputs flye_outputs graphs log_phase preprocessing_data root.log vcf

Do you know why I don't get the output files?

Thanks,

Bram

[katerinakazantseva]

Hello Bram!

Thank you for the report! Could you please sharelog_phase dir ?

[mikolmogorov]

Hi Bram,

It looks like you may re running an older version of strainy, based on theh output that you see.

I recommend either reinstalling the latest version from github into a fresh bioconda envinorment, or alternatively use the docker container. Before running on a larger dataset, you can verify that the toy example produces the expected output (https://github.com/katerinakazantseva/strainy?tab=readme-ov-file#quick-usage). You can also try a larger dataset from the tutorial (https://github.com/katerinakazantseva/strainy?tab=readme-ov-file#strainy-tutorial).

[mikolmogorov]

P.S. if you are updating a github repository via pull, make sure to run git submodule update --init to update submodules. A failsafe method is to do a fresh clone into a new directory..

[brambloemen]

Hi @fenderglass @katerinakazantseva ,

My bad, it looks like I was indeed running an older version instead of the latest release. I will update and try rerunning the tool. Thank you