Could incomplete gene_info.tsv file be due to a lack of matches between sample reads and database genes?

[AprilJauhal]

I recently ran Instrain (v.1.8.0) on a set of metagenomes, and even though I ran a loop to run all of the samples, the gene output file for one of the profiles only had a subset of the columns (“scaffold, gene, coverage, breadth, start, end, direction, and partial”), and I was wondering if this could be due to this sample lacking matches of the sample to the genes or genomes from the database I used?

I also noticed in the log file that it had a line that said “Skipping genes_clonality gene calculation; you have none”, which didn’t appear in any of the other log files.

I followed the instructions in Tutorial 2 ran each profile as a loop with the command: "inStrain profile ${bamfile} ${db_path_prefix}.fa -o ${output_file} -g ${genesfile} -p 5 -s ${stb_file}"

[MrOlm]

Hi @AprilJauhal - is it possible that the sample with no genes called was a very small metagenome with no genes detected? I've seen that happen before. To check, can you let me know if there are any robustly detected genomes in the same with no genes called?

Best,
Matt