Troubleshooting

Troubleshooting

"mash" was not found

genome-comparator uses the mash found in your PATH first, then the one installed next to its own Python interpreter (the bin/ folder of the conda environment). Calling /path/to/envs/genome_comparator/bin/genome-comparator without activating the environment therefore works if Mash is installed in that environment. The log shows which mash was used.

If Mash cannot be found in either place, install it in the environment: conda install -c bioconda mash.

mash: error while loading shared libraries: libgsl.so.25

Older bioconda builds of Mash are linked to GSL 2.6. Recreate the environment from environment.yml, which requires gsl>=2.8 and a matching Mash build, and do not use the defaults channel:

conda env remove -n genome_comparator
conda env create -f environment.yml

Ambiguous sample names

Two input files give the same sample name. Rename or remove the files listed in the message. See Usage for how sample names are derived from file names.

Could not sketch "<sample>"

Mash could not read the file: it may be empty, truncated or not a fasta/fastq file. The sample is flagged as failed in sample_stats.tsv and left out; the run continues if at least 3 samples remain.

Some distances are not significant

The largest Mash p-value is above 0.01. Some samples may be unrelated (e.g. a contaminant or a wrong species), or the sketch size is too small. Check all_dist.tsv for samples with unusually large distances, or increase --sketch-size.

The tree has low bootstrap support

See Bootstrap support.

Getting more details

Run with -v to log every Mash command and show the full Python traceback of errors. The log is also saved in <output>/genome_comparator.log.