Testing Propagate: "Error: The SAM/BAM file appears to be empty, was not converted properly, or no reads aligned. Exiting."

[cwillian1]

Hi, first thank for this interest tool. After I installed the propagAtE into the computer I having some troubles in running the examples commands such as : "Propagate -f example_sequence.fasta -r sample_forward_reads.fastq.gz sample_reverse_reads.fastq.gz -v VIBRANT_integrated_prophage_coordinates_example.tsv -o PropagAtE_example_results_dormant --clean -t 2"

After that I getting the ERROR "Error: The SAM/BAM file appears to be empty, was not converted properly, or no reads aligned. Exiting."

I already installed all the required tools and dependencies and I getting an empty bam file inside the folder "PropagAtE_example_results_dormant". I wonder if the bowtie2 isn't generating any index previous the alignment.

Here is also the log file generated PropagAtE_example_results_dormant.log

[cwillian1]

Hi. It seems like it was a problem with the samtools software. In my environment created for propagate I run the command line "conda install -c bioconda samtools=1.16.1 --force-reinstall" and reinstalled the samtools succefully. After that Propagate worked pretty well.