sniffles: error: the following arguments are required: -i/--input SV detection output not found, exiting...

[Kiliankleemann]

Got the installation to work and sample seem to be loaded properly and processing starts but then i get the following:

[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 1100962 reads
[bam_sort_core] merging from 2 files and 1 in-memory blocks...
usage: sniffles --input SORTED_INPUT.bam [--vcf OUTPUT.vcf] [--snf MERGEABLE_OUTPUT.snf] [--threads 4] [--mosaic]

Sniffles2: A fast structural variant (SV) caller for long-read sequencing data
 Version 2.2
 Contact: [email protected]

sniffles: error: the following arguments are required: -i/--input
SV detection output not found, exiting...

[shunhuahan]

Hi @Kiliankleemann,

This suggests that Sniffles 2.2 is in your current environment. However, TELR requires an old version of Sniffles (1.0.12). It's odd that Sniffles 2.2 was installed even though the conda recipe explicitly requests 1.0.12 (see https://bioconda.github.io/recipes/telr/README.html).

Could you try the following conda/mamba installation to replace Sniffles version before running TELR?

conda activate TELR
conda install Sniffles=1.0.12 -c bioconda

If it still doesn't work, I'm happy to run TELR on your dataset and share results for you to analyze. Sorry for the troubles.

Shunhua