FilTar error message

[ntinamu001]

Hi. Dr. Thomas Bradley,

I found your paper, FilTar: using RNA-Seq data to improve microRNA target prediction accuracy in animals, and your program really fit into my project.

On the first attempt with default parameters, the following error message is displayed:

Error in rule salmon_index_for_lib_types:
Error in rule salmon_index:
jobid: 810
jobid: 575
output: results/salmon/indexes/lib_type_identification/hsa
output: results/salmon/indexes/hsa
conda-env: /home/wooje/NGS_tools/FilTar-master/.snakemake/conda/3399c010
conda-env: /home/wooje/NGS_tools/FilTar-master/.snakemake/conda/3399c010
shell:
salmon index --threads 8 -t data/Homo_sapiens.GRCh38.cdna.all.fa -i results/salmon/indexes/lib_type_identification/hsa --type quasi -k 31
(exited with non-zero exit code)
shell:
salmon index --threads 8 -t data/Homo_sapiens.GRCh38.cdna.all.fa -i results/salmon/indexes/hsa --type quasi -k 31
(exited with non-zero exit code)

Because I also receive "Exception : [Error: RapMap-based indexing is not supported in this version of salmon.]", I may need to replace the latest version of Salmon with V.0.11.3.
But I am new to computer programming, so I don't know how to replace it.
Could you please help me how to solve the problem?

Thank you.

Best regards,
Wooje

[TBradley27]

Hi @ntinamu001,

Apologies for the delayed response.

Could you try editing modules/quant_reads/salmon/envs/salmon.yaml and specifying a recently released version of salmon and rerun please?

I will test this on my end some time soon