PyamilySeq will die without warning if CD-HIT is presented with incompatible options #7
Description
cd-hit and cd-hit-est have a minimum -c pident and word size and when incompatible options are provided, PyamilySeq just dies.
Running PyamilySeq v1.1.1 in Full mode: Traceback (most recent call last): File "...PyamilySeq/src/PyamilySeq/PyamilySeq.py", line 326, in <module> main() File "...PyamilySeq/src/PyamilySeq/PyamilySeq.py", line 312, in main species_cluster(clustering_options) File "...PyamilySeq/src/PyamilySeq/PyamilySeq_Species.py", line 138, in cluster genome_dict, pangenome_clusters_First, pangenome_clusters_First_genomes, pangenome_clusters_First_sequences, reps = cluster_CDHIT(options, '|') File "...PyamilySeq/src/PyamilySeq/clusterings.py", line 9, in cluster_CDHIT First_in = open(options.clusters, 'r') FileNotFoundError: [Errno 2] No such file or directory: '...../clustering_CD-HIT.clstr'