run_gnomon_biotype parameter error #197
Description
Hello, my YAML settings are as follows,I want to know exactly how to set the "-max_prok_hits_pct" parameter:
V 0.4.1
genome: H4080.clean.fasta
taxid: 4530
long_reads:
-H4080limapolyA.fasta
short_reads:H4080_short.txt
locus_tag_prefix: H4080
tasks:
gnomon:
gnomon_biotype:
gnomon_biotype: -max_prok_hits_pct 75
Despite having displayed/printed the valid parameters:
Command executed:
mkdir -p output
mkdir -p ./asncache/
prime_cache -cache ./asncache/ -ifmt asnb-seq-entry -i swissprot.asnb -oseq-ids spids -split-sequences
prime_cache -cache ./asncache/ -ifmt asnb-seq-entry -i scored.models.asn -oseq-ids gnids -split-sequences
lds2_indexer -source genome/ -db LDS2
echo "hits.diamond.asn" > raw_blastp_hits.mft
merge_blastp_hits -asn-cache ./asncache/ -nogenbank -lds2 LDS2 -input-manifest raw_blastp_hits.mft -o prot_hits.asn
echo "scored.models.asn" > models.mft
echo "prot_hits.asn" > prot_hits.mft
echo "" > splices.mft
export effective_params=-max_prok_hits_pct 75
if [ -n "swissprot_organelle_bacteria.gi" ]; then
effective_params="${effective_params} -prot_denylist swissprot_organelle_bacteria.gi"
fi
gnomon_biotype -name_cleanup_rules_file name_cleanup_rules_file.txt ${effective_params} -logfile - -gc H4080.clean-gencoll.asn -asn-cache ./asncache/ -lds2 ./LDS2 -nogenbank -gnomon_models models.mft -o output/biotypes.tsv -o_prots_rpt output/prots_rpt.tsv -o_contam_rpt output/contam_rpt.tsv -prot_hits prot_hits.mft -prot_splices splices.mft -reftrack-server 'NONE' -allow_lt631 true
But the parameter error still occurred:
+ export effective_params=-max_prok_hits_pct 75
+ effective_params=-max_prok_hits_pct
.command.sh: line 12: export: `75': not a valid identifier
++ kill 36