Hybpiper gives same output for paralogs_all and paralogs_no_chimeras

[leminch]

I ran hybpiper assemble with the following command in Hybpiper v.2.1.2:

hybpiper assemble -t_dna ../..//Detarioideae_baits_v.1.fasta \
-r ${tdir}/"$name"_trimmed_1.fastq.gz ${tdir}/"$name"_trimmed_2.fastq.gz \
--unpaired ${tdir}/"$name"_trimmed_u.fastq.gz \
--prefix "$prefix" --run_intronerate --cov_cutoff 4 --cpu 10

and hybpiper paralog_retriever with the following in Hybpiper v.2.1.6:

hybpiper paralog_retriever -t_dna ../../Detarioideae_baits_v.1.fasta \
detarieae_reduced_namelist.txt \
--fasta_dir_all detarieae_reduced_paralogs_all \
--fasta_dir_no_chimeras detarieae_reduced_paralogs_no_chimeras \
--paralog_report_filename detarieae_reduced_paralog_report.txt \
--paralogs_above_threshold_report_filename detarieae_reduced_threshold_report.txt \
--heatmap_filename detarieae_reduced_paralog_heatmap

However the output in the paralogs_all and paralogs_no_chimeras folders seem to be exactly the same, with the fasta headers for the paralogs_all.fasta being >Sample multi_hit_stitched_contig_comprising_3_hits and the fasta headers for paralogs_no_chimeras.fasta being >Sample multi_hit_stitched_contig_comprising_3_hits when I assume it should end with >Sample Flag no_stitched_contig used. Single longest hit.

Is this a problem with using different versions of Hybpiper for different steps?