basic works, but duo and trio fail

[fakedrtom]

I seem to be able to successfully run needLR_3.4_basic.sh, but whenever I try and run the duo or trio scripts, there seems to be a problem finding the temporary files that the script should be generating in the initial steps of the shell. Here is some of the output from my last attempt to run the trio script:

[E::hts_open_format] Failed to open file "needLR_output/RD_021.sniffles.vcf.gz_needLR_3.4_trio/preprocessed_temp_RD_021.sniffles*.vcf.gz" : No such file or directory
Failed to open needLR_output/RD_021.sniffles.vcf.gz_needLR_3.4_trio/preprocessed_temp_RD_021.sniffles*.vcf.gz: No such file or directory
tbx_index_build failed: needLR_output/RD_021.sniffles.vcf.gz_needLR_3.4_trio/RD_021.sniffles.vcf.gz_needLR_3.4_trio_bcftools_merged_with_UWONT450_temp.vcf.gz
2025-10-09 16:49:55,999 [INFO] Truvari v4.2.2
2025-10-09 16:49:55,999 [INFO] Command /uufs/chpc.utah.edu/common/HIPAA/u0055382/src/miniforge3/envs/needLR_env/bin/truvari collapse -i needLR_output/RD_021.sniffles.vcf.gz_needLR_3.4_trio/RD_021.sniffles.vcf.gz_needLR_3.4_trio_bcftools_merged_with_UWONT450_temp.vcf.gz -o needLR_output/RD_021.sniffles.vcf.gz_needLR_3.4_trio/RD_021.sniffles.vcf.gz_needLR_3.4_trio_truvari_merged_temp.vcf -c needLR_output/RD_021.sniffles.vcf.gz_needLR_3.4_trio/RD_021.sniffles.vcf.gz_needLR_3.4_trio_truvari_collapsed_temp.vcf -f /scratch/ucgd/lustre-core/common/data/Reference/homo_sapiens/GRCh38/primary_assembly_decoy_phix.fa -k common -r 2000 -p 0 -B 50 -P 0.2 -O 0.2 --chain -s 50 -S 10000000 --passonly
2025-10-09 16:49:56,000 [ERROR] File needLR_output/RD_021.sniffles.vcf.gz_needLR_3.4_trio/RD_021.sniffles.vcf.gz_needLR_3.4_trio_bcftools_merged_with_UWONT450_temp.vcf.gz does not exist
2025-10-09 16:49:56,000 [ERROR] Input vcf index needLR_output/RD_021.sniffles.vcf.gz_needLR_3.4_trio/RD_021.sniffles.vcf.gz_needLR_3.4_trio_bcftools_merged_with_UWONT450_temp.vcf.gz.tbi does not exist. Must be indexed
Couldn't run Truvari. Please fix parameters
[E::hts_open_format] Failed to open file "needLR_output/RD_021.sniffles.vcf.gz_needLR_3.4_trio/RD_021.sniffles.vcf.gz_needLR_3.4_trio_truvari_merged_temp.vcf" : No such file or directory
Failed to read from needLR_output/RD_021.sniffles.vcf.gz_needLR_3.4_trio/RD_021.sniffles.vcf.gz_needLR_3.4_trio_truvari_merged_temp.vcf: No such file or directory
Writing to /tmp/bcftools.RxKpnG
Merging 0 temporary files
Cleaning
Done

It completes, but all resulting files are empty. When I try the duo script, I run into the same problem. Confused why the basic script would work for me, but these other versions fail. Any suggestions?

Thanks