REF_GENOME is hardcoded in the trio shell script #5
Description
running the trio fails because REF_GENOME is hardcoded in the trio shell script.
I commented out that line and set to my own.
But I am using the -g parameter so I assume that line is not needed at all and should be commented or removed.
(needLR) [dmulder@gphost09 needLR_local]$ /projects/dmulder_prj/results/bin/needLR_local/needLR_trio_3.3.sh \
> -p /projects/rapidomics/DM/RLR-027/prelim/results-medium-trio-both/RLR-027/RLR-027_proband-F154748_sniffles.vcf.gz \
> -m /projects/rapidomics/DM/RLR-027/prelim/results-medium-trio-both/RLR-027/RLR-027_mother-F155189_sniffles.vcf.gz \
> -f /projects/rapidomics/DM/RLR-027/prelim/results-medium-trio-both/RLR-027/RLR-027_father-F155190_sniffles.vcf.gz \
> -g /projects/alignment_references/Homo_sapiens/hg38_no_alt/genome/fasta/hg38_no_alt.fa
2025-04-10 01:38:29,088 [INFO] Truvari v4.2.2
2025-04-10 01:38:29,089 [INFO] Command /home/dmulder/miniconda3/envs/needLR/bin/truvari collapse -i needLR_output/RLR-027_proband-F154748_sniffles_needLR-3.3_trio_UWONT150/RLR-027_proband-F154748_sniffles_needLR-3.3_trio_UWONT150_bcftools_merged_with_UWONT150.vcf.gz -o needLR_output/RLR-027_proband-F154748_sniffles_needLR-3.3_trio_UWONT150/RLR-027_proband-F154748_sniffles_needLR-3.3_trio_UWONT150_truvari_merged.vcf -c needLR_output/RLR-027_proband-F154748_sniffles_needLR-3.3_trio_UWONT150/RLR-027_proband-F154748_sniffles_needLR-3.3_trio_UWONT150_truvari_collapsed.vcf -f /n/users/jgust1/reference_files/hg38_reference_genome/hg38.no_alt.fa -k first -s 50 -S 10000000 --passonly -B 50 -r 2000 -p 0 -P 0.2 -O 0.2 --chain
Traceback (most recent call last):
File "/home/dmulder/miniconda3/envs/needLR/bin/truvari", line 10, in <module>
sys.exit(main())
File "/home/dmulder/miniconda3/envs/needLR/lib/python3.9/site-packages/truvari/__main__.py", line 105, in main
TOOLS[args.cmd](args.options)
File "/home/dmulder/miniconda3/envs/needLR/lib/python3.9/site-packages/truvari/collapse.py", line 790, in collapse_main
matcher = truvari.Matcher(args=args)
File "/home/dmulder/miniconda3/envs/needLR/lib/python3.9/site-packages/truvari/matching.py", line 95, in __init__
self.reference = pysam.FastaFile(self.params.reference)
File "pysam/libcfaidx.pyx", line 121, in pysam.libcfaidx.FastaFile.__cinit__
File "pysam/libcfaidx.pyx", line 153, in pysam.libcfaidx.FastaFile._open
OSError: file `/n/users/jgust1/reference_files/hg38_reference_genome/hg38.no_alt.fa` not found