Comments (4)
ACEnglish
commented on September 27, 2024
Funny story, this is the third ticket in a row related to pysam.bcftools.consensus. Luckily, the first ticket required me to replace the haplotype consensus creation step with something more stable. Therefore, you may not see the error if you install directly from develop and try again. Please install from develop and let me know if you still see an error.
git clone https://github.com/spiralgenetics/truvari.git
python3 -m pip install truvarifrom truvari.
nate-d-olson
commented on September 27, 2024
Unfortunately, the replacement didn't address this error. Looks like it is an issue with extract_references, specifically the call to pysam.faidx(). Here is the log file.
2024-01-04 17:33:39,857 [INFO] Truvari v4.2.0rc1
2024-01-04 17:33:39,858 [INFO] Command /home/nolson/mambaforge/envs/truvari_eval/bin/truvari refine --threads 1 --align mafft --use-original --reference resources/references/GRCh38_chr21.fa --regions results/evaluations/truvari/eval14_testC/GRCh38_chr21_CMRGv1.00-stvar_asm17aChr21_stvar_dipcall-default/candidate.refine.bed results/evaluations/truvari/eval14_testC/GRCh38_chr21_CMRGv1.00-stvar_asm17aChr21_stvar_dipcall-default
2024-01-04 17:33:39,858 [INFO] Params:
{
"benchdir": "results/evaluations/truvari/eval14_testC/GRCh38_chr21_CMRGv1.00-stvar_asm17aChr21_stvar_dipcall-default",
"reference": "resources/references/GRCh38_chr21.fa",
"regions": "results/evaluations/truvari/eval14_testC/GRCh38_chr21_CMRGv1.00-stvar_asm17aChr21_stvar_dipcall-default/candidate.refine.bed",
"use_original_vcfs": true,
"use_region_coords": false,
"recount": false,
"threads": 1,
"align": "mafft",
"mafft_params": "--auto --thread 1",
"debug": false
}
2024-01-04 17:33:39,858 [INFO] Setting up regions
2024-01-04 17:33:39,859 [INFO] 26 --includebed reduced to 7 after intersecting with 10 from --regions
2024-01-04 17:33:39,934 [INFO] 0 regions to be refined
2024-01-04 17:33:39,950 [INFO] Preparing regions
2024-01-04 17:33:39,951 [INFO] Extracting haplotypes
Traceback (most recent call last):
File "/home/nolson/mambaforge/envs/truvari_eval/bin/truvari", line 8, in <module>
sys.exit(main())
File "/home/nolson/mambaforge/envs/truvari_eval/lib/python3.9/site-packages/truvari/__main__.py", line 102, in main
TOOLS[args.cmd](args.options)
File "/home/nolson/mambaforge/envs/truvari_eval/lib/python3.9/site-packages/truvari/refine.py", line 413, in refine_main
truvari.phab(to_eval_coords, base_vcf, args.reference, phab_vcf, buffer=PHAB_BUFFER,
File "/home/nolson/mambaforge/envs/truvari_eval/lib/python3.9/site-packages/truvari/phab.py", line 338, in phab
ref_haps_fn = extract_reference(region_fn, ref_fn)
File "/home/nolson/mambaforge/envs/truvari_eval/lib/python3.9/site-packages/truvari/phab.py", line 80, in extract_reference
fout.write(samtools.faidx(ref_fn, "-r", reg_fn))
File "/home/nolson/mambaforge/envs/truvari_eval/lib/python3.9/site-packages/pysam/utils.py", line 83, in __call__
raise SamtoolsError(
pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr='```
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ACEnglish
commented on September 27, 2024
My mistake. I saw pysam and guess I stopped reading the error. I just pushed a guard into develop that should work.
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nate-d-olson
commented on September 27, 2024
Thanks! That works. I'll close the issue. Here the log from my run 2024-01-04 17:50:07,230 [INFO] Truvari v4.2.0rc1 2024-01-04 17:50:07,230 [INFO] Command /home/nolson/mambaforge/envs/truvari_eval/bin/truvari refine --threads 1 --align mafft --use-original --reference resources/references/GRCh38_chr21.fa --regions results/evaluations/truvari/eval14_testC/GRCh38_chr21_CMRGv1.00-stvar_asm17aChr21_stvar_dipcall-default/candidate.refine.bed results/evaluations/truvari/eval14_testC/GRCh38_chr21_CMRGv1.00-stvar_asm17aChr21_stvar_dipcall-default 2024-01-04 17:50:07,230 [INFO] Params: { "benchdir": "results/evaluations/truvari/eval14_testC/GRCh38_chr21_CMRGv1.00-stvar_asm17aChr21_stvar_dipcall-default", "reference": "resources/references/GRCh38_chr21.fa", "regions": "results/evaluations/truvari/eval14_testC/GRCh38_chr21_CMRGv1.00-stvar_asm17aChr21_stvar_dipcall-default/candidate.refine.bed", "use_original_vcfs": true, "use_region_coords": false, "recount": false, "threads": 1, "align": "mafft", "mafft_params": "--auto --thread 1", "debug": false } 2024-01-04 17:50:07,230 [INFO] Setting up regions 2024-01-04 17:50:07,231 [INFO] 26 --includebed reduced to 7 after intersecting with 10 from --regions 2024-01-04 17:50:07,280 [INFO] 0 regions to be refined 2024-01-04 17:50:07,293 [INFO] Preparing regions 2024-01-04 17:50:07,294 [CRITICAL] No regions to be refined. Exiting
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Related Issues (20)
- No FP or TP calls HOT 2
- Unable to run MAFFT HOT 9
- md5sum FIPS issue HOT 1
- Support vector for intra-sample merge HOT 6
- some questions about the results in fp.vcf.gz
- some questions about the results in fp.vcf.gz HOT 1
- Getting same numbers of TP-base and TP-comp HOT 4
- Suggested minor documentation changes
- Truvari, STRs and Expansion Hunter - Query HOT 2
- Bug in benchmarking HOT 4
- Request: truvari collapse --keep option to mantain the ALT sequence HOT 1
- Inquiry on the Determination of Representative Structural Variants in Merged VCF Sets HOT 2
- Truvari Collapse error HOT 1
- Same SV failed to merge HOT 1
- Q: stratify produces all-zero columns HOT 2
- INFO/END field not carried through from input VCF to output VCF HOT 3
- How to handle the "./." genotype in the merged project-level VCF? HOT 2
- Question: meaning of the parameter MINHAPLEN HOT 2
- Collapsed INFO column HOT 1
- wrong collapse? HOT 1
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