vcfeval: Error: An IO problem occurred: "Expected file missing"

[Charles Warden]

Hi,

I am test vcfeval based upon some feedback from this Biostars discussion.

To start, I am testing an example of VCF compared to itself (since the discussion related to such a situation and whether the calculated F1 value was equal to 1).

The specified output folder was created, and I have attached a copy of the vcfeval.txt (from within that folder).

The output captured from the command was "Error: An IO problem occurred: "Expected file missing".

The command being run is as follows:

TEST=../../GIAB-hg38_latest-230726/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
REF=../../GIAB-hg38_latest-230726/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
OUT=CALLABLE-GAIB_v4.2.1-vs-GAIB_v4.2.1
SDF=../../../EPI2ME/giab_lsk114_2022.12/copied_files/analysis/benchmarking/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.sdf
BED=../../GIAB-hg38_latest-230726/SupplementaryFiles/HG002_GRCh38_1_22_v4.2.1_callablemultinter_gt0.bed
THREADS=4

/path/to/rtg-tools-3.12.1/rtg vcfeval -T $THREADS -Z --bed-regions=$BED -b $REF -c $TEST -o $OUT -t $SDF

Can you please help me determine what file or files are not being recognized (or what other issue is occurring)?

With "less" or "ls" commands, I believe the file paths should all be correct.

Thank you very much!

Sincerely,

Charles

[Len Trigg]

Hi Charles,

That error is produced when there is some corruption in the SDF (in particular one of the files within the SDF directory is missing). I would suggest using rtg format to re-create the reference SDF from your original fasta.

Cheers,

Len.

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[Charles Warden]

Hi Len,

Thank you very much for your prompt response.

I was using a .sdf file/folder downloaded from Nanopore (for this dataset).

I have gone back to create a file from the original reference sequence file using the following command:

FA=../../../EPI2ME/giab_lsk114_2022.12/copied_files/analysis/benchmarking/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
SDF=GCA_000001405.15_GRCh38_no_alt_analysis_set.sdf

/path/to/rtg format -o $SDF $FA

I then used this .sdf file for running rtg vcfeval, instead of the provided .sdf file.

This solves that particular error message - so, thank you!

I believe this is the main output summary when that VCF is compared to itself:

Threshold  True-pos-baseline  True-pos-call  False-pos  False-neg  Precision  Sensitivity  F-measure
----------------------------------------------------------------------------------------------------
   25.000            4022526        4022526          0      17539     1.0000       0.9957     0.9978
     None            4040028        4040028         37         37     1.0000       1.0000     1.0000

Again, thank you very much!

Sincerely,

Charles