Unable to use the tool

[adhisadi]

I am unable to use the tool. I installed vartrix with the source code. I also installed Rust from within the directory containing the VarTrix source code. I have these inside my directory : Cargo.lock Cargo.toml LICENSE README.md VarTrix_WorkFlow.png ci construct_linux_binary.py src target test

These are my issues: I get this error with cargo build --release [ERROR] The resulting matrix has a sum of 0. Did you use the --umi flag on data without UMIs?

I do not see vartrix inside "target/release/"

And I get vartrix: command not found. Could you help me installation or usage issue I am dealing with?

[XUEbaogai0101]

Hi @adhisadi, I am encountering the same "issue". Were you able to solve this?

Here I share the command line I am using and the results:

cargo test --release

Compiling vartrix v1.1.22 (/data/user/*/vartrix-1.1.22)
Finished release [optimized + debuginfo] target(s) in 24.28s
Running unittests src/main.rs (target/release/deps/vartrix-c59c3ec5b2fc0f12)
running 7 tests
test tests::test_frac_matrix ... ok
test tests::test_coverage_matrices_umi ... ok
test tests::test_consensus_matrix ... ok
test tests::test_coverage_matrices_umi_gzipped_bcs ... ok
test tests::test_coverage_matrices ... ok
22:48:17 [ERROR] The resulting matrix has a sum of 0. Did you use the --umi flag on data without UMIs?
test tests::test_coverage_matrices_umi_dna ... ok
test tests::test_coverage_matrices_dna ... ok
test result: ok. 7 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.96s

Best, XUE

[pmarks]

@XUEbaogai0101 You need to run cargo build --release - that will create the vartrix program at target/release/vartrix. Here you've run cargo test --release which just runs the built-in unit tests. @adhisadi is that potentially the same problem you were seeing? I'll close this issue - please re-open if you're still having problems.

[ErminZ]

Update, the [ERROR] The resulting matrix has a sum of 0. Did you use the --umi flag on data without UMIs in my case is caused by the barcodes (TTGGAACAGTACGACG-1) are not matched in the BAM file (TTGGAACAGTACGACG).

VarTrix installation: wget https://github.com/10XGenomics/vartrix/releases/download/v1.1.22/vartrix_linux

mv vartrix_linux vartrix
chmod +x vartrix
./vartrix --help

To run vartrix, no matter use --umi or not, using different bam input, always get the same error: The resulting matrix has a sum of 0. Did you use the --umi flag on data without UMIs

./vartrix -v ../clair3/merge_output.vcf -b ../.tagged.bam \
-f GCA_set.fna \
-c barcodes.tsv.gz \
--out-matrix ../vartrix/out_matrix.mtx \
--umi --threads 4