Correct path for conda environment

[yifangt]

Following my other post I was trying to create vcf from maf files with following line:

export PATH=/storage/proj/Pea_hapmap/yifang/data/phg2/phg/bin:${PATH}
export JVM_OPTS="-Xmx500g"

phg create-maf-vcf \
    --db-path ${DIR_PROJ}/data/phg2/vcf_dbs \
    --bed ${DIR_PROJ}/data/phg2/output/ranges.bed \
    --reference-file ${REF_FASTA} \
    --maf-dir ${DIR_IN} \
    --metrics-file ${DIR_OUT}/VCFMetrics.tsv \
    --output-dir ${DIR_OUT} \
    --conda-env-prefix ${DIR_PROJ}/miniforge3/envs/phgv2-conda

and I got errors:

queryAgc: Running Agc Command:
conda run -p phgv2-conda agc getctg /storage/proj/Pea_hapmap/yifang/data/phg2/vcf_dbs/assemblies.agc 
chr1LG6@Ref:35278-46135 
chr1LG6@Ref:46136-58346 
...

[main] ERROR net.maizegenetics.phgv2.utils.SeqUtils 2025-03-10 09:13:42,148: queryAgc: errors found in errorStream: 3
Exception in thread "main" java.lang.IllegalArgumentException: 
Error running AGC command: 
conda run -p phgv2-conda agc getctg /storage/proj/Pea_hapmap/yifang/data/phg2/vcf_dbs/assemblies.agc 

chr1LG6@Ref:35278-46135

****

chr1LG6@Ref:372142870-372145594

Error: [, EnvironmentLocationNotFound: Not a conda environment: /storage/proj/Pea_hapmap/yifang/data/phg2/scripts/phgv2-conda, ]

        at net.maizegenetics.phgv2.utils.SeqUtilsKt.queryAgc(SeqUtils.kt:386)

which tells the path to phgv2-conda environment is wrong.
I believe the option --conda-env-prefix ${DIR_PROJ}/miniforge3/envs/phgv2-conda is correct as there was no error to run phg create-ref-vcf and the assemblies.agc was successfully generated without error.
What did I miss?
Thank you!

[btmonier]

Hi @yifangt - I believe this is a bug due to the Conda environment prefix not being passed properly to one of the internal process builder functions. I will submit a bugfix for this issue soon.

[yifangt]

Thank you!

[btmonier]

Hi @yifangt - a new release of PHGv2 is out that should resolve this issue:

https://github.com/maize-genetics/phg_v2/releases/tag/2.4.48.203

[yifangt]

For your reference after I gave it a try for this new version.
The conda env path error went away, but with a new error:

conda run -p /storage/ppl/yifang/miniforge3/envs/phgv2-conda agc getctg /storage/proj/Pea_hapmap/yifang/data/phg2/vcf_dbs/assemblies.agc chr1LG6@Ref:3...
Exception in thread "main" java.lang.NullPointerException
        at net.maizegenetics.phgv2.cli.CreateMafVcf.buildSeq(CreateMafVcf.kt:526)
        at net.maizegenetics.phgv2.cli.CreateMafVcf.addSequencesToMetaData(CreateMafVcf.kt:510)
        at net.maizegenetics.phgv2.cli.CreateMafVcf.convertGVCFToHVCFForChrom(CreateMafVcf.kt:276)
        at net.maizegenetics.phgv2.cli.CreateMafVcf.convertGVCFToHVCF(CreateMafVcf.kt:182)
        at net.maizegenetics.phgv2.cli.CreateMafVcf.createASMHvcfs(CreateMafVcf.kt:103)
        at net.maizegenetics.phgv2.cli.CreateMafVcf.run(CreateMafVcf.kt:631)
        at com.github.ajalt.clikt.parsers.Parser.parse(Parser.kt:306)
        at com.github.ajalt.clikt.parsers.Parser.parse(Parser.kt:319)
        at com.github.ajalt.clikt.parsers.Parser.parse(Parser.kt:40)
        at com.github.ajalt.clikt.core.CliktCommand.parse(CliktCommand.kt:458)
        at com.github.ajalt.clikt.core.CliktCommand.parse$default(CliktCommand.kt:455)
        at com.github.ajalt.clikt.core.CliktCommand.main(CliktCommand.kt:475)
        at com.github.ajalt.clikt.core.CliktCommand.main(CliktCommand.kt:482)
        at net.maizegenetics.phgv2.cli.PhgKt.main(Phg.kt:42)

No further error information can be found to debug.
This is following the leftover of my last run continued with all the existing results. Maybe I should restart the whole process from the beginning. Thanks again!

[zrm22]

This looks like there is likely a chromosome naming issue between your files. If a redo does not fix please submit an Issue so we can accurately track it specifically.