dxCompiler fails to compile example scripts like bam_chrom_counter

[tprodanov]

Similar to problems, reported by this user, I cannot compile any WDL scripts on my machine, even standard ones like HLA arcas or Bam chrom coutner.

I have java

openjdk 21.0.2-internal 2024-01-16
OpenJDK Runtime Environment (build 21.0.2-internal-adhoc.conda.src)
OpenJDK 64-Bit Server VM (build 21.0.2-internal-adhoc.conda.src, mixed mode, sharing)

and I tried dxCompiler 2.14.0, 2.10.9 and 2.4.10, all failed with error

  bad constant pool index: 0 at pos: 48461
     while compiling: <no file>
        during phase: globalPhase=<no phase>, enteringPhase=<some phase>
     library version: version 2.13.7
    compiler version: version 2.13.7
  reconstructed args: -dependencyfile none -deprecation -Wconf:cat=deprecation:w -Wconf:cat=deprecation:ws -Wconf:cat=feature:ws -Wconf:cat=optimizer:ws -classpath /home/tim>

  last tree to typer: EmptyTree
       tree position: <unknown>
            tree tpe: <notype>
              symbol: null
           call site: <none> in <none>

You can find the full log here.

Thank you in advance,
Timofey

[tprodanov]

In respect to my own script, I get even stranger error invalid runtime keyword docker,

version 2.0

struct Reference {
    File fasta
    File fai
    File kmer_counts
}

struct Cram {
    File cram
    File crai
}

task locityper_preproc {
    input {
        Cram cram
        Reference ref
        Int threads
    }
    String prefix = basename(cram.cram, ".cram")

    command <<<
        set -x -e -o pipefail
        out=bg.${RANDOM}${RANDOM}
        time locityper preproc \
            -a ~{cram.cram} \
            -o ${out} \
            -r ~{ref.fasta} \
            -j ~{ref.kmer_counts} \
            -@ ~{threads}
        mv ${out}/distr.gz ~{prefix}.gz
        rm -r ${out}
    >>>
    output {
        File bg = "~{prefix}.gz"
    }
    runtime {
        docker: "dx://project-...:/Timofey/Locityper/locityper.v1.0.0.tar.gz"
        dx_timeout: "48H"
        dx_instance_type: "mem1_ssd1_v2_x8"
    }
}

You can find corresponding log file here.

[e-dorigatti]

Ran into the same problem with my own workflow, it's probably an issue with java rather than dxCompiler. Anyways, I could compile my workflow using the docker image.