giraffe.wdl run failed with "ERROR task indexReference"

[gsc74]

@adamnovak , @edawson
I have used the following command to run the giraffe.wdl workflow with the miniwdl (v1.11.1)

Command used run wdl workflow

miniwdl run --as-me ../workflows/giraffe.wdl -i giraffe.json

Error:

2024-01-24 04:51:01.997 wdl.w:Giraffe.t:call-indexReference NOTICE docker image :: tag: "quay.io/cmarkello/samtools_picard:latest", id: "sha256:519e0674c0a68a0f8f24012689c14a735775b1347b559ded44ac29a30dfa7829", RepoDigest: false
2024-01-24 04:51:02.962 wdl.w:Giraffe.t:call-runVGGIRAFFEpe-04-04fq_chunk_1part NOTICE docker task running :: service: "lia3wppb8s", task: "ymlwwixbzj", node: "fq1i9mz6t9", message: "started"
2024-01-24 04:51:05.337 wdl.w:Giraffe.t:call-indexReference NOTICE docker task running :: service: "7xxfkl8pgi", task: "dx8sm5u3d8", node: "fq1i9mz6t9", message: "started"
2024-01-24 04:51:06.566 wdl.w:Giraffe.t:call-indexReference ERROR docker task failed :: service: "7xxfkl8pgi", task: "dx8sm5u3d8", node: "fq1i9mz6t9", message: "task: non-zero exit (255)"
2024-01-24 04:51:06.566 wdl.w:Giraffe.t:call-indexReference ERROR docker task exit :: state: "failed", exit_code: 255
2024-01-24 04:51:06.602 wdl.w:Giraffe.t:call-indexReference ERROR task indexReference (../tasks/bioinfo_utils.wdl Ln 3 Col 1) failed :: dir: "/home/ghanshyam/Project_Y/WDL/vg_wdl/data_mg/20240123_192046_Giraffe/call-indexReference", error: "CommandFailed", exit_status: 255, stderr_file: "/home/ghanshyam/Project_Y/WDL/vg_wdl/data_mg/20240123_192046_Giraffe/call-indexReference/stderr.txt", stdout_file: "/home/ghanshyam/Project_Y/WDL/vg_wdl/data_mg/20240123_192046_Giraffe/call-indexReference/stdout.txt"
2024-01-24 04:51:06.696 wdl.w:Giraffe ERROR call failure propagating :: from: "call-indexReference", dir: "/home/ghanshyam/Project_Y/WDL/vg_wdl/data_mg/20240123_192046_Giraffe"
2024-01-24 04:51:06.697 wdl.w:Giraffe NOTICE aborting workflow
2024-01-24 04:51:06.788 wdl.w:Giraffe.t:call-runVGGIRAFFEpe-04-04fq_chunk_1part ERROR task runVGGIRAFFE (../tasks/vg_map_hts.wdl Ln 33 Col 1) failed :: dir: "/home/ghanshyam/Project_Y/WDL/vg_wdl/data_mg/20240123_192046_Giraffe/call-runVGGIRAFFEpe-04-04fq_chunk_1part", error: "Terminated

The output of the error file /home/ghanshyam/Project_Y/WDL/vg_wdl/data_mg/20240123_192046_Giraffe/call-indexReference/stderr.txt

+ ln -s /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/ref.fa ref.fa
+ samtools faidx ref.fa
Could not build fai index ref.fa.fai

The size of /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/ref.fa is 0.

The input graph is generated from the Minigraph-Cactus (v2.6.7) pipeline with the following commands:

cactus-pangenome ./js-chm13_mg ./hprc-v1.1-mc.seqfile --outName hprc-v1.1-mg-chm13 --outDir hprc-v1.1-mg-chm13 --reference CHM13 --filter 9 --giraffe clip filter  --gbz clip filter  --maxCores 48  --indexCores 32 --mapCores 8 --batchSystem single_machine

Input hprc-v1.1-mc.seqfile has the following haplotypes

CHM13   haps/CHM13Y.fa
HG00438.1   haps/HG00438.1.fa
HG00438.2   haps/HG00438.2.fa
HG005.1 haps/HG005.1.fa
HG005.2 haps/HG005.2.fa
HG00621.1   haps/HG00621.1.fa
HG00621.2   haps/HG00621.2.fa
HG00673.1   haps/HG00673.1.fa
HG00673.2   haps/HG00673.2.fa
HG00733.1   haps/HG00733.1.fa
HG00733.2   haps/HG00733.2.fa
HG00735.1   haps/HG00735.1.fa
HG00735.2   haps/HG00735.2.fa
HG00741.1   haps/HG00741.1.fa
HG00741.2   haps/HG00741.2.fa
HG01071.1   haps/HG01071.1.fa
HG01071.2   haps/HG01071.2.fa
HG01106.1   haps/HG01106.1.fa
HG01106.2   haps/HG01106.2.fa

I have used filtered graphs and the giraffe.json file has the following inputs

 {
  "Giraffe.INPUT_READ_FILE_1": "../../../WGS/HG002.NovaSeq.pcr-free.35x.R1.fastq.gz",
  "Giraffe.INPUT_READ_FILE_2": "../../../WGS/HG002.NovaSeq.pcr-free.35x.R2.fastq.gz",
  "Giraffe.GBZ_FILE": "hprc-v1.1-mg-chm13.d9.gbz",
  "Giraffe.REFERENCE_PREFIX": "CHM13",
  "Giraffe.SAMPLE_NAME": "CHM13_HG002_mg_",
  "Giraffe.MIN_FILE": "hprc-v1.1-mg-chm13.d9.min",
  "Giraffe.DIST_FILE": "hprc-v1.1-mg-chm13.d9.dist",
  "Giraffe.OUTPUT_GAF": true,
  "Giraffe.OUTPUT_CALLING_BAMS": true,
  "Giraffe.OUTPUT_SINGLE_BAM": true,
  "Giraffe.MAP_MEM": 150,
  "Giraffe.HAPLOTYPE_SAMPLING": true,
  "Giraffe.IN_DIPLOID": true
}

Also, the ref.fa and ref.fa.fai files are present in the ./ folder, which is CHM13Y.fa and its index file.

It seems vg is not able to extract the ref.fa from the graph. Can't we just pass ref.fa and ref.fa.fai from giraffe.json file?