Failed to liftover chromosomes with picard

[tahashmi]

Hi, can someone look what is causing this issue? my *.ini file is attached as text. Thanks.

hatchet.txt

        snps: https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/GATK/00-All.vcf.gz
        reference: /data/references/grch38_chr.fasta
        j: 16
        q: 0
        Q: 11
        E: False
        mincov: 8
        maxcov: 300
        outputsnps: /gpfs/gsfs12/users/ahmadt2/hatchet/output/snps
        verbose: False
^[[0m^[[1m^[[95m[2023-Jul-21 23:52:40]# Inferring SNPs from the normal sample
^[[0m^[[2K^M^[[96mProgress:^[[0m |----------------------------------------| ^[[96m0.0% Complete^[[0m ^[[96m[[2023-Jul-21 23:52:40]Caller-1 starts on Normal for chr3)]^[[0m^[[2K^M^[[96mProgress:^[[0m |████████████████████████████████████████| ^[[96m100.0% Complete^[[0m ^[[96m[[2023-Jul-22 00:28:26]Caller-1 ends on Normal for chr3)]^[[0m
^[[1m^[[95m[2023-Jul-22 00:28:26]# Counting number of identified SNPs
^[[0m^[[92m695473 SNPs have been identified in total
^[[0m^[[1m^[[95m[2023-Jul-22 00:28:26]# SNP Calling is concluded
^[[0m^[[92m## Called SNPs have been written per chromosome in:
/gpfs/gsfs12/users/ahmadt2/hatchet/output/snps/chr3.vcf.gz
^[[0m^[[1m^[[95m[2023-Jul-22 00:28:26]# log notes
^[[0m^[[92m
        refpaneldir: data/panel
        j: 16
        chromosomes: ['3']
        snps: {'3': 'output/snps/chr3.vcf.gz'}
        refvers: hg38
        chrnot: True
        refgenome: /data/references/grch38_chr.fasta
        outdir: /gpfs/gsfs12/users/ahmadt2/hatchet/output/phase
        shapeit: shapeit
        picard: picard -Xmx8g
        bcftools: bcftools
        bgzip: bgzip
^[[0m^[[91mpicard -Xmx8g LiftoverVcf -I output/snps/chr3.vcf.gz -O /gpfs/gsfs12/users/ahmadt2/hatchet/output/phase/3_lifted.vcf.gz -CHAIN data/panel/hg38ToHg19.chr.chain -R data/panel/hg19_no_chr.fa -REJECT /gpfs/gsfs12/users/ahmadt2/hatchet/output/phase/3_rejected.vcf.gz --WARN_ON_MISSING_CONTIG true^[[0m^[[91mFailed to liftover chromosomes with picard on output/snps/chr3.vcf.gz.^[[0m^[[2K^M^[[96m[2023-Jul-22 00:28:27]^[[0m
^[[96mProgress:^[[0m |████████████████████████████████████████| ^[[96m100.0% Complete^[[0m
Traceback (most recent call last):
  File "/gpfs/gsfs12/users/ahmadt2/conda/envs/hatchet/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/gpfs/gsfs12/users/ahmadt2/conda/envs/hatchet/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/gpfs/gsfs12/users/ahmadt2/conda/envs/hatchet/lib/python3.9/site-packages/hatchet/__main__.py", line 65, in <module>
    sys.exit(main())
  File "/gpfs/gsfs12/users/ahmadt2/conda/envs/hatchet/lib/python3.9/site-packages/hatchet/__main__.py", line 61, in main
    globals()[command](args)
  File "/gpfs/gsfs12/users/ahmadt2/conda/envs/hatchet/lib/python3.9/site-packages/hatchet/utils/run.py", line 155, in main
    phase_snps(
  File "/gpfs/gsfs12/users/ahmadt2/conda/envs/hatchet/lib/python3.9/site-packages/hatchet/utils/phase_snps.py", line 88, in main
    vcfs = phaser.run(work=phaser_args, n_instances=n_instances)
  File "/gpfs/gsfs12/users/ahmadt2/conda/envs/hatchet/lib/python3.9/site-packages/hatchet/utils/multiprocessing.py", line 98, in run
    raise result.__class__(f'WORK {work_i} FAILED\n\n{error_string}')
RuntimeError: WORK 0 FAILED

Traceback (most recent call last):
  File "/gpfs/gsfs12/users/ahmadt2/conda/envs/hatchet/lib/python3.9/site-packages/hatchet/utils/multiprocessing.py", line 32, in run
    result = self.worker.work(*args)
  File "/gpfs/gsfs12/users/ahmadt2/conda/envs/hatchet/lib/python3.9/site-packages/hatchet/utils/phase_snps.py", line 198, in work
    vcf_toFilter = self.liftover(
  File "/gpfs/gsfs12/users/ahmadt2/conda/envs/hatchet/lib/python3.9/site-packages/hatchet/utils/phase_snps.py", line 278, in liftover
    error(
  File "/gpfs/gsfs12/users/ahmadt2/conda/envs/hatchet/lib/python3.9/site-packages/hatchet/utils/Supporting.py", line 137, in error
    return log(
  File "/gpfs/gsfs12/users/ahmadt2/conda/envs/hatchet/lib/python3.9/site-packages/hatchet/utils/Supporting.py", line 124, in log
    raise exception_class(msg)
ValueError: Failed to liftover chromosomes with picard on output/snps/chr3.vcf.gz.