Error with snp phasing

[lilypeck]

Hello

Firstly thanks for making this great tool.

I installed duet using mamba.

I have run duet as follows

module load mamba
mamba activate duet

mkdir -p duet_out/

duet ${barcode}_haploid.final.sorted.bam \
        ${barcode}_haploid.final.fa \
        duet_out \
        -t 10

However it is hitting an error when it starts snp phasing (jobscript attached):

15:09:53 [INFO] ************************* SV CALLING COMPLETED IN 13860.038s *************************
15:09:53 [INFO] ************************* SNP PHASING STARTED *************************
[E::idx_find_and_load] Could not retrieve index file for 'duet_out/snp_calling/pileup.vcf.gz'
Could not load .tbi index of duet_out/snp_calling/pileup.vcf.gz: No such file or directory
Traceback (most recent call last):
  File "/u/home/l/ldpeck/.conda/envs/duet/bin/duet", line 31, in <module>
    main(sys.argv[1:])
  File "/u/home/l/ldpeck/.conda/envs/duet/bin/duet", line 25, in main
    snp_phasing(args.OUTPUT, args.REFERENCE, args.BAM, args.thread)
  File "/u/home/l/ldpeck/.conda/envs/duet/lib/python3.9/site-packages/duet/snp_phasing.py", line 17, in snp_phasing
    ctgs = subprocess.check_output(shlex.split('tabix --list-chroms ' + pileup_vcf_path)).decode('ascii').split('\n')[:-1]
  File "/u/home/l/ldpeck/.conda/envs/duet/lib/python3.9/subprocess.py", line 420, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "/u/home/l/ldpeck/.conda/envs/duet/lib/python3.9/subprocess.py", line 524, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['tabix', '--list-chroms', 'duet_out/snp_calling/pileup.vcf.gz']' returned non-zero exit status 1.

The output directories are as follows:

ls -l snp_calling/
4096 Mar 18 11:18 log
16108 Mar 18 11:18 merge_output.vcf.gz
72 Mar 18 11:18 merge_output.vcf.gz.tbi
4744 Mar 18 11:18 run_clair3.log
4096 Mar 18 11:18 tmp

ls -l sv_calling/
195589632 Mar 18 15:09 variants.vcf

ls -l snp_phasing/
total 0

Do you know why the snp_calling/pileup.vcf.gz is not being created?

Thanks

Lily

joblog.7969774.txt