smoove genotype - could not import: bam_hdr_destroy

[heidihyang]

Hi,

I get this error for a lot of the samples I'm running, although I do seem to have a complete genotyped file for each bam I have.

[smoove] 2023/09/06 14:45:21 [W::vcf_parse_info] INFO/END=60935357 is smaller than POS at CM012294.1:60935394
[smoove] 2023/09/06 14:45:48 2023/09/06 14:45:48 time to merge 2 files: 31.395
[smoove] 2023/09/06 14:45:49 [W::tbx_parse1] VCF INFO/END=60935357 is smaller than POS at CM012294.1:60935393
This tag will be ignored. Note: only one invalid END tag will be reported.
[smoove] 2023/09/06 14:45:49 [smoove] 2023/09/06 14:45:49 starting with version 0.2.8
[smoove] 2023/09/06 14:45:49 [smoove] 2023/09/06 14:45:49 running duphold on 1 files in 36 processes
[smoove] 2023/09/06 14:45:49 [smoove] 2023/09/06 14:45:49 **could not import: bam_hdr_destroy**
[smoove] 2023/09/06 14:45:49 2023/09/06 14:45:49 exit status 1
2023/09/06 14:45:49 exit status 1

I ran this command:

smoove genotype -d -x -p 1 --name ${sample}-joint --outdir \
$SCRATCH/smoove_output_test/results_genotyped/ --fasta $HOME/ref/Qlob.ref.v3.2.fasta \
--vcf merged.test.sites.vcf.gz $SCRATCH/merged_bams/${sample}

I was wondering what the bam_hdr_destroy file is and why it's not importing? Or if the issue is related to the former part of the joblog about the end position being smaller. Thanks!

Heidi

[Sreelekshmi-291]

Hey Does anybody have any insights as to why this might be happening? I ran into the same issue.

This was my command smoove call --name VY04480246BQ_smoove_d --fasta Human_hg38/GRCh38_full_analysis_set_plus_decoy_hla.fa -p 50 -o SV_analysis_Smoove/VY04480246BQ_smoove_d --duphold --genotype VY04480246BQ.bam

It ran without any error when I did not use --duphold. Do you think it is because there is some version issue for htslib? I have htslib 1.17 .

Thank you

[Sreelekshmi-291]

Also, just to be clear, calling Smoove separately shows that I already have duphold installed.

Calling duphold alone gives me the same error as mentioned in the above comment, but when its called with smoove it works.

[Sreelekshmi-291]

I tried running it with smoove duphold, smoove duphold --fasta GRCh38_full_analysis_set_plus_decoy_hla.fa --vcf SV_analysis_Smoove/CO70607861FC_smoove/CO70607861FC_smoove-smoove.genotyped.vcf.gz --processes 50 --outvcf SV_analysis_Smoove/CO70607861FC_smoove-smoove.genotyped_duphold.vcf.gz CO70607861FC.bam

It gives the same error