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

[C-YONG]

I'd like to ask you, has the problem been solved?

[afurches]

I am also having the same problem.

[brentp]

Hi, this means you need to use a newer version of htslib.

[afurches]

Hi, I'm using htslib v1.20 and duphold v0.1.4 (both bioconda). I've tried different versions of htslib to no avail. I also tried updating duphold but conda tells me "All requested packages are already installed" if I don't specify a version, and that newer specified versions are incompatible with other packages in the environment (in a fresh conda environment install of smoove and all dependencies). Smoove ran just fine if duphold was omitted. Thanks.

[benstemon]

I am having the same problem. I have tried different versions of htslib as well (including initial v1.20) and duphold always gives error message: "could not import: bam_hdr_destroy". Even a clean install of the conda version of duphold(v0.1.4) produces this error. It appears the conda install for duphold is the issue.

To get around this, I installed duphold from the github version here and replaced the default install (v0.1.4) with this new install (v0.2.3) in the bin for the conda environment for smoove. This appears to have fixed the problem

[brentp]

@benstemon that's the best way. The github version is a static binary so has no dependencies. I don't know what's going on with the conda version.