gimbleprep: error code 255 - unknown file type

[juanitagutierrez]

Hi,

I am using gimbleprep. The job proceeds as expected until it has to create the filtered vcf (note: it does create multi_callable.bed).

These are the commands I am using: source activate gimbleprep_again conda activate gimbleprep_again

Then: gimbleprep --fasta_file assembly_final_corrected.fa --vcf_file prefiltered.biallelic_snp.inv.masked_reps.ab_0.2_0.8.subset_6000000.vcf.gz --bam_dir bam_files --snpgap 2 --min_qual 8 --min_depth 10 --max_depth 2 --threads 6 --keep_tmp --outprefix test_gimbleprep

The error: bcftools norm --threads 6 -Ov -f path/to/assembly_final_corrected.fa path/to/prefiltered.biallelic_snp.inv.masked_reps.ab_0.2_0.8.subset_6000000.vcf.gz | vcfallelicprimitives --keep-info --keep-geno -t decomposed | bcftools plugin fill-AN-AC --threads 6 -Oz | bcftools filter --threads 6 -Oz -s Qual -m+ -e 'QUAL<10' | bcftools filter --threads 6 -Oz -m+ -s+ --SnpGap 2 | bcftools filter --threads 6 -Oz -e 'TYPE!="snp"' -s NonSnp -m+ > tmp_gimble_ape6un8i/vcf.filtered.vcf.gz (STDERR): 'Failed to read from standard input: unknown file type\nFailed to read from standard input: unknown file type\nFailed to read from standard input: unknown file type\nFailed to read from standard input: unknown file type'

Also, I must clarify that I used bcftools instead of freebayes to create the vcf. Is this expected to cause issues of this kind? Since I knew that the main problem would be that allele imbalance filters couldn't be applied unless freebayes was used, I also pre-filtered for allele imbalance using bcftools. Thanks in advance for any help you can provide!

[XieHongX]

Hi I met with the same issue. Any idea of the problem?

[GertjanBisschop]

Hi both, At the moment gimbleprep only supports vcfs generated by freebayes. I totally get this is probably frustrating from your end. What we actually need is a parser that translates any vcf into an array to be used by gimble, using sgkit for example. If any of you would be up for that challenge then definitely let us know and we'll give you pointers on how to get started. (see #19)

[XieHongX]

Hi, it turns out this is not an issue with the input but the software setup. check here: https://github.com/LohseLab/gimbleprep/issues/18

[XieHongX]

installing gimbleprep using conda install -c bioconda vcflib=1.0.3 tabixpp=1.1.0 gimbleprep solves the problem. I highly recommend adding this to the condo package or in the user manual

[GertjanBisschop]

Thanks @XieHongX for looking into this! I will pin these package requirements.