IndexError from Smoove calls

[cagaser]

Hi Brent,

I have calls from 4 SV-callers for all my 5 samples then ran DUPHOLD before merging. In 2/5 samples, DUPHOLD failed on predictions from 1 SV-caller (SMOOVE), the rest were fine. This was the error message I got:

fatal.nim(39)            sysFatal
Error: unhandled exception: index -1 not in 0 .. 185590 [IndexError]  

Is there any way I can find out why this happening? I am using this current version: quay.io/biocontainers/duphold:0.2.1--h516909a_1

Thanks in advance!

[brentp]

Hi, can you try with v0.2.3, the latest version to make sure this hasn't been fixed?

[cagaser]

Sorry, but how can I run the new release? The bioconda has not been updated yet.

[brentp]

you can download the binary from here: https://github.com/brentp/duphold/releases/tag/v0.2.3

[cagaser]

I am not really sure how to run this as I have been using either the conda env. or dockerimage. I tried installing nim and compile the source code but I don't think I'm doing it the right way :(

nim compile src/duphold.nim.cfg 
Error: invalid module name: duphold.nim

Tried also running it but:

nim r src/duphold.nim
duphold-0.2.3/src/duphold.nim(1, 8) Error: cannot open file: hts

[brentp]

just download it:

wget https://github.com/brentp/duphold/releases/download/v0.2.3/duphold
chmod +x ./duphold
./duphold -h

[brentp]

you could also check that the smoove file is valid. and if you can provide the full command you ran and/or a small file so i can reproduce the error, i can look into it more.

[cagaser]

just download it:

wget https://github.com/brentp/duphold/releases/download/v0.2.3/duphold
chmod +x ./duphold
./duphold -h

I did but: -bash: ./duphold: cannot execute binary file: Exec format error I'm running it on Mac btw.

you could also check that the smoove file is valid. and if you can provide the full command you ran and/or a small file so i can reproduce the error, i can look into it more.

        export DUPHOLD_SAMPLE_NAME=~{sample}
        duphold \
        -v ~{inputVcf} \
        -b ~{bamFile} \
        -f ~{referenceFasta} \
        -o ~{outputPath}

[cagaser]

Hi,

I managed to run duphold on ubuntu. I ran it and I get the following:

./duphold -v smoove.vcf -b markdup.bam -f reference.fa -o smoove.duphold.vcf                            
[duphold] trying sample name from env:D
[W::vcf_parse_info] INFO/END=15195 is smaller than POS at chr17_GL000205v2_random:4294967296                                     
weird variant:Variant(chr17_GL000205v2_random:4294967296 N/<DUP>)                                                                
SIGSEGV: Illegal storage access. (Attempt to read from nil?)

This is from the VCF.

chr17_GL000205v2_random 4294967296      chr17_GL000205v2_random_0       N       <DUP>   675.05  .       AC=1;AN=2;CIEND=-30,395;CIEND95=-2,244;CIPOS=0,506;CIPOS95=0,355;END=15195;IMPRECISE;PE=6;SR=0;STRANDS=-+:6;SU=6;SVLEN=15195;SVTYPE=DUP GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB   0/1:99:675.05:-69,-1,-11:418:340:77:339:76:168:2:55:171:19:0.18

Is this SMOOVE-related issue then with END having a smaller value than POS?