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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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SVTyper Unknown argument #176

Closed janawold1 closed 2 years ago

janawold1 commented 2 years ago

Hello, I have installed smoove through the bioconda repo. I used to run v2.6, but started having some merge issues and decided to upgrade. However, I now get the error below across the 3 latest versions of smoove.

An example of the error is below: smoove call --name AU01 --outdir smoove/SVcalls/ --fasta reference/bSteHir1.pri.cur.20190820.fasta --genotype alignments/merged_bam/AU01.bam

[smoove] 2021/10/15 17:54:46 Super_scaffold_1 1000000 [smoove] 2021/10/15 17:54:46 > gsort version 0.1.4 [smoove] 2021/10/15 17:54:46 Calculating library metrics from alignments/merged_bam/AU01.bam... [smoove] 2021/10/15 17:54:58 Super_scaffold_2 1000000 [smoove] 2021/10/15 17:55:11 done Writing library metrics to /tmp/tempclean-366548679/333575853svtype-lib... [smoove] 2021/10/15 17:55:11 done [smoove] 2021/10/15 17:55:11 usage: svtyper [-h] [-i FILE] [-o FILE] -B FILE [-T FILE] [-l FILE] [-m INT] [-n INT] [-q] [--max_reads INT] [--split_weight FLOAT] [--disc_weight FLOAT] [-w FILE] [smoove] 2021/10/15 17:55:11 usage: svtyper [-h] [-i FILE] [-o FILE] -B FILE [-T FILE] [-l FILE] [-m INT] [-n INT] [-q] [--max_reads INT] [--split_weight FLOAT] [--disc_weight FLOAT] [-w FILE] [smoove] 2021/10/15 17:55:11 svtyper: error: unrecognized arguments: --max_ci_dist 0 [smoove] 2021/10/15 17:55:11 svtyper: error: unrecognized arguments: --max_ci_dist 0 [smoove] 2021/10/15 17:55:11 usage: svtyper [-h] [-i FILE] [-o FILE] -B FILE [-T FILE] [-l FILE] [-m INT] [-n INT] [-q] [--max_reads INT] [--split_weight FLOAT] [--disc_weight FLOAT] [-w FILE] [smoove] 2021/10/15 17:55:11 svtyper: error: unrecognized arguments: --max_ci_dist 0 panic: exit status 2

goroutine 31081 [running]: github.com/brentp/smoove/svtyper.check(...) /home/brentp/go/go/src/github.com/brentp/smoove/svtyper/svtyper.go:33 github.com/brentp/smoove/svtyper.Svtyper.func2(0xc001e7a000, 0xc000121600, 0x1, 0x1, 0x7ffe15c2227e, 0x29, 0xc001e7c0c0, 0x2c, 0xc001d7ab48, 0xc001d7ab60, ...) /home/brentp/go/go/src/github.com/brentp/smoove/svtyper/svtyper.go:179 +0x90b created by github.com/brentp/smoove/svtyper.Svtyper /home/brentp/go/go/src/github.com/brentp/smoove/svtyper/svtyper.go:165 +0xab2

brentp commented 2 years ago

Hi, you must have a very old version of svtyper. You should be able to run svtyper -h and see this in the help:

  --max_ci_dist INT     maximum size of a confidence interval before 95% CI is used intead (default: 1e10)

and you can also see the version in the output, it should be v0.7.0 (or higher)

janawold1 commented 2 years ago

That'll be it, the version installed with conda install smoove is svtyper v.0.1.4. I'll see if I can update it to the appropriate version now. *Edit To get this solution to work, I had to uninstall smoove, explicitly uninstall SVTyper, then explicitly install it before installing smoove. Fingers crossed this is all that's needed. Thank you so much for your help!

user-tq commented 1 year ago

I met the same problem，because i install smoove from conda，It's like a prank。conda install all softs，but the svtyper cant be used. finally, i run this cmd to install newst version by conda，Now it runs smoothly.

conda install  smoove=0.2.8  -c bioconda
conda install  svtyper=0.7.1  -c bioconda