AnnotSV BioConda Environment: Reference Issues For GRCh38

[yr542]

I used the commands to create a reference for AnnotSV:

wget http://ftp.ensembl.org/pub/release-
111/gtf/homo_sapiens/Homo_sapiens.GRCh38.111.chr.gtf.gz
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred
chmod +x gtfToGenePred
gunzip Homo_sapiens.GRCh38.111.chr.gtf.gz
./gtfToGenePred -genePredExt -geneNameAsName2 -includeVersion \
Homo_sapiens.GRCh38.111.chr.gtf refGene.txt
for i in 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7 8 9 M MT X Y;do \
awk -v chr=$i '$2 ==chr {print
$2"\t"$4"\t"$5"\t"$3"\t"$12"\t"$1"\t"$6"\t"$7"\t"$9"\t"$10}' \
refGene.txt | sed 's/^MT/M/' | sort -k1,1 -k2,2n -k3,3n >>
refGene.sorted.tmp.tmp.bed; done
grep -v "none" refGene.sorted.tmp.tmp.bed > refGene.sorted.tmp.bed
rm gtfToGenePred Homo_sapiens.GRCh38.111.chr.gtf refGene.txt
refGene.sorted.tmp.tmp.bedhttp://ftp.ensembl.org/pub/release-111/gtf/homo_sapiens/Homo_sapiens.GRCh38.111.chr.gtf.gzhttp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred

but AnnotSV would not accept it saying:

...checking the annotation data sources (September 05 2024 - 13:23)
############################################################################
"" file doesn't exist
Please check your install - Exit with error.
############################################################################

My commands for AnnotSV in both cases:

AnnotSV -SVinputFile "path/to/my/vcf/file" \
        -outputDir "/full/path/to/my/output/directory" \
        -genomeBuild GRCh38 \
        -annotationsDir "/the/full/path/to/my/reference/directory"

I also tried the work around using INSTALL_annotations.shbut I do not believe the annotations are for Ensembl?

[lgmgeo]

I'm quite surprised by your request.
Why did you try to update the refGene.sorted.bed file with the same ENSEMBL version (GRCh38.111) as the one distributed?

Can you show me the output of the following command lines:

ls -l $ANNOTSV/share/AnnotSV/Annotations_Human/Genes/GRCh38/
ls -l $ANNOTSV/share/AnnotSV/Annotations_Human/*

[yr542]

Hello @lgmgeo I was trying to test it out so I can modify the reference as needed but so far:

I activate the conda environment then I did the commands you suggested:

Suggested command 1:

ls -l $ANNOTSV/share/AnnotSV/Annotations_Human/Genes/GRCh38/

Result Of Command 1:

ls: cannot access '/share/AnnotSV/Annotations_Human/Genes/GRCh38/': No such file or directory

Suggested Command 2:

ls -l $ANNOTSV/share/AnnotSV/Annotations_Human/*

Result Of Command 2:

ls: cannot access '/share/AnnotSV/Annotations_Human/*': No such file or directory

This was why I had to try with the references. But I did find a work around using the INSTALL_annotations.sh command in the BioConda environment. But I believe it uses RefSeq annotations not Ensembl?

[lgmgeo]

The ANNOTSV environment variable is not defined in your conda environment.
That's why it's not working.

[yr542]

Thank you for your response. Then what path would you suggest to define this $ANNOTSV variable given this in a bioconda environment? Is there an example?

[lgmgeo]

I can't understand totally, because this should work by using the -annotationsDir option.

see #184:

can you try binding the directory with your input files and annotations directory to the container? This can be done with --bind (see here for more information about this).

[yr542]

I am not sure what I did wrong? I had to create references using the INSTALL_annotations.sh command -

1. there was no path for $ANNOTSV,
2. I did try the binding with singularity but it did not work.
3. It rendered AnnotSV un-usable via Singularity. I am now using the bioconda.

[lgmgeo]

Sorry, I'm definitely not an expert with singularity or bioconda.

@nvnieuwk, can you help @yr542 ?

[nvnieuwk]

Have you tried installing annotsv in a fresh conda environment?

[yr542]

@nvnieuwk yes I have used a fresh conda environment. The issue still remains.

[nvnieuwk]

Strange :/ Can you give me some more information on your system? What OS are you using? What conda/mamba version are you using?

[yr542]

@nvnieuwk

### Basic Information:

System version: Debian 10
Conda Version: 23.11.0
Python Version: 3.11.5

[nvnieuwk]

Hmm all looks fine :/ It's very weird that you are getting these issues, I usually run the tool on a HPC too with singularity and have never encountered any issues. I'm not a expert on these systems either so I'm not sure my suggestions will help...

Can try downloading the annotations on another system and rsyncing them to your HPC? Maybe this can help?

[yr542]

@nvnieuwk I have tried this before, it didn't work regrettably.

[nvnieuwk]

Then I'm not really sure this is something I can help you with :/ It doesn't seem like it's a singularity error, @lgmgeo could it be some bug in the INSTALL_annotations.sh script that only downloads parts of the annotations, or some issue with the source of the annotations?