First try of AnnotSV (How to set ANNOTSV environment variable)

Question

First try of AnnotSV (How to set ANNOTSV environment variable)

handoko12u opened this issue 10 months ago · 22 comments

handoko12u commented 10 months ago

fail to run AnnotSV in conda environment with error:

(annotsv) sysadmin@sysadmin:~/Downloads/R_practice$ AnnotSV -SVinputFile s1_sv.vcf
AnnotSV 3.3.6

Please feel free to contact me for any suggestions or bug reports
email: veronique.geoffroy@inserm.fr

Tcl/Tk version: 8.6

Application name used:
/home/sysadmin/mambaforge/envs/annotsv

...downloading the configuration data (January 11 2024 - 10:08)
...configuration data by default
...configuration data from /home/sysadmin/mambaforge/envs/annotsv/etc/AnnotSV/configfile
...configuration data given in arguments
...checking all these configuration data

...VCF to BED (January 11 2024 - 10:08)

...checking the annotation data sources (January 11 2024 - 10:08)
can't read "hpoVersion": no such variable
while executing
"file exist $g_AnnotSV(annotationsDir)/Annotations_Exomiser/$hpoVersion/application.properties"
(procedure "checkExomiserInstallation" line 18)
invoked from within
"checkExomiserInstallation"
(file "/home/sysadmin/mambaforge/envs/annotsv/bin/AnnotSV" line 180)

Initially I though exomiser has not been installed, then I also install: conda install bioconda::exomiser-rest-prioritiser, but still fail.

please advice, what's wrong?

lgmgeo commented 9 months ago

Any news?

Answer 1 · 2024-01-15T15:49:38.000Z

Hi @handoko12u,

Thank you for this bug report.
I just added a fix (v3.3.9).
Can you confirm that everything is back to normal?

Best,

Véronique

Answer 2 · 2024-01-16T06:07:19.000Z

Hello @lgmgeo
Here is the result:

(annotsv) sysadmin@sysadmin:~/Downloads/R_practice$ AnnotSV -SVinputFile s1_sv.vcf -genomeBuild GRCh38
AnnotSV 3.3.9

Please feel free to contact me for any suggestions or bug reports
email: veronique.geoffroy@inserm.fr

Tcl/Tk version: 8.6

Application name used:
/home/sysadmin/mambaforge/envs/annotsv

...downloading the configuration data (January 16 2024 - 13:00)
...configuration data by default
...configuration data from /home/sysadmin/mambaforge/envs/annotsv/etc/AnnotSV/configfile
...configuration data given in arguments
...checking all these configuration data

...VCF to BED (January 16 2024 - 13:00)

...checking the annotation data sources (January 16 2024 - 13:00)

WARNING: No Exomiser annotations available in /home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Exomiser/

   >>> creation of /home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Human/SVincludedInFt/BenignSV/GRCh37/overlappedGenes_RefSeq_in_benign_Loss_SV_GRCh37.tsv] (January 16 2024 - 13:00)

-- checkOverlappedGenesBenignFiles, GRCh37, RefSeq, Loss --
bedtools intersect -sorted -a -b -wa -wb > 20240116_AnnotSV/1705384826_overlappedGenes_RefSeq_in_benign_Loss_SV_GRCh37.tmp.bed
Error: Unable to open file . Exiting.
Exit with error

Still doesn't work.

Answer 3 · 2024-01-16T13:23:03.000Z

Sorry I can't reproduce the bug.
Quite difficult to help you.

1 - Does the following file exist in your installation:
/home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Human/SVincludedInFt/BenignSV/GRCh37/overlappedGenes_RefSeq_in_benign_Loss_SV_GRCh37.tsv

If so, in your conda environment, can you access this file?

2 - More generally, can you run this command in your conda environment and give me the result:
ls /home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Human/*/*

Answer 4 · 2024-01-16T13:59:46.000Z

Here is the command you used to run AnnotSV:

AnnotSV -SVinputFile s1_sv.vcf -genomeBuild GRCh38

3 - What is your current directory? Can you give me the path (pwd) in the conda environment?

4 - Can you run AnnotSV by using the "bin" path?
Something like:
/home/sysadmin/mambaforge/envs/annotsv/bin/AnnotSV -SVinputFile s1_sv.vcf -genomeBuild GRCh38

Answer 5 · 2024-01-18T01:19:10.000Z

Hello @lgmgeo

This is my current directory: /home/sysadmin/Downloads/R_practice

I have also run using bin path:

(annotsv) sysadmin@sysadmin:~/Downloads/R_practice$ /home/sysadmin/mambaforge/envs/annotsv/bin/AnnotSV -SVinputFile s1_sv.vcf -genomeBuild GRCh38
AnnotSV 3.3.9

Please feel free to contact me for any suggestions or bug reports
email: veronique.geoffroy@inserm.fr

Tcl/Tk version: 8.6

Application name used:
/home/sysadmin/mambaforge/envs/annotsv

...downloading the configuration data (January 18 2024 - 08:14)
...configuration data by default
...configuration data from /home/sysadmin/mambaforge/envs/annotsv/etc/AnnotSV/configfile
...configuration data given in arguments
...checking all these configuration data

...VCF to BED (January 18 2024 - 08:14)

...checking the annotation data sources (January 18 2024 - 08:14)

WARNING: No Exomiser annotations available in /home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Exomiser/

   >>> creation of /home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Human/SVincludedInFt/BenignSV/GRCh37/overlappedGenes_RefSeq_in_benign_Loss_SV_GRCh37.tsv] (January 18 2024 - 08:14)

-- checkOverlappedGenesBenignFiles, GRCh37, RefSeq, Loss --
bedtools intersect -sorted -a -b -wa -wb > 20240118_AnnotSV/1705540478_overlappedGenes_RefSeq_in_benign_Loss_SV_GRCh37.tmp.bed
Error: Unable to open file . Exiting.
Exit with error
(annotsv) sysadmin@sysadmin:~/Downloads/R_practice$ pwd
/home/sysadmin/Downloads/R_practice

I checked there is no overlappedGenes_RefSeq_in_benign_Loss_SV_GRCh37.tsv created. Is it supposed to be created automatically?

Answer 6 · 2024-01-18T01:20:48.000Z

This is my ls result:

(annotsv) sysadmin@sysadmin:~/Downloads/R_practice$ ls /home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Human//
/home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Human/Gene-based/NCBIgeneID:
geneSymbol_NCBIgeneID.txt results.txt

/home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Human/Genes/GRCh38:
genes.RefSeq.sorted.bed

Answer 7 · 2024-01-18T09:07:28.000Z

The bug can be visualize in your output with this command:

bedtools intersect -sorted -a -b -wa -wb

This should be:

bedtools intersect -sorted -a /home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Human/Genes/GRCh37/genes.RefSeq.sorted.bed -b /home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Human/SVincludedInFt/BenignSV/GRCh37/benign_Loss_SV_GRCh37.sorted.bed -wa -wb

To debug, can you please:

download and uncompress the attached file
AnnotSV-benignsv.tcl.gz
save then replace this file in your install:
/home/sysadmin/mambaforge/envs/annotsv/share/tcl/AnnotSV/AnnotSV-benignsv.tcl
run AnnotSV
give me the output

Else, have you already installed and run AnnotSV with a previous version? Or is this the first time?

Answer 8 · 2024-01-19T07:24:42.000Z

Hello @lgmgeo

This is my first time running AnnotSV

I have done as your instruction. This is the result:
(annotsv) sysadmin@sysadmin:~/Downloads/R_practice$ /home/sysadmin/mambaforge/envs/annotsv/bin/AnnotSV -SVinputFile s1_sv.vcf -genomeBuild GRCh38
AnnotSV 3.3.9

Please feel free to contact me for any suggestions or bug reports
email: veronique.geoffroy@inserm.fr

Tcl/Tk version: 8.6

Application name used:
/home/sysadmin/mambaforge/envs/annotsv

...downloading the configuration data (January 19 2024 - 14:19)
...configuration data by default
...configuration data from /home/sysadmin/mambaforge/envs/annotsv/etc/AnnotSV/configfile
...configuration data given in arguments
...checking all these configuration data

...VCF to BED (January 19 2024 - 14:19)

...checking the annotation data sources (January 19 2024 - 14:19)

WARNING: No Exomiser annotations available in /home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Exomiser/

--- g_AnnotSV(annotationsDir) : /home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV
g_AnnotSV(organism) : Human
genomeBuild : GRCh37
benignDir : /home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Human/SVincludedInFt/BenignSV/GRCh37
genesDir : /home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Human/Genes/GRCh37
--- tx : RefSeq

    GenesfileFormatted :
       >> $genesDir/genes.${tx}.sorted.bed 
       >> /home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Human/Genes/GRCh37/genes.RefSeq.sorted.bed
       >>  ($GenesfileFormatted)

ls: cannot access '/home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Human/Genes/GRCh37/genes.RefSeq.sorted.bed': No such file or directory
while executing
"exec ls /home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Human/Genes/GRCh37/genes.RefSeq.sorted.bed"
("eval" body line 1)
invoked from within
"eval exec ls $genesDir/genes.${tx}.sorted.bed"
(procedure "checkOverlappedGenesBenignFiles" line 23)
invoked from within
"checkOverlappedGenesBenignFiles"
(file "/home/sysadmin/mambaforge/envs/annotsv/bin/AnnotSV" line 188)

Answer 9 · 2024-01-19T08:05:48.000Z

I don't know why, but your annotation directory is not correct.
This following file is distributed with AnnotSV and should exist:
/home/sysadmin/mambaforge/envs/annotsv/share/AnnotSV/Annotations_Human/Genes/GRCh37/genes.RefSeq.sorted.bed
(even if you run AnnotSV with -genomeBuild GRCh38)

This does not seem to be the case.

Can you try another AnnotSV install from scratch:

To install AnnotSV, please follow these instructions:
https://github.com/lgmgeo/AnnotSV/blob/master/docs/quickstart.md
The following step is mandatory:

make PREFIX=. install-human-annotation

Answer 10 · 2024-01-26T02:03:41.000Z

Hello @lgmgeo

I have removed the whole thing and install again.

stil does not work. The annotations files are supposed to be downloaded automatically (when we install AnnotSV), is that right? why it doesn't seem to be the case for me.

Thanks

Answer 11 · 2024-01-26T07:06:18.000Z

The annotations files are supposed to be downloaded automatically when running:

make PREFIX=. install-human-annotation

Can you give me the output of this command?

Answer 12 · 2024-01-26T10:19:20.000Z

Here is the result:

(annotsv) sysadmin@sysadmin:~/Downloads/R_practice/sv_vcf$ make PREFIX=. install-human-annotation
make: *** No rule to make target 'install-human-annotation'. Stop.

Answer 13 · 2024-01-26T10:27:53.000Z

OK, at least we know why you don't have annotation files... The install is not done correctly...

Please run the following instructions:

cd ~/Downloads/R_practice/sv_vcf
git clone https://github.com/lgmgeo/AnnotSV.git
cd ~/Downloads/R_practice/sv_vcf/AnnotSV
make PREFIX=. install
make PREFIX=. install-human-annotation

And paste me the outputs of each step if it does not work (but it should work).

Answer 14 · 2024-01-26T11:35:05.000Z

Installation looks successful:

But when I run again:

the annotation downloaded is this:

please advice, some adjustment is needed, but I don't know how!
Thanks

Answer 15 · 2024-01-26T12:06:39.000Z

I'm a little lost, I've never had feedback like this and I can't reproduce the bug...

Can you try not to run AnnotSV from the AnnotSV bin directory? Or to redirect the output elsewhere than in the AnnotSV install (-outputFile /home/sysadmin/Downloads/R_practice/sv_vcf/s1_phased.annotated.tsv).

(This is something that is not done, the installation must remain clean)

But this will not explain your bug.

Your output is quite strange:

The AnnotSV path install is:
/home/sysadmin/Downloads/R_practice/sv_vcf/AnnotSV

But then, AnnotSV search for annotation in:
/home/sysadmin/mambaforge/envs/annotsv/

That's not normal.

What is the result when printing the ANNOTSV env variable?

echo $ANNOTSV

Answer 16 · 2024-01-26T12:16:56.000Z

this is the result:

Answer 17 · 2024-01-26T12:35:39.000Z

The ANNOTSV environment variable must be set:

Answer 18 · 2024-01-26T16:42:24.000Z

Have done it correctly? but it is still the same

Answer 19 · 2024-01-26T17:02:16.000Z

Can you add the export ANNOTSV=/home/sysadmin/Downloads/R_practice/sv_vcf/AnnotSV command in your ~/.bashrc file?
Then :

cd /home/sysadmin/Downloads/R_practice/sv_vcf/
echo $SHELL
source ~/.bashrc
echo $ANNOTSV
$ANNOTSV/bin/AnnotSV -SVinputFile /home/sysadmin/Downloads/R_practice/sv_vcf/s1_phased.vcf -outputFile /home/sysadmin/Downloads/R_practice/sv_vcf/s1_phased.annotated.tsv

Answer 20 · 2024-01-29T10:27:51.000Z

Thank you very much @lgmgeo . It works now.

Answer 21 · 2024-01-29T11:18:40.000Z

Great!
Have fun with AnnotSV!