issue with annotation of input vcf file

[dasn588]

Hi, I have downloaded and installed the AnnotSV tool in my linux system. then compiled as: sudo make PREFIX=. install sudo make PREFIX=. install-human-annotation

Next when I tried running the tool with given command , i am getting error ("" file doesn't exist Please check your install - Exit with error.)

command run

AnnotSV -SVinputFile input.vcf -outputFile output_AnnotSV.txt -genomeBuild GRCh38 -bedtools bin/bedtools -REreport 0 -annotationsDir programs/AnnotSV AnnotSV 3.4.3

Copyright (C) 2017-2024 GEOFFROY Veronique

Please feel free to create a Github issue for any suggestions or bug reports (https://github.com/lgmgeo/AnnotSV/issues)

Tcl/Tk version: 8.6

Application name used: programs/AnnotSV

...downloading the configuration data (September 06 2024 - 13:12) ...configuration data by default ...configuration data from programs/AnnotSV/etc/AnnotSV/configfile ...configuration data given in arguments ...checking all these configuration data

...VCF to BED (September 06 2024 - 13:12)

...checking the annotation data sources (September 06 2024 - 13:16) ############################################################################ "" file doesn't exist Please check your install - Exit with error.

How to resolve the issue in order to annotate the SV vcf.

[lgmgeo]

You installed AnnotSV with root rights. But you are using it with other user rights. I think that is the problem.

The best would be to run:

sudo chmod -R 777 $ANNOTSV

Can you have a try and tell me if it works?

[dasn588]

Hi, Thank you for the response. I have tried the command (sudo chmod -R 777 /data/programs/AnnotSV) as per your suggestion but still getting same error.

Please help me to resolve the issue.

[lgmgeo]

Really strange... Did you have any error during the install? (sudo make PREFIX=. install-human-annotation) Because it looks like your annotation files are not present.

Else, let's investigate.

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

  ls -l $ANNOTSV/share/AnnotSV/Annotations_Human/Genes/GRCh38/genes.RefSeq.sorted.bed
  ls -l $ANNOTSV/share/AnnotSV/Annotations_Human/*

• Can you download the AnnotSV-genes.tcl.txt attached file. Then run:

  cp $ANNOTSV/share/tcl/AnnotSV/AnnotSV-genes.tcl $ANNOTSV/share/tcl/AnnotSV//AnnotSV-genes.tcl.sauv
  mv AnnotSV-genes.tcl.txt $ANNOTSV/share/tcl/AnnotSV/AnnotSV-genes.tcl

Then run AnnotSV and show me the output?

[dasn588]

Hi,

I am sharing the output for make PREFIX=. install and make PREFIX=. install-human-annotation after using sudo chmod -R 777 . make PREFIX=. install

Installation of AnnotSV-3.4.4:

DESTDIR= PREFIX=. TCLVERSION=tcl8.5

/bin/mv License.txt changeLog.txt commandLineOptions.txt README.AnnotSV_3.4.1_Mouse.pdf README.AnnotSV_3.4.1.pdf ./share/doc/AnnotSV /bin/mv share/tcl ./share/tcl8.5

variantconvert installation

touch ./share/python3/variantconvert/pipinstall.flag chmod 777 ./share/python3/variantconvert/pipinstall.flag pip3 install -e ./share/python3/variantconvert/. &> ./tmp.variantconvert.txt || pip install -e ./share/python3/variantconvert/. &> ./tmp.variantconvert.txt || rm -f ./share/python3/variantconvert/pipinstall.flag rm -f ./tmp.variantconvert.txt ls -l ./share/python3/variantconvert/pipinstall.flag || echo "variantconvert not installed" -rwxrwxrwx 1 it it 0 Sep 9 11:21 ./share/python3/variantconvert/pipinstall.flag touch ./share/python3/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_bed.combined.local.json touch ./share/python3/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_bed.full.local.json touch ./share/python3/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_bed.fullsplit.local.json touch ./share/python3/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_vcf.combined.local.json touch ./share/python3/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_vcf.full.local.json touch ./share/python3/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_vcf.fullsplit.local.json touch ./share/python3/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_bed.combined.local.json touch ./share/python3/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_bed.full.local.json touch ./share/python3/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_bed.fullsplit.local.json touch ./share/python3/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_vcf.combined.local.json touch ./share/python3/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_vcf.full.local.json touch ./share/python3/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_vcf.fullsplit.local.json /bin/chmod -R 777 ./share/python3/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_bed.combined.local.json /bin/chmod -R 777 ./share/python3/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_bed.full.local.json /bin/chmod -R 777 ./share/python3/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_bed.fullsplit.local.json /bin/chmod -R 777 ./share/python3/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_vcf.combined.local.json /bin/chmod -R 777 ./share/python3/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_vcf.full.local.json /bin/chmod -R 777 ./share/python3/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_vcf.fullsplit.local.json /bin/chmod -R 777 ./share/python3/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_bed.combined.local.json /bin/chmod -R 777 ./share/python3/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_bed.full.local.json /bin/chmod -R 777 ./share/python3/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_bed.fullsplit.local.json /bin/chmod -R 777 ./share/python3/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_vcf.combined.local.json /bin/chmod -R 777 ./share/python3/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_vcf.full.local.json /bin/chmod -R 777 ./share/python3/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_vcf.fullsplit.local.json

Done

WARNING: Annotations need to be installed: make DESTDIR= PREFIX=. install-human-annotation make DESTDIR= PREFIX=. install-mouse-annotation

================================================================================================================= make PREFIX=. install-human-annotation

Download AnnotSV supporting data files:

curl -C - -LO https://www.lbgi.fr/~geoffroy/Annotations/Annotations_Human_3.4.4.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 2025M 100 2025M 0 0 459k 0 1:15:09 1:15:09 --:--:-- 525k

Download Exomiser supporting data files:

curl -C - -LO https://www.lbgi.fr/~geoffroy/Annotations/2309_hg19.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 111M 100 111M 0 0 680k 0 0:02:47 0:02:47 --:--:-- 591k curl -C - -LO https://data.monarchinitiative.org/exomiser/data/2309_phenotype.zip % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 2747M 100 2747M 0 0 6074k 0 0:07:43 0:07:43 --:--:-- 7567k

Installation of Exomiser data:

install -d -p ./share/AnnotSV/Annotations_Exomiser/2309 tar -xf 2309_hg19.tar.gz -C ./share/AnnotSV/Annotations_Exomiser/2309/ unzip 2309_phenotype.zip -d ./share/AnnotSV/Annotations_Exomiser/2309/ Archive: 2309_phenotype.zip creating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/ inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/hp.obo
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/rw_string_10.mv
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/2309_phenotype.h2.db
creating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/ creating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/ inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/4.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/10.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/20.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/17_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/3_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/15.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/11.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/4_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/16.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/5_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/12.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/12_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/17.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/13.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/11_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/15_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/14_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/16_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/18.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/7_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/14.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/10_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/3.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/19.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/18_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/2.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/9_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/9.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/1.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/20_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/8.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/7.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/2_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/6_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/13_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/6.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/8_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/1_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/19_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/out/5.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/hp.obo
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype/phenix/ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt
inflating: ./share/AnnotSV/Annotations_Exomiser/2309/2309_phenotype.sha256
/bin/rm -rf 2309_phenotype.zip /bin/rm -rf 2309_hg19.tar.gz

--> Exomiser data installed

Installation of human annotation:

tar -xf Annotations_Human_3.4.4.tar.gz -C ./share/AnnotSV/ /bin/rm -rf Annotations_Human3.4.4.tar.gz /bin/chmod -R 777 ./share/AnnotSV/Annotations*

--> Human annotation installed

================================================================================================

Then tried following approach

cp $ANNOTSV/share/tcl/AnnotSV/AnnotSV-genes.tcl $ANNOTSV/share/tcl/AnnotSV//AnnotSV-genes.tcl.sauv mv AnnotSV-genes.tcl.txt $ANNOTSV/share/tcl/AnnotSV/AnnotSV-genes.tcl

annotationsDir = /data/ngs/programs/AnnotSV. genesDir = /data/ngs/programs/AnnotSV/Annotations_Human/Genes/GRCh37. genesFileDownloaded = . genesFileFormatted = . ############################################################################ "" file doesn't exist Please check your install - Exit with error.

Now getting some new error.

[lgmgeo]

The install looks correct.

This time, you seem to run AnnotSV with GRCh37 (not GRCh38 as in your command line from the first comment).

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/Genes/GRCh37/ ls -l $ANNOTSV/share/AnnotSV/Annotations_Human/*

[dasn588]

ls -l share/AnnotSV/Annotations_Human/Genes/GRCh38/ total 97484 -rwxrwxrwx 1 it it 43481272 Feb 17 2024 genes.ENSEMBL.sorted.bed -rwxrwxrwx 1 it it 49819536 Feb 17 2024 genes.RefSeq.sorted.bed -rwxrwxrwx 1 it it 4006943 Feb 17 2024 transcript_version.ENSEMBL.tsv -rwxrwxrwx 1 it it 2508459 Feb 17 2024 transcript_version.RefSeq.tsv

ls -l share/AnnotSV/Annotations_Human/Genes/GRCh37/ total 59600 -rwxrwxrwx 1 it it 35092793 Feb 17 2024 genes.ENSEMBL.sorted.bed -rwxrwxrwx 1 it it 21472665 Feb 17 2024 genes.RefSeq.sorted.bed -rwxrwxrwx 1 it it 3338018 Feb 17 2024 transcript_version.ENSEMBL.tsv -rwxrwxrwx 1 it it 1121558 Feb 17 2024 transcript_version.RefSeq.tsv

ls -l share/AnnotSV/Annotations_Human/ total 28 drwxrwxrwx 3 it it 4096 Feb 17 2024 AnyOverlap drwxrwxrwx 7 it it 4096 Feb 17 2024 BreakpointsAnnotations drwxrwxrwx 7 it it 4096 Feb 17 2024 FtIncludedInSV drwxrwxrwx 10 it it 4096 Feb 17 2024 Gene-based drwxrwxrwx 4 it it 4096 Feb 17 2024 Genes drwxrwxrwx 3 it it 4096 Feb 17 2024 SVincludedInFt drwxrwxrwx 4 it it 4096 Feb 17 2024 Users

[lgmgeo]

Following the issue https://github.com/lgmgeo/AnnotSV/issues/255, I have an idea of your problem. Did you use a conda environment? Did you set the ANNOTSV environment variable in that environment?