Exomiser Network unreachable

[abrusell]

Hi,
I can't get Exomiser annotation work with AnnotSV v3.5.3
It says ```
...running Exomiser on 15238 gene names (November 10 2025 - 11:37)
...on port 10001
...starting the REST service
...idService = 15163

geneName: PATJ
unexpected token "END" at position 0; expecting VALUE

http://localhost:10001/exomiser/api/prioritise/?phenotypes=HP:0001548,HP:0001250,HP:0002463,HP:0007010,HP:0001999,HP:0001863&prioritiser=hiphive&prioritiser-params=human,mouse,fish,ppi&genes=10207
geneName: PATL1
connect failed network is unreachable

http://localhost:10001/exomiser/api/prioritise/?phenotypes=HP:0001548,HP:0001250,HP:0002463,HP:0007010,HP:0001999,HP:0001863&prioritiser=hiphive&prioritiser-params=human,mouse,fish,ppi&genes=219988
geneName: PATZ1
connect failed network is unreachable

...

for every gene!

Network is available because exomiser annotation works well with AnnotSV v3.4

[lgmgeo]

Exomiser (annotation +execution files) was updated between AnnotSV 3.4 and 3.5.
The same installation cannot work for both.
It appears that your installation for AnnotSV 3.5 was not done correctly. Did you do it from scratch?

[abrusell]

Yes, absolutely.
cloned with git and installed with human annotations
Thanks

[lgmgeo]

Do you have the output of:
make PREFIX=. install-human-annotation

[abrusell]

I didt have the output but I'm sure I didn't have any error.
Anyway, I've re-done it:

make PREFIX=. install-human-annotation

Download AnnotSV supporting data files:

curl -C - -LO https://www.lbgi.fr/~geoffroy/Annotations/Annotations_Human_3.5.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 5067M  100 5067M    0     0  11.7M      0  0:07:11  0:07:11 --:--:-- 13.1M

Download Exomiser supporting data files:

curl -C - -LO https://data.monarchinitiative.org/exomiser/data/2406_phenotype.zip
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 5947M  100 5947M    0     0  58.4M      0  0:01:41  0:01:41 --:--:-- 58.0M

Installation of Exomiser data:

install -d -p ./share/AnnotSV/Annotations_Exomiser/2406
unzip 2406_phenotype.zip -d ./share/AnnotSV/Annotations_Exomiser/2406/
Archive:  2406_phenotype.zip
replace ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/2406_phenotype.mv.db? [y]es, [n]o, [A]ll, [N]one, [r]ename: y
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/2406_phenotype.mv.db  
replace ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/hp.obo? [y]es, [n]o, [A]ll, [N]one, [r]ename: y
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/hp.obo  
replace ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/rw_string_10.mv? [y]es, [n]o, [A]ll, [N]one, [r]ename: y
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/rw_string_10.mv  y

replace ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/4.out? [y]es, [n]o, [A]ll, [N]one, [r]ename:   inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/4.out  
replace ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/10.out? [y]es, [n]o, [A]ll, [N]one, [r]ename: A
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/10.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/20.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/17_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/3_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/15.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/11.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/4_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/16.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/5_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/12.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/12_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/17.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/13.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/11_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/15_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/14_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/16_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/18.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/7_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/14.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/10_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/3.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/19.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/18_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/2.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/9_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/9.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/1.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/20_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/8.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/7.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/2_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/6_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/13_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/6.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/8_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/1_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/19_symmetric.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/out/5.out  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/hp.obo  
  inflating: ./share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/phenix/ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt  
/bin/rm -rf 2406_phenotype.zip
curl -C - -LO https://github.com/exomiser/Exomiser/releases/download/14.1.0/exomiser-rest-prioritiser-14.1.0.jar
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  114M  100  114M    0     0  26.8M      0  0:00:04  0:00:04 --:--:-- 29.3M
install -d -p ./share/AnnotSV/jar
install -p -m 0755 exomiser-rest-prioritiser-14.1.0.jar ./share/AnnotSV/jar/
/bin/rm exomiser-rest-prioritiser-14.1.0.jar

--> Exomiser data installed

Installation of human annotation:

tar -xf Annotations_Human_3.5.tar.gz -C ./share/AnnotSV/
/bin/rm -rf Annotations_Human_3.5.tar.gz
/bin/chmod -R 777 ./share/AnnotSV/Annotations_*

--> Human annotation installed

[lgmgeo]

I admit I'm a little lost...

The installation via the Makefile seems to have gone smoothly...

1. Is this indeed version 2406 in the Makefile and application.properties:

grep 2406 $ANNOTSV/Makefile

install-exomiser-1: 2406_phenotype.zip
$(MKDIR) -p $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/Annotations_Exomiser/2406
unzip 2406_phenotype.zip -d $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/Annotations_Exomiser/2406/
$(RM) -rf 2406_phenotype.zip

grep 2406 $ANNOTSV/etc/AnnotSV/application.properties

exomiser.phenotype.data-version=2406

2. Is the .jar present?

ls -l $ANNOTSV/share/AnnotSV/jar/exomiser-rest-prioritiser-14.1.0.jar

3. Are the exomiser annotations present?

ls -l $ANNOTSV/share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/

total 6.1G
drwxrwsr-x 3 vgeoffroy bioinfo    6 Aug 29 10:19 ./
drwxrwsr-x 3 vgeoffroy bioinfo    3 Aug 29 10:18 ../
-rwxrwxr-x 1 vgeoffroy bioinfo 8.7G Aug 29 10:19 2406_phenotype.mv.db*
-rwxrwxr-x 1 vgeoffroy bioinfo 9.7M Aug 29 10:18 hp.obo*
drwxrwsr-x 3 vgeoffroy bioinfo    5 Aug 29 10:19 phenix/
-rwxrwxr-x 1 vgeoffroy bioinfo 707M Aug 29 10:18 rw_string_10.mv*

[lgmgeo]

If everything is correct, can you run the service manually?

1. Copy the file $ANNOTSV/etc/AnnotSV/application.properties

2. Modify your copy of application.properties:

Replace XXXX and YYYY in

server.port=XXXX
exomiser.data-directory=YYYY

by replacing XXXX with 10001 and YYYY with $ANNOTSV/share/AnnotSV/Annotations_Exomiser/2406/ (insert your path without the variable name $ANNOTSV)

3. Run the service

bash
jarFile=$ANNOTSV/share/AnnotSV/jar/exomiser-rest-prioritiser-14.1.0.jar
port=10001
applicationProperties=/path of your copy/

java -Xmx4g -jar $jarFile --server.port=$port --spring.config.location=$applicationProperties &

4. Run exomiser

url="http://localhost:10001/exomiser/api/prioritise/?phenotypes=HP:0001548,HP:0001250,HP:0002463,HP:0007010,HP:0001999,HP:0001863&prioritiser=hiphive&prioritiser-params=human,mouse,fish,ppi&genes=10207"
response=$(curl -s "$url")
echo $response

5. Shut down the service

jobs | grep "applicationProperties"

[1]+  Running                 java -Xmx4g -jar $jarFile --server.port=$port --spring.config.location=$applicationProperties & 

pkill -f "java -Xmx4g -jar $jarFile"

[abrusell]

Thank you for your reply.
Everything looks correct:

ls -l $ANNOTSV/share/AnnotSV/jar/exomiser-rest-prioritiser-14.1.0.jar
-rwxr-xr-x 1 abrusell interactive Nov 10 /g100_work/OPBG2_prod2023//NGS_tools/AnnotSV_3.5.3/share/AnnotSV/jar/exomiser-rest-prioritiser-14.1.0.jar
grep 2406 $ANNOTSV/Makefile
install-exomiser-1: 2406_phenotype.zip
	$(MKDIR) -p $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/Annotations_Exomiser/2406
	unzip 2406_phenotype.zip -d $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/Annotations_Exomiser/2406/
	$(RM) -rf 2406_phenotype.zip
grep 2406 $ANNOTSV/etc/AnnotSV/application.properties
exomiser.phenotype.data-version=2406
ls -l $ANNOTSV/share/AnnotSV/jar/exomiser-rest-prioritiser-14.1.0.jar
-rwxr-xr-x 1 abrusell interactive Nov 10 /g100_work/OPBG2_prod2023//NGS_tools/AnnotSV_3.5.3/share/AnnotSV/jar/exomiser-rest-prioritiser-14.1.0.jar
ls -l $ANNOTSV/share/AnnotSV/Annotations_Exomiser/2406/2406_phenotype/
total 9806500
-rwxrwxrwx 1 abrusell interactive 9290592256 Jun 18  2024 2406_phenotype.mv.db
-rwxrwxrwx 1 abrusell interactive   10155910 Jun 18  2024 hp.obo
drwxrwxrwx 3 abrusell interactive      12288 Nov 10 14:45 phenix
-rwxrwxrwx 1 abrusell interactive  740933632 Jun 18  2024 rw_string_10.mv

and running the Exomiser service manually works too...
AnnotSV_3.4 works
AnnotSV_3.5.3 doesn't work (using the same application.properties file used for previous manual attempt)!

...running Exomiser on 18820 gene names (November 18 2025 - 13:56)
	...on port 10000
	...starting the REST service
	...idService = 2090911

geneName: MIR22HG
unexpected token "END" at position 0; expecting VALUE

http://localhost:10000/exomiser/api/prioritise/?phenotypes=HP:0000252,HP:0011729,HP:0000968,HP:0001999,HP:0032323,HP:0020110,HP:0007021&prioritiser=hiphive&prioritiser-params=human,mouse,fish,ppi&genes=84981
geneName: MIR2355
connect failed network is unreachable

http://localhost:10000/exomiser/api/prioritise/?phenotypes=HP:0000252,HP:0011729,HP:0000968,HP:0001999,HP:0032323,HP:0020110,HP:0007021&prioritiser=hiphive&prioritiser-params=human,mouse,fish,ppi&genes=100423036
geneName: MIR25
connect failed network is unreachable

http://localhost:10000/exomiser/api/prioritise/?phenotypes=HP:0000252,HP:0011729,HP:0000968,HP:0001999,HP:0032323,HP:0020110,HP:0007021&prioritiser=hiphive&prioritiser-params=human,mouse,fish,ppi&genes=407014
geneName: MIR26A1
connect failed network is unreachable

Curiously, it's using port 10000, even if port 10001 is specified in the application.properties file:

grep server.port $ANNOTSV/etc/AnnotSV/application.properties 
server.port=10001

[lgmgeo]

Curiously, it's using port 10000, even if port 10001 is specified in the application.properties file:

Great, we’ve identified a potential direction to resolve the bug.

[lgmgeo]

Does this work manually with port 10000?

[lgmgeo]

Hmm…
With the following command:

grep server.port $ANNOTSV/etc/AnnotSV/application.properties

You should see:
server.port=XXXX
and not:
server.port=10001

AnnotSV generates a temporary application file at each execution. This is because, when multiple jobs run simultaneously, they cannot all use the same server.port.

[abrusell]

I think that's the point!
I've tried several port numbers and it seems to respond only on port 10001...
(I've restored server.port=XXXX in application.properties)
Can I force the service to use port 10001 (avoiding running simultaneous jobs)?

[lgmgeo]

Perfect, it's good that you were able to pinpoint the problem.

Can I force the service to use port 10001 (avoiding running simultaneous jobs)?

Yes
The port is created by the script $ANNOTSV/share/bash/AnnotSV/searchForAFreePortNumber.bash.
You can hack this file as follows, but the installation will not be very clean.

#!/bin/bash

# com: Compare two sorted files line by line. Output the lines that are common, plus the lines that are unique.
#      comm [options]... File1 File2
#       -2 Suppress lines unique to file2
#       -3 Suppress lines that appear in both files
#
# seq: print a sorted sequence of numbers from 5000 to 50000
#
# ss: used to dump socket statistics.
#       -H, --no-header
#       -n, --numeric
#              Do not try to resolve service names. Show exact bandwidth
#              values, instead of human-readable.
#       -t, --tcp
#              Display TCP sockets.
#     e.g. "ss -Htan" >>> "LISTEN    0      5                       0.0.0.0:63864                  0.0.0.0:*"

#comm -23 <(seq 5000 50000 | sort) <(ss -Htan | awk '{print $4}' | cut -d':' -f2 | sort -u) | head -n 1
echo 10001

[abrusell]

Thank you, but the mystery thickens...
as I said, the service runs manually using port 10001

port=10001
(base) 11:01:12 abrusell@login02:/g100_work/OPBG2_prod2023/NGS_tools/AnnotSV_3.5.3 $ java -Xmx4g -jar $jarFile --server.port=$port --spring.config.location=$applicationProperties &
[1] 47481
(base) 11:01:15 abrusell@login02:/g100_work/OPBG2_prod2023/NGS_tools/AnnotSV_3.5.3 $   _____ _            _____                     _
 |_   _| |__   ___  | ____|_  _____  _ __ ___ (_)___  ___ _ __
   | | | '_ \ / _ \ |  _| \ \/ / _ \| '_ ` _ \| / __|/ _ \ '__|
   | | | | | |  __/ | |___ >  < (_) | | | | | | \__ \  __/ |
   |_| |_| |_|\___| |_____/_/\_\___/|_| |_| |_|_|___/\___|_|

 === Prioritiser Server ===                              v14.1.0

2025-11-21T11:01:16.678+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] o.m.e.r.p.ExomiserPrioritiserServer      : Starting ExomiserPrioritiserServer using Java 24.0.2 with PID 47481 (/g100_work/OPBG2_prod2023/NGS_tools/AnnotSV_3.5.3/share/AnnotSV/jar/exomiser-rest-prioritiser-14.1.0.jar started by abrusell in /g100_work/OPBG2_prod2023/NGS_tools/AnnotSV_3.5.3)
2025-11-21T11:01:16.688+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] o.m.e.r.p.ExomiserPrioritiserServer      : No active profile set, falling back to 1 default profile: "default"
WARNING: A restricted method in java.lang.System has been called
WARNING: java.lang.System::load has been called by org.apache.tomcat.jni.Library in an unnamed module (jar:nested:/g100_work/OPBG2_prod2023/NGS_tools/AnnotSV_3.5.3/share/AnnotSV/jar/exomiser-rest-prioritiser-14.1.0.jar/!BOOT-INF/lib/tomcat-embed-core-10.1.19.jar!/)
WARNING: Use --enable-native-access=ALL-UNNAMED to avoid a warning for callers in this module
WARNING: Restricted methods will be blocked in a future release unless native access is enabled

2025-11-21T11:01:18.146+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] o.s.b.w.embedded.tomcat.TomcatWebServer  : Tomcat initialized with port 10001 (http)
2025-11-21T11:01:18.158+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] o.apache.catalina.core.StandardService   : Starting service [Tomcat]
2025-11-21T11:01:18.158+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] o.apache.catalina.core.StandardEngine    : Starting Servlet engine: [Apache Tomcat/10.1.19]
2025-11-21T11:01:18.187+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] o.a.c.c.C.[.[.[/exomiser/api/prioritise] : Initializing Spring embedded WebApplicationContext
2025-11-21T11:01:18.187+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] w.s.c.ServletWebServerApplicationContext : Root WebApplicationContext: initialization completed in 1405 ms
2025-11-21T11:01:18.391+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] o.m.e.r.p.config.ControllerConfig        : Loading gene identifiers...
2025-11-21T11:01:18.392+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] com.zaxxer.hikari.HikariDataSource       : 2406_phenotype - Starting...
2025-11-21T11:01:18.812+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] com.zaxxer.hikari.pool.HikariPool        : 2406_phenotype - Added connection conn0: url=jdbc:h2:file:/g100_work/OPBG2_prod2023/NGS_tools/ExomiserData/data//2406_phenotype/2406_phenotype user=SA
2025-11-21T11:01:18.814+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] com.zaxxer.hikari.HikariDataSource       : 2406_phenotype - Start completed.
2025-11-21T11:01:18.923+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] o.m.e.r.p.config.ControllerConfig        : Loaded 19762 gene identifiers
2025-11-21T11:01:19.372+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] o.m.e.a.DataDirectoryAutoConfiguration   : Exomiser data directory set to: /g100_work/OPBG2_prod2023/NGS_tools/ExomiserData/data
2025-11-21T11:01:19.377+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] o.m.e.a.p.PrioritiserAutoConfiguration   : Pre-loading in-memory random-walk matrix from /g100_work/OPBG2_prod2023/NGS_tools/ExomiserData/data/2406_phenotype/rw_string_10.mv
2025-11-21T11:01:21.288+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] o.m.e.r.p.api.PrioritiserController      : Started PrioritiserController with GeneIdentifier cache of 19762 entries
2025-11-21T11:01:21.808+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] o.s.b.a.e.web.EndpointLinksResolver      : Exposing 1 endpoint(s) beneath base path '/actuator'
2025-11-21T11:01:21.873+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] o.s.b.w.embedded.tomcat.TomcatWebServer  : Tomcat started on port 10001 (http) with context path '/exomiser/api/prioritise'
2025-11-21T11:01:21.887+01:00  INFO 47481 --- [exomiser-prioritiser-service] [           main] o.m.e.r.p.ExomiserPrioritiserServer      : Started ExomiserPrioritiserServer in 5.711 seconds (process running for 6.197)

(base) 11:01:38 abrusell@login02:/g100_work/OPBG2_prod2023/NGS_tools/AnnotSV_3.5.3 $ response=$(curl -s "$url")
2025-11-21T11:01:41.247+01:00  INFO 47481 --- [exomiser-prioritiser-service] [io-10001-exec-1] o.a.c.c.C.[.[.[/exomiser/api/prioritise] : Initializing Spring DispatcherServlet 'dispatcherServlet'
2025-11-21T11:01:41.247+01:00  INFO 47481 --- [exomiser-prioritiser-service] [io-10001-exec-1] o.s.web.servlet.DispatcherServlet        : Initializing Servlet 'dispatcherServlet'
2025-11-21T11:01:41.248+01:00  INFO 47481 --- [exomiser-prioritiser-service] [io-10001-exec-1] o.s.web.servlet.DispatcherServlet        : Completed initialization in 1 ms
2025-11-21T11:01:41.295+01:00  INFO 47481 --- [exomiser-prioritiser-service] [io-10001-exec-1] o.m.e.r.p.api.PrioritiserController      : PrioritiserRequest{phenotypes=[HP:0001548, HP:0001250, HP:0002463, HP:0007010, HP:0001999, HP:0001863], genes=[10207], prioritiser='hiphive', prioritiserParams='human,mouse,fish,ppi', limit=0}
2025-11-21T11:01:42.695+01:00  INFO 47481 --- [exomiser-prioritiser-service] [io-10001-exec-1] o.m.e.r.p.api.PrioritiserController      : Finished HIPHIVE_PRIORITY
(base) 11:01:42 abrusell@login02:/g100_work/OPBG2_prod2023/NGS_tools/AnnotSV_3.5.3 $ echo $response
{"params":{"phenotypes":["HP:0001548","HP:0001250","HP:0002463","HP:0007010","HP:0001999","HP:0001863"],"genes":[10207],"prioritiser":"hiphive","prioritiserParams":"human,mouse,fish,ppi","limit":0},"queryTime":1402,"results":[{"priorityType":"HIPHIVE_PRIORITY","geneId":10207,"geneSymbol":"PATJ","score":0.0,"ppiScore":0.0,"candidateGeneMatch":false,"queryPhenotypeTerms":[{"id":"HP:0001548","label":"Overgrowth"},{"id":"HP:0001250","label":"Seizure"},{"id":"HP:0002463","label":"Language impairment"},{"id":"HP:0007010","label":"Poor fine motor coordination"},{"id":"HP:0001999","label":"Abnormal facial shape"},{"id":"HP:0001863","label":"Toe clinodactyly"}],"phenotypeEvidence":[],"diseaseMatches":[],"ppiEvidence":[],"humanScore":0.0,"mouseScore":0.0,"fishScore":0.0}]}

but it doesn't reach the network when running inside AnnotSV:

$AnnotSV -SVinputFile $famID"_sniffles_sv.bnd.vcf.gz" -genomeBuild GRCh38 -annotationMode both         -includeCI 0 -missingGTinSamplesid 0 -hpo $hpo -outputDir $outdir -outputFile $prob"_sniffles_sv.Annot.tsv" 
AnnotSV 3.5.3

Copyright (C) 2017-current 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:
/g100_work/OPBG2_prod2023/NGS_tools/AnnotSV_3.5.3


...downloading the configuration data (November 21 2025 - 13:35)
	...configuration data by default
	...configuration data from /g100_work/OPBG2_prod2023/NGS_tools/AnnotSV_3.5.3/etc/AnnotSV/configfile
	...configuration data given in arguments
	...checking all these configuration data

...VCF to BED (November 21 2025 - 13:35)
...checking the annotation data sources (November 21 2025 - 13:36)
	INFO: AnnotSV takes use of Exomiser (Smedley et al., 2015) for the phenotype-driven analysis.
	INFO: AnnotSV is using the Human Phenotype Ontology (version 2406). Find out more at http://www.human-phenotype-ontology.org
	INFO: AnnotSV takes use of PhenoGenius (Yauy et al., 2023) for the phenotype-driven analysis.

...listing arguments
	******************************************
	AnnotSV has been run with these arguments:
	******************************************
	-PhenoGeniusCli 1
	-REreport 0
	-REselect1 1
	-REselect2 1
	-SVinputFile Multi_sniffles_sv.bnd.vcf.gz
	-SVinputInfo 1
	-SVminSize 50
	-annotationMode both
	-annotationsDir /g100_work/OPBG2_prod2023/NGS_tools/AnnotSV_3.5.3/share/AnnotSV
	-bcftools bcftools
	-bedtools bedtools
	-benignAF 0.01
	-candidateGenesFiltering 0
	-cytoband 1
	-genomeBuild GRCh38
	-hpo HP:0000252,HP:0011729,HP:0000968,HP:0001999,HP:0032323,HP:0020110,HP:0007021
	-includeCI 0
	-metrics us
	-miRNAann 1
	-minTotalNumber 500
	-missingGTinSamplesid 0
	-organism Human
	-outputDir /g100_scratch/userexternal/abrusell/ONT/Sniffles
	-outputFile prob_U03485607_sniffles_sv.Annot.tsv
	-overlap 100
	-overwrite 1
	-promoterSize 500
	-rankFiltering 1 2 3 4 5 NA
	-reciprocal 0
	-samplesidBEDcol -1
	-snvIndelPASS 0
	-svtBEDcol -1
	-tx RefSeq
	-variantconvertDir /g100_work/OPBG2_prod2023/NGS_tools/AnnotSV_3.5.3/share/python3/variantconvert/
	-variantconvertMode combined
	-vcf 0
	******************************************

...searching for SV overlaps with a gene or a regulatory elements
	...7632 genes overlapped with an SV
	...16481 genes regulated by a regulatory element which is overlapped with an SV

...running PhenoGeniusCli for 18820 gene names (November 21 2025 - 13:39)

...running Exomiser on 18820 gene names (November 21 2025 - 13:40)
	...on port 10001
	...starting the REST service
	...idService = 29411

geneName: LINC01859
unexpected token "END" at position 0; expecting VALUE

http://localhost:10001/exomiser/api/prioritise/?phenotypes=HP:0000252,HP:0011729,HP:0000968,HP:0001999,HP:0032323,HP:0020110,HP:0007021&prioritiser=hiphive&prioritiser-params=human,mouse,fish,ppi&genes=101929164
geneName: LINC01864
connect failed network is unreachable

http://localhost:10001/exomiser/api/prioritise/?phenotypes=HP:0000252,HP:0011729,HP:0000968,HP:0001999,HP:0032323,HP:0020110,HP:0007021&prioritiser=hiphive&prioritiser-params=human,mouse,fish,ppi&genes=101928886
geneName: LINC01865
connect failed network is unreachable

http://localhost:10001/exomiser/api/prioritise/?phenotypes=HP:0000252,HP:0011729,HP:0000968,HP:0001999,HP:0032323,HP:0020110,HP:0007021&prioritiser=hiphive&prioritiser-params=human,mouse,fish,ppi&genes=105373350
geneName: LINC01870
connect failed network is unreachable

http://localhost:10001/exomiser/api/prioritise/?phenotypes=HP:0000252,HP:0011729,HP:0000968,HP:0001999,HP:0032323,HP:0020110,HP:0007021&prioritiser=hiphive&prioritiser-params=human,mouse,fish,ppi&genes=107985925
geneName: LINC01880
connect failed network is unreachable
...
...

[lgmgeo]

I'm lost...

[lgmgeo]

Are you using AnnotSV in a conda environment?