Error: can't read the LOF genes file /home/tud03125/CancerVar/cancervardb/PVS1.LOF.genes

[tud03125]

Hi,

I'm receiving this error message when running this code:

python3 /home/tud03125/CancerVar/CancerVar.py
-b hg38
-i /home/tud03125/input.avinput
--input_type=AVinput
-o /home/tud03125/output_cancervar
--table_annovar=/home/tud03125/annovar/table_annovar.pl
--annotate_variation=/home/tud03125/annovar/annotate_variation.pl
--convert2annovar=/home/tud03125/annovar/convert2annovar.pl
-d /home/tud03125/annovar/humandb
-t /home/tud03125/CancerVar/cancervardb

This image is the output of what it looks like. I'm also attaching my "input.avinput" input file here (as TXT instead of AVINPUT file since the format won't be accepted here):

input.avinput.txt

It's similar to this Issue: #25, which I had the same problem before, regarding " LOF.genes.exac_me_cancers," and solved it by "-t /home/tud03125/CancerVar/cancervardb." I will also attach the "LOF.genes.exac_me_cancers" file here too, just in case (also as TXT):

LOF.genes.exac_me_cancers.txt

Anyway, the error message graduated from "Error: can't read the LOF genes file cancervardb/LOF.genes.exac_me_cancers" to "Error: can't read the LOF genes file /home/tud03125/CancerVar/cancervardb/PVS1.LOF.genes." But, the "CancerVar/cancervardb" directory is very much like yours: https://github.com/WGLab/CancerVar/tree/master/cancervardb, and that the "LOF.genes.exac_me_cancers" file does not mention "PVS1" anywhere in that list. So, where is "PVS1.LOF.genes" coming from?

[ShvartsmanIrina]

Hi, I encountered exactly the same error. Were you able to resolve it?

[tud03125]

@ShvartsmanIrina Nope! What about you?

[ShvartsmanIrina]

@ShvartsmanIrina Nope! What about you?

No(

[quanliustc]

do you try to using -c config.ini, will upload new version to avoid these wrong file names

[ShvartsmanIrina]

do you try to using -c config.ini, will upload new version to avoid these wrong file names

Thank you - it's work!

[Karthick99-S]

python3 CancerVar.py -c config.ini -i 202509131709_AE01-250201014_4P250708136US293231D2_B_LBPRUN250083-DetaGen-WES_CTP0109250007
5_L00_annovar.hg19_multianno.txt --input_type AVinput --output cancervar_out -b hg19 -t cancervardb -d /DATADR/Oncology/annovar/humandb --table_annovar table_annovar.pl --conv
ert2annovar convert2annovar.pl --annotate_variation annotate_variation.pl

I have used the command -c config.ini, but I am still encountering the same error.

[quanliustc]

Could you post out the config.ini, as this PVS1.LOF.genes should be not used here. Best, Quan LI, Ph.D ***@***.*** http://www.quanli.org <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.quanli.org%2F&data=05%7C01%7CGUOY%40chop.edu%7C1737ed2dc43f4054cdef08da3e8d0e5d%7Ca611241607b041a59bb1d146b575c975%7C0%7C0%7C637891072799646498%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=M2z3UZ6KkcLGltScnueVhFljaEHTgbisutQLIJ%2Fe%2BYA%3D&reserved=0> From: Karthick S ***@***.***> Sent: Monday, September 22, 2025 1:30 AM To: WGLab/CancerVar ***@***.***> Cc: Quan LI ***@***.***>; Comment ***@***.***> Subject: Re: [WGLab/CancerVar] Error: can't read the LOF genes file /home/tud03125/CancerVar/cancervardb/PVS1.LOF.genes (Issue #27) <https://avatars.githubusercontent.com/u/131851867?s=20&v=4> Karthick99-S left a comment (WGLab/CancerVar#27) <#27 (comment)> Screenshot.2025-09-22.105614.png (view on web) <https://github.com/user-attachments/assets/cb5095ae-744b-421b-a3c1-c01868bee117> python3 CancerVar.py -c config.ini -i 202509131709_AE01-250201014_4P250708136US293231D2_B_LBPRUN250083-DetaGen-WES_CTP0109250007 5_L00_annovar.hg19_multianno.txt --input_type AVinput --output cancervar_out -b hg19 -t cancervardb -d /DATADR/Oncology/annovar/humandb --table_annovar table_annovar.pl --conv ert2annovar convert2annovar.pl --annotate_variation annotate_variation.pl I have used the command -c config.ini, but I am still encountering the same error. — Reply to this email directly, view it on GitHub <#27 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADYPUJCSC2PPSWFQVZRKBV33T6CN3AVCNFSM6AAAAACHEBQFH2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTGMJXGAYDGMRSGM> . You are receiving this because you commented. <https://github.com/notifications/beacon/ADYPUJCVYCAXXYRHCFDYCDT3T6CN3A5CNFSM6AAAAACHEBQFH2WGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTWFWVZ5O.gif> Message ID: ***@***.*** ***@***.***> >