ValueError: could not convert string to float: X

[stanedav]

Hello, I am trying to run your tool with this command:
./InterVar.py -b hg19 --table_annovar='/annovar/table_annovar.pl' --convert2annovar='/annovar/convert2annovar.pl' --annotate_variation='/annovar/annotate_variation.pl' -i '/vcf_wes/sample.vcf' --input_type=VCF -o '/vcf_wes/sample_output'

After few moment I am getting this error:
``
NOTICE: Multianno output file is written to /home/lab/galaxy-Win-Lin/David/vcf_wes/6788_output.hg19_multianno.txt
Notice: Begin the variants interpretation by InterVar

Traceback (most recent call last):

File "./InterVar.py", line 2022, in
main()

File "./InterVar.py", line 1996, in main
sum2=my_inter_var(annovar_outfile)

File "./InterVar.py", line 1771, in my_inter_var
intervar_bp=assign(BP,line,Freqs_flgs,Funcanno_flgs,Allels_flgs)

File "./InterVar.py", line 1599, in assign
PM2=check_PM2(line,Freqs_flgs,Allels_flgs,Funcanno_flgs,mim2gene_dict,mim2gene_dict2)

File "./InterVar.py", line 1055, in check_PM2
if(cls[Freqs_flgs[key]]!='.' and float(cls[Freqs_flgs[key]])>=cutoff_maf):
ValueError: could not convert string to float: X
``

In attachment you can see few lines of my vcf,
error_intervar.txt

Can you help? Thank you in advancei

[quanliustc]

I tested your provided vcf,it is no prolem. Please show your version of python, config,ini and full output of the screen. Also make sure all the files you using are updated. Best, Quan LI leequan@gmail.com From: stanedav [mailto:notifications@github.com] Sent: Wednesday, March 01, 2017 7:44 AM To: WGLab/InterVar <InterVar@noreply.github.com> Cc: Subscribed <subscribed@noreply.github.com> Subject: [WGLab/InterVar] ValueError: could not convert string to float: X (#3) Hello, I am trying to run your tool with this command: ./InterVar.py -b hg19 --table_annovar='/annovar/table_annovar.pl' --convert2annovar='/annovar/convert2annovar.pl' --annotate_variation='/annovar/annotate_variation.pl' -i '/vcf_wes/sample.vcf' --input_type=VCF -o '/vcf_wes/sample_output' After few moment I am getting this error: `` NOTICE: Multianno output file is written to /home/lab/galaxy-Win-Lin/David/vcf_wes/6788_output.hg19_multianno.txt Notice: Begin the variants interpretation by InterVar Traceback (most recent call last): File "./InterVar.py", line 2022, in main() File "./InterVar.py", line 1996, in main sum2=my_inter_var(annovar_outfile) File "./InterVar.py", line 1771, in my_inter_var intervar_bp=assign(BP,line,Freqs_flgs,Funcanno_flgs,Allels_flgs) File "./InterVar.py", line 1599, in assign PM2=check_PM2(line,Freqs_flgs,Allels_flgs,Funcanno_flgs,mim2gene_dict,mim2gene_dict2) File "./InterVar.py", line 1055, in check_PM2 if(cls[Freqs_flgs[key]]!='.' and float(cls[Freqs_flgs[key]])>=cutoff_maf): ValueError: could not convert string to float: X `` In attachment you can see few lines of my vcf, error_intervar.txt <https://github.com/WGLab/InterVar/files/810484/error_intervar.txt> Can you help? Thank you in advancei — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3> , or mute the thread <https://github.com/notifications/unsubscribe-auth/APD6JLwbH5zyX2OTDZRwTJxivXZBBVxeks5rhVLtgaJpZM4MPhZ2> . <https://github.com/notifications/beacon/APD6JIxcBjmM1KjGR4Wo9sxzC8UvzffOks5rhVLtgaJpZM4MPhZ2.gif>

[quanliustc]

please update the intervar. The value error has been fixed for this issue.

[stanedav]

Hello, thank you for quick response, I updated annovar and intervar and everything works fine! Thank you very much David Stanek 2017-03-01 14:22 GMT+01:00 Quan LI <notifications@github.com>:

…

please update the intervar. The value error has been fixed for this issue. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ANrs46NdB6vOChdnVWHx9F1rbeRpyJwVks5rhXETgaJpZM4MPhZ2> .

[yinbinqiu]

Hello, I am using intervar (2021-8-update), annovar (Version: $Date: 2020-06-07), but the above error still occurs, how can I solve it?

[WhiteKnightZMA]

please update the intervar. The value error has been fixed for this issue.

Hello, I have the same error with the latest Intervar version.

Notice: Begin the variants interpretation by InterVar
Traceback (most recent call last):
File "./Intervar.py", line 2126, in
main()
File "./Intervar.py", line 2095, in main
sum2=my_inter_var(annovar_outfile)
File "./Intervar.py", line 1844, in my_inter_var
intervar_bp=assign(BP,line,Freqs_flgs,Funcanno_flgs,Allels_flgs)
File "./Intervar.py", line 1715, in assign
BP7=check_BP7(line,Funcanno_flgs,Allels_flgs)
File "./Intervar.py", line 1627, in check_BP7
if float(cls[Funcanno_flgs['dbscSNV_RF_SCORE']])<0.6 and float(cls[Funcanno_flgs['dbscSNV_ADA_SCORE']])<0.6:
ValueError: could not convert string to float: X